Variant report

Variant	rs12744132
Chromosome Location	chr1:155663326-155663327
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr1:155662296..155664287-chr1:155670196..155672385,2	MCF-7	breast:
2	chr1:155656565..155660782-chr1:155662182..155667108,10	MCF-7	breast:
3	chr1:155656893..155661917-chr1:155662515..155668604,13	MCF-7	breast:

Variant related genes	Relation type
ENSG00000132676	Chromatin interaction
ENSG00000163374	Chromatin interaction

Extended variants
information (count: 96 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:61)

rs_ID	r²[population]
rs10752611	0.80[CEU][hapmap];0.91[JPT][hapmap]
rs10908469	0.92[JPT][hapmap]
rs10908470	0.80[CEU][hapmap];0.91[JPT][hapmap]
rs10908471	0.81[CEU][hapmap];0.92[JPT][hapmap]
rs10908479	0.84[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.83[AMR][1000 genomes];0.84[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10908481	0.90[CHB][hapmap];1.00[JPT][hapmap];0.80[ASN][1000 genomes]
rs10908482	0.80[ASN][1000 genomes]
rs11264380	0.80[CEU][hapmap];0.91[JPT][hapmap]
rs11264381	0.80[CEU][hapmap];0.81[CHB][hapmap];0.91[JPT][hapmap]
rs11264387	0.80[CEU][hapmap];0.82[JPT][hapmap]
rs11264397	0.86[AMR][1000 genomes];0.81[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs11264398	0.88[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs11264409	0.80[ASN][1000 genomes]
rs12022088	0.88[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs12035524	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12039893	0.87[AMR][1000 genomes];0.81[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs12040100	0.86[AMR][1000 genomes];0.81[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs12047626	0.81[AMR][1000 genomes]
rs12047756	0.95[CHB][hapmap];1.00[JPT][hapmap];0.87[AMR][1000 genomes];0.83[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs12079134	0.92[JPT][hapmap]
rs12091730	0.88[EUR][1000 genomes]
rs12143948	0.91[JPT][hapmap]
rs12740629	0.89[AMR][1000 genomes];0.83[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12746592	0.80[CEU][hapmap];0.91[JPT][hapmap]
rs12758945	0.88[AMR][1000 genomes];0.81[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1360554	0.91[JPT][hapmap]
rs1556488	0.81[CEU][hapmap];0.81[JPT][hapmap]
rs2048431	0.84[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.88[AMR][1000 genomes];0.83[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2175391	0.84[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.81[AMR][1000 genomes];0.83[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2666826	0.91[CHB][hapmap];1.00[JPT][hapmap];0.97[ASN][1000 genomes]
rs28662267	0.83[ASN][1000 genomes]
rs34124416	0.81[EUR][1000 genomes]
rs34620961	0.88[AMR][1000 genomes];0.83[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs348186	0.83[AMR][1000 genomes];0.82[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs348192	0.85[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs348196	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.84[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35615695	0.91[JPT][hapmap]
rs3738590	0.84[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.90[AMR][1000 genomes];0.84[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs3820594	0.86[CHB][hapmap];0.82[JPT][hapmap]
rs3851912	0.81[EUR][1000 genomes]
rs3892792	0.80[CEU][hapmap];0.92[JPT][hapmap]
rs4278368	0.81[ASN][1000 genomes]
rs475550	0.84[CEU][hapmap];0.90[CHB][hapmap];1.00[JPT][hapmap];0.83[AMR][1000 genomes];0.84[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs490608	0.85[ASN][1000 genomes]
rs4971095	0.81[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs6427286	0.95[CHB][hapmap];1.00[JPT][hapmap]
rs644853	0.84[JPT][hapmap]
rs6665227	0.80[ASN][1000 genomes]
rs6672128	0.83[AMR][1000 genomes];0.84[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6688636	0.91[JPT][hapmap]
rs6696888	0.91[JPT][hapmap]
rs670876	1.00[CEU][hapmap];0.95[CHB][hapmap];0.87[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs678157	1.00[CEU][hapmap];0.91[CHB][hapmap];1.00[JPT][hapmap];0.85[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs708611	0.90[CHB][hapmap]
rs7521594	0.83[AMR][1000 genomes];0.84[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7541060	0.91[CHB][hapmap];1.00[JPT][hapmap]
rs821551	0.81[CHB][hapmap];0.91[JPT][hapmap]
rs822478	0.80[CHB][hapmap]
rs822490	0.86[CHB][hapmap];0.82[JPT][hapmap]
rs860295	0.90[CHB][hapmap];0.82[JPT][hapmap]
rs9426933	0.84[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:35 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv529709	chr1:155154933-155757219	Strong transcription Weak transcription Flanking Active TSS Enhancers Active TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	450 gene(s)	inside rSNPs	diseases
2	esv33869	chr1:155223283-155917961	Flanking Active TSS Strong transcription Weak transcription Active TSS Bivalent/Poised TSS Enhancers Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	187 gene(s)	inside rSNPs	diseases
3	esv3431739	chr1:155514331-155664183	Active TSS Weak transcription Enhancers Flanking Active TSS ZNF genes & repeats Genic enhancers Strong transcription Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	61 gene(s)	inside rSNPs	diseases
4	nsv1002390	chr1:155553423-155706930	Strong transcription Weak transcription Enhancers Flanking Active TSS Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	42 gene(s)	inside rSNPs	diseases
5	nsv428246	chr1:155558197-155785831	Weak transcription Strong transcription Enhancers Active TSS Flanking Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	43 gene(s)	inside rSNPs	diseases
6	nsv436522	chr1:155559513-155674249	Strong transcription Enhancers Flanking Active TSS Active TSS Genic enhancers ZNF genes & repeats Weak transcription Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	40 gene(s)	inside rSNPs	diseases
7	esv3360339	chr1:155562157-155683127	Active TSS Flanking Active TSS Genic enhancers Enhancers Strong transcription ZNF genes & repeats Weak transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	41 gene(s)	inside rSNPs	diseases
8	nsv547965	chr1:155563152-155688600	Weak transcription Enhancers Genic enhancers Strong transcription Flanking Active TSS Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	41 gene(s)	inside rSNPs	diseases
9	esv3381327	chr1:155582853-155718436	Enhancers Flanking Active TSS Strong transcription Weak transcription Active TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	34 gene(s)	inside rSNPs	diseases
10	esv3436971	chr1:155618172-155733386	Weak transcription Strong transcription Enhancers Active TSS Flanking Active TSS Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	32 gene(s)	inside rSNPs	diseases
11	esv3338099	chr1:155618190-155733359	Weak transcription Strong transcription Enhancers Flanking Active TSS Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	32 gene(s)	inside rSNPs	diseases
12	nsv3054	chr1:155653835-155673509	Flanking Active TSS Weak transcription Enhancers Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Strong transcription Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	22 gene(s)	inside rSNPs	n/a
13	esv3529730	chr1:155658528-155665576	Active TSS ZNF genes & repeats Flanking Active TSS Enhancers Bivalent/Poised TSS Weak transcription Transcr. at gene 5' and 3' Genic enhancers Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	20 gene(s)	inside rSNPs	n/a
14	esv3529724	chr1:155659028-155665126	Weak transcription Flanking Active TSS ZNF genes & repeats Active TSS Strong transcription Enhancers Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	n/a
15	esv3319429	chr1:155659028-155665326	Flanking Active TSS Genic enhancers Enhancers Weak transcription Active TSS Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	n/a
16	esv3452512	chr1:155659621-155664566	Weak transcription Active TSS Flanking Active TSS Enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Strong transcription Genic enhancers Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region	10 gene(s)	inside rSNPs	n/a
17	esv3529726	chr1:155659644-155664581	Weak transcription Strong transcription Active TSS Enhancers Flanking Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region	10 gene(s)	inside rSNPs	n/a
18	esv3529725	chr1:155659667-155664604	Weak transcription Strong transcription Enhancers Active TSS Flanking Active TSS Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region	10 gene(s)	inside rSNPs	n/a
19	esv3452511	chr1:155659675-155664534	Active TSS Weak transcription Strong transcription Enhancers Genic enhancers Transcr. at gene 5' and 3' Flanking Active TSS ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region	10 gene(s)	inside rSNPs	n/a
20	esv3529727	chr1:155659701-155664609	Weak transcription ZNF genes & repeats Active TSS Flanking Active TSS Transcr. at gene 5' and 3' Enhancers Genic enhancers Strong transcription Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region	10 gene(s)	inside rSNPs	n/a
21	esv3452510	chr1:155659746-155664469	Active TSS Enhancers Weak transcription Strong transcription Genic enhancers Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region	10 gene(s)	inside rSNPs	n/a
22	esv15603	chr1:155659754-155664482	Weak transcription Active TSS Enhancers Flanking Active TSS Strong transcription ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region	8 gene(s)	inside rSNPs	n/a
23	esv3529731	chr1:155659756-155664467	Flanking Active TSS Active TSS Enhancers Strong transcription Weak transcription Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region	8 gene(s)	inside rSNPs	n/a
24	esv3452513	chr1:155659760-155664465	Enhancers Weak transcription Strong transcription Active TSS ZNF genes & repeats Genic enhancers Flanking Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region	8 gene(s)	inside rSNPs	n/a
25	esv3529732	chr1:155659760-155664465	Strong transcription Enhancers ZNF genes & repeats Active TSS Weak transcription Bivalent/Poised TSS Genic enhancers Flanking Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	8 gene(s)	inside rSNPs	n/a
26	nsv514012	chr1:155659776-155664208	Flanking Active TSS Enhancers Strong transcription Weak transcription Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region	8 gene(s)	inside rSNPs	n/a
27	esv3319431	chr1:155660853-155664201	Genic enhancers Weak transcription Strong transcription Enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	4 gene(s)	inside rSNPs	n/a
28	esv3319432	chr1:155660853-155664201	ZNF genes & repeats Enhancers Weak transcription Genic enhancers Strong transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	4 gene(s)	inside rSNPs	n/a
29	esv2421343	chr1:155661227-155663357	Weak transcription Strong transcription ZNF genes & repeats Genic enhancers Enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	4 gene(s)	inside rSNPs	n/a
30	nsv442072	chr1:155661227-155663357	Strong transcription Weak transcription ZNF genes & repeats Enhancers Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	4 gene(s)	inside rSNPs	n/a
31	nsv547966	chr1:155661917-155663326	Weak transcription Strong transcription ZNF genes & repeats Enhancers Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region	4 gene(s)	inside rSNPs	n/a
32	esv1806943	chr1:155661917-155664376	Weak transcription Genic enhancers Enhancers Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	4 gene(s)	inside rSNPs	n/a
33	esv3393626	chr1:155662028-155666426	Enhancers Strong transcription Weak transcription Flanking Active TSS Genic enhancers ZNF genes & repeats Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	5 gene(s)	inside rSNPs	n/a
34	esv1804717	chr1:155662247-155664439	Weak transcription Enhancers Genic enhancers Strong transcription Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region	2 gene(s)	inside rSNPs	n/a
35	esv1813640	chr1:155662247-155664439	Weak transcription Strong transcription Enhancers Genic enhancers ZNF genes & repeats Active TSS	TF binding region CpG island Chromatin interactive region	2 gene(s)	inside rSNPs	n/a

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs12744132	RIT1	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:120 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:155659400-155668200	Weak transcription	Aorta	Aorta
2	chr1:155659600-155664600	Weak transcription	Placenta Amnion	Placenta Amnion
3	chr1:155659600-155666400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
4	chr1:155659800-155664600	Weak transcription	Brain Germinal Matrix	brain
5	chr1:155660000-155667600	ZNF genes & repeats	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
6	chr1:155660200-155663400	ZNF genes & repeats	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
7	chr1:155660200-155664200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
8	chr1:155660200-155664200	Weak transcription	Thymus	Thymus
9	chr1:155660200-155664600	Weak transcription	NHDF-Ad	bronchial
10	chr1:155660200-155665000	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
11	chr1:155660200-155665000	Weak transcription	Rectal Smooth Muscle	rectum
12	chr1:155660200-155665400	Weak transcription	Ovary	ovary
13	chr1:155660200-155666800	Weak transcription	Fetal Stomach	stomach
14	chr1:155660200-155667000	ZNF genes & repeats	HUES6 Cell Line	embryonic stem cell
15	chr1:155660200-155667000	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
16	chr1:155660200-155668000	ZNF genes & repeats	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
17	chr1:155660200-155698800	Weak transcription	NHLF	lung
18	chr1:155660400-155663800	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
19	chr1:155660400-155664000	Weak transcription	Left Ventricle	heart
20	chr1:155660400-155664000	Weak transcription	Psoas Muscle	Psoas
21	chr1:155660400-155664000	Weak transcription	Right Ventricle	heart
22	chr1:155660400-155664000	Weak transcription	Skeletal Muscle Female	skeletal muscle
23	chr1:155660400-155664200	Weak transcription	Pancreas	Pancrea
24	chr1:155660400-155664200	Weak transcription	Sigmoid Colon	Sigmoid Colon
25	chr1:155660400-155664400	Weak transcription	Colon Smooth Muscle	Colon
26	chr1:155660400-155664800	Weak transcription	Brain Anterior Caudate	brain
27	chr1:155660400-155665000	Weak transcription	H9 Cell Line	embryonic stem cell
28	chr1:155660400-155665000	Weak transcription	Brain Cingulate Gyrus	brain
29	chr1:155660400-155665000	Weak transcription	Gastric	stomach
30	chr1:155660400-155668400	Weak transcription	Fetal Intestine Large	intestine
31	chr1:155660400-155671000	Weak transcription	Esophagus	oesophagus
32	chr1:155660400-155675000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
33	chr1:155660400-155682800	Weak transcription	Stomach Smooth Muscle	stomach
34	chr1:155660400-155688800	Weak transcription	Lung	lung
35	chr1:155660400-155706200	Weak transcription	Colonic Mucosa	Colon
36	chr1:155660600-155663800	Weak transcription	Skeletal Muscle Male	skeletal muscle
37	chr1:155660600-155664000	Weak transcription	Stomach Mucosa	stomach
38	chr1:155660600-155664200	Weak transcription	Liver	Liver
39	chr1:155660600-155664200	Weak transcription	Brain Angular Gyrus	brain
40	chr1:155660600-155664200	Weak transcription	Brain Hippocampus Middle	brain
41	chr1:155660600-155664200	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
42	chr1:155660600-155665000	Weak transcription	Primary neutrophils fromperipheralblood	blood
43	chr1:155660600-155665000	Weak transcription	Brain Substantia Nigra	brain
44	chr1:155660600-155665000	Weak transcription	Duodenum Smooth Muscle	Duodenum
45	chr1:155660600-155668000	Weak transcription	Muscle Satellite Cultured Cells	--
46	chr1:155660600-155679000	Weak transcription	Fetal Brain Female	brain
47	chr1:155660600-155680200	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
48	chr1:155660800-155663800	Weak transcription	Right Atrium	heart
49	chr1:155660800-155664200	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
50	chr1:155660800-155682600	Weak transcription	Spleen	Spleen

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