Variant report

Variant	rs644853
Chromosome Location	chr1:155706217-155706218
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr1:155706061-155706350	K562	blood:	n/a	n/a
2	POLR2A	chr1:155706155-155706293	MCF-7	breast:	n/a	n/a
3	POLR2A	chr1:155706128-155706362	K562	blood:	n/a	n/a
4	POLR2A	chr1:155706042-155706292	K562	blood:	n/a	n/a
5	POLR2A	chr1:155705954-155706306	HepG2	liver:	n/a	n/a

Variant related genes	Relation type
DAP3	TF binding region

Extended variants
information (count: 45 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:35)

rs_ID	r²[population]
rs10752611	1.00[JPT][hapmap]
rs10908470	1.00[JPT][hapmap]
rs10908471	0.92[JPT][hapmap]
rs10908479	0.84[JPT][hapmap]
rs10908481	0.91[JPT][hapmap]
rs10908482	0.87[AFR][1000 genomes]
rs11264380	1.00[JPT][hapmap]
rs11264381	1.00[JPT][hapmap]
rs11264387	0.83[JPT][hapmap]
rs12035524	0.91[JPT][hapmap]
rs12047756	0.84[JPT][hapmap]
rs12143948	1.00[JPT][hapmap]
rs12744132	0.84[JPT][hapmap]
rs1556488	0.90[JPT][hapmap]
rs2048431	0.91[JPT][hapmap]
rs2175391	0.91[JPT][hapmap]
rs2666826	0.82[JPT][hapmap]
rs348196	0.91[JPT][hapmap]
rs3738590	0.91[JPT][hapmap]
rs3892792	0.92[JPT][hapmap]
rs475550	0.91[JPT][hapmap]
rs490608	0.87[AFR][1000 genomes]
rs6427286	0.84[JPT][hapmap];0.94[YRI][hapmap];0.88[AFR][1000 genomes]
rs6427287	0.88[AFR][1000 genomes]
rs6696888	1.00[JPT][hapmap]
rs678157	0.84[JPT][hapmap]
rs708611	0.87[YRI][hapmap]
rs7541060	0.84[JPT][hapmap];0.94[YRI][hapmap];0.88[AFR][1000 genomes]
rs7550402	0.87[AFR][1000 genomes]
rs821551	0.85[CHB][hapmap];1.00[JPT][hapmap]
rs822478	0.84[CHB][hapmap];0.81[JPT][hapmap]
rs822490	0.93[YRI][hapmap]
rs822527	0.81[AFR][1000 genomes]
rs860295	0.93[YRI][hapmap]
rs9426933	0.88[AFR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:10 , 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	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
4	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
5	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
6	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
7	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
8	esv3423892	chr1:155664084-155901487	Flanking Active TSS Weak transcription Enhancers Strong transcription Active TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	28 gene(s)	inside rSNPs	diseases
9	nsv3065	chr1:155682768-155727524	Strong transcription Weak transcription Genic enhancers Enhancers Flanking Active TSS Active TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	7 gene(s)	inside rSNPs	diseases
10	nsv947547	chr1:155698814-155708436	Weak transcription Strong transcription Enhancers ZNF genes & repeats Genic enhancers	TF binding region CpG island Chromatin interactive region	1 gene(s)	inside rSNPs	n/a

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs644853	RIT1	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:124 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:155661600-155707800	Weak transcription	HUVEC	blood vessel
2	chr1:155665200-155708000	Weak transcription	Placenta Amnion	Placenta Amnion
3	chr1:155665600-155707200	Weak transcription	Psoas Muscle	Psoas
4	chr1:155665800-155707000	Weak transcription	Small Intestine	intestine
5	chr1:155673800-155707800	Weak transcription	Aorta	Aorta
6	chr1:155679400-155710400	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
7	chr1:155681600-155707800	Weak transcription	iPS-15b Cell Line	embryonic stem cell
8	chr1:155683200-155715000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
9	chr1:155683400-155707800	Weak transcription	Fetal Heart	heart
10	chr1:155683800-155709000	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
11	chr1:155683800-155715000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
12	chr1:155684000-155707800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
13	chr1:155687200-155715000	Weak transcription	Esophagus	oesophagus
14	chr1:155688400-155711200	Strong transcription	Fetal Muscle Leg	muscle
15	chr1:155688800-155710800	Strong transcription	Fetal Stomach	stomach
16	chr1:155688800-155711000	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
17	chr1:155689200-155709400	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
18	chr1:155691000-155709000	Strong transcription	HUES64 Cell Line	embryonic stem cell
19	chr1:155695000-155709400	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
20	chr1:155695600-155707400	Weak transcription	Pancreas	Pancrea
21	chr1:155695600-155714600	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
22	chr1:155695800-155714600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
23	chr1:155698800-155709200	Strong transcription	Foreskin Fibroblast Primary Cells skin01	Skin
24	chr1:155699000-155707000	Weak transcription	Brain Substantia Nigra	brain
25	chr1:155699000-155714800	Weak transcription	Stomach Mucosa	stomach
26	chr1:155699200-155710800	Strong transcription	Fetal Intestine Small	intestine
27	chr1:155699600-155707400	Weak transcription	Rectal Smooth Muscle	rectum
28	chr1:155700200-155708600	Strong transcription	Duodenum Mucosa	Duodenum
29	chr1:155700200-155709600	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
30	chr1:155700400-155706400	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
31	chr1:155701000-155709400	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
32	chr1:155701000-155714600	Weak transcription	Primary T killer memory cells from peripheral blood	blood
33	chr1:155701200-155709000	Strong transcription	Adipose Nuclei	Adipose
34	chr1:155701400-155706600	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
35	chr1:155701600-155708200	Strong transcription	Breast Myoepithelial Primary Cells	Breast
36	chr1:155701600-155708600	Strong transcription	Primary T helper 17 cells PMA-I stimulated	--
37	chr1:155701800-155707800	Weak transcription	Colon Smooth Muscle	Colon
38	chr1:155702000-155714600	Weak transcription	Pancreatic Islets	Pancreatic Islet
39	chr1:155702200-155709000	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
40	chr1:155702400-155707000	Strong transcription	Cortex derived primary cultured neurospheres	brain
41	chr1:155702600-155708600	Strong transcription	Sigmoid Colon	Sigmoid Colon
42	chr1:155703200-155708800	Strong transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
43	chr1:155704400-155706400	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
44	chr1:155704600-155706400	Weak transcription	Hela-S3	cervix
45	chr1:155704600-155706600	Weak transcription	Brain Anterior Caudate	brain
46	chr1:155704600-155707200	Weak transcription	Fetal Brain Female	brain
47	chr1:155704600-155714800	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
48	chr1:155704600-155714800	Weak transcription	Fetal Lung	lung
49	chr1:155704800-155706600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
50	chr1:155704800-155707600	Weak transcription	Primary T helper naive cells from peripheral blood	blood

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