Variant report

Variant	rs6438159
Chromosome Location	chr3:113217341-113217342
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:5)
CpG islands
(count:0)
Chromatin interactive
region (count:6)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:5 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	FOS	chr3:113217321-113217835	HUVEC	blood vessel:	n/a	n/a
2	SP1	chr3:113217235-113217907	A549	lung:	n/a	n/a
3	CEBPB	chr3:113217128-113217425	A549	lung:	n/a	n/a
4	CEBPB	chr3:113217096-113217797	Hela-S3	cervix:	n/a	n/a
5	CEBPB	chr3:113217078-113217722	IMR90	lung:	n/a	n/a

No data

(count:6 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr3:113217243..113219124-chr3:113250664..113252376,2	MCF-7	breast:
2	chr3:113215849..113222351-chr3:113231718..113236655,12	MCF-7	breast:
3	chr3:113216822..113219310-chr3:113237513..113239458,2	MCF-7	breast:
4	chr3:113215914..113218639-chr3:113252642..113255587,3	MCF-7	breast:
5	chr3:113216065..113219439-chr3:113250291..113253077,5	MCF-7	breast:
6	chr3:113216951..113219431-chr3:113270962..113272792,3	MCF-7	breast:

No data

Variant related genes	Relation type
SPICE1	TF binding region
ENSG00000072858	Chromatin interaction
ENSG00000163611	Chromatin interaction

Extended variants
information (count: 88 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:84)

rs_ID	r²[population]
rs10511326	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11537650	0.81[AMR][1000 genomes]
rs13064411	0.90[CHD][hapmap];0.96[GIH][hapmap]
rs13066742	0.81[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs13067967	0.86[CHB][hapmap];1.00[JPT][hapmap];0.92[ASN][1000 genomes]
rs13082603	0.81[AMR][1000 genomes]
rs13087452	0.98[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs13092925	0.81[AMR][1000 genomes]
rs13098166	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs13325046	0.94[CEU][hapmap];0.86[CHD][hapmap];1.00[GIH][hapmap];0.82[MEX][hapmap];0.85[TSI][hapmap];0.83[EUR][1000 genomes]
rs1386336	0.94[CEU][hapmap];0.90[CHD][hapmap];1.00[GIH][hapmap];0.91[MEX][hapmap];0.89[TSI][hapmap];0.87[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs1463643	0.81[AMR][1000 genomes]
rs1486894	1.00[ASW][hapmap];1.00[CEU][hapmap];0.88[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.83[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1486897	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[YRI][hapmap];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1552432	1.00[CEU][hapmap];0.86[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs16860849	0.90[CHD][hapmap];0.96[GIH][hapmap]
rs16861103	0.90[MKK][hapmap];0.93[TSI][hapmap]
rs16861158	0.86[CHB][hapmap];1.00[CHD][hapmap];0.96[GIH][hapmap];1.00[JPT][hapmap];0.89[ASN][1000 genomes]
rs1872747	0.80[AMR][1000 genomes];0.90[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2087129	0.94[CEU][hapmap];0.85[EUR][1000 genomes]
rs2087130	0.81[AMR][1000 genomes]
rs2129434	0.94[CEU][hapmap];0.90[CHD][hapmap];1.00[GIH][hapmap];0.91[MEX][hapmap];0.89[TSI][hapmap];0.87[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs2399477	0.95[MKK][hapmap];0.93[TSI][hapmap];0.81[AMR][1000 genomes]
rs2399479	1.00[CEU][hapmap];0.86[CHB][hapmap];1.00[JPT][hapmap];0.83[YRI][hapmap];0.96[AMR][1000 genomes];0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2399480	0.81[AMR][1000 genomes]
rs28536176	0.87[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs28710051	0.87[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs34286076	0.92[ASN][1000 genomes]
rs34844841	0.92[ASN][1000 genomes]
rs35274817	0.92[ASN][1000 genomes]
rs35278902	0.93[ASN][1000 genomes]
rs35860985	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs36054418	0.97[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs3732803	0.82[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs3773697	0.86[CHD][hapmap];0.96[GIH][hapmap]
rs4396864	0.83[CEU][hapmap];0.81[AMR][1000 genomes]
rs4425226	0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4484165	0.86[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs60634072	0.81[AMR][1000 genomes]
rs6438149	0.89[AMR][1000 genomes];0.97[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs6438156	0.82[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6438157	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6438158	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6438161	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs67211112	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6766615	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[YRI][hapmap];0.90[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6768648	1.00[CEU][hapmap];0.86[CHB][hapmap];0.84[JPT][hapmap];0.91[YRI][hapmap];0.84[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6768979	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6769516	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6773497	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.96[TSI][hapmap];0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs6778800	0.85[EUR][1000 genomes]
rs6783965	0.92[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.81[MKK][hapmap];0.96[TSI][hapmap];0.83[YRI][hapmap];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6786974	1.00[CEU][hapmap];0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs6787026	0.94[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.82[MEX][hapmap];0.93[TSI][hapmap];0.80[AMR][1000 genomes];0.90[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs6798938	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6799610	1.00[CEU][hapmap];0.86[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.96[TSI][hapmap];0.93[AMR][1000 genomes];0.92[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6808394	0.94[CEU][hapmap];0.87[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs722392	1.00[AMR][1000 genomes];0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7610638	0.87[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs7613546	0.91[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7618226	0.81[AMR][1000 genomes]
rs7622740	0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7628945	0.81[AMR][1000 genomes]
rs7631082	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7631138	1.00[CEU][hapmap];0.89[JPT][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7631335	0.81[AMR][1000 genomes]
rs7636128	0.85[EUR][1000 genomes]
rs869342	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs869343	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9808893	1.00[CEU][hapmap];0.86[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9814395	0.87[AMR][1000 genomes];0.96[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs9825827	0.87[AMR][1000 genomes];0.96[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs9835848	0.87[AMR][1000 genomes];0.96[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs9836396	1.00[CEU][hapmap];1.00[CHB][hapmap];0.89[JPT][hapmap];0.87[AMR][1000 genomes];0.96[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs9839921	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs9844447	0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs9846539	0.81[AMR][1000 genomes]
rs9851378	0.87[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs9860549	0.94[CEU][hapmap];0.85[EUR][1000 genomes]
rs9869119	0.87[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs9869318	0.94[CEU][hapmap];0.90[CHD][hapmap];1.00[GIH][hapmap];0.91[MEX][hapmap];0.89[TSI][hapmap];0.87[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs9872168	0.82[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9875025	0.84[EUR][1000 genomes]
rs9877649	0.81[AMR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1013506	chr3:112890608-113680951	Weak transcription Bivalent/Poised TSS Enhancers Strong transcription ZNF genes & repeats Genic enhancers Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	51 gene(s)	inside rSNPs	diseases
2	nsv1004000	chr3:113116778-113513899	Weak transcription Strong transcription ZNF genes & repeats Active TSS Enhancers Flanking Active TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	34 gene(s)	inside rSNPs	diseases
3	nsv877349	chr3:113208224-113323787	Enhancers Flanking Active TSS Strong transcription Active TSS Weak transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	13 gene(s)	inside rSNPs	diseases
4	nsv877350	chr3:113208224-113332235	Strong transcription Weak transcription Enhancers Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	13 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs6438159	SIDT1	Cis_1M	lymphoblastoid	RTeQTL
rs6438159	BOC	cis	parietal	SCAN
rs6438159	CHD4	trans	cerebellum	SCAN

Chromatin state (count:114 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:113160800-113224800	Weak transcription	Placenta	Placenta
2	chr3:113160800-113232600	Weak transcription	Right Ventricle	heart
3	chr3:113172800-113232800	Weak transcription	HSMMtube	muscle
4	chr3:113176400-113233200	Weak transcription	Gastric	stomach
5	chr3:113177400-113225800	Weak transcription	Pancreatic Islets	Pancreatic Islet
6	chr3:113177600-113224400	Weak transcription	Spleen	Spleen
7	chr3:113179600-113232400	Weak transcription	Rectal Smooth Muscle	rectum
8	chr3:113179600-113232800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
9	chr3:113184000-113233200	Weak transcription	Pancreas	Pancrea
10	chr3:113187200-113224400	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
11	chr3:113201400-113232600	Weak transcription	Brain Hippocampus Middle	brain
12	chr3:113202400-113232800	Weak transcription	Fetal Brain Female	brain
13	chr3:113203200-113223600	Weak transcription	iPS-18 Cell Line	embryonic stem cell
14	chr3:113203400-113229200	Weak transcription	Lung	lung
15	chr3:113204000-113221200	Weak transcription	Skeletal Muscle Male	skeletal muscle
16	chr3:113204000-113223400	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
17	chr3:113204400-113224600	Weak transcription	Aorta	Aorta
18	chr3:113204400-113230600	Weak transcription	HUES6 Cell Line	embryonic stem cell
19	chr3:113204600-113223000	Weak transcription	HepG2	liver
20	chr3:113204600-113232800	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
21	chr3:113204600-113233200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
22	chr3:113204600-113233200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
23	chr3:113204600-113233200	Weak transcription	Esophagus	oesophagus
24	chr3:113204800-113221400	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
25	chr3:113204800-113222400	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
26	chr3:113204800-113232400	Weak transcription	Placenta Amnion	Placenta Amnion
27	chr3:113204800-113232600	Weak transcription	Primary T helper naive cells from peripheral blood	blood
28	chr3:113204800-113232800	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
29	chr3:113204800-113233200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
30	chr3:113205000-113224200	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
31	chr3:113205000-113224400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
32	chr3:113205200-113220600	Weak transcription	K562	blood
33	chr3:113206200-113217400	Weak transcription	Brain Cingulate Gyrus	brain
34	chr3:113207600-113232600	Weak transcription	NHEK	skin
35	chr3:113207600-113233000	Weak transcription	Psoas Muscle	Psoas
36	chr3:113207800-113233000	Weak transcription	H9 Cell Line	embryonic stem cell
37	chr3:113208200-113223800	Weak transcription	Skeletal Muscle Female	skeletal muscle
38	chr3:113209000-113232600	Weak transcription	Fetal Kidney	kidney
39	chr3:113209200-113232800	Weak transcription	H1 Cell Line	embryonic stem cell
40	chr3:113209400-113232800	Weak transcription	Stomach Mucosa	stomach
41	chr3:113209800-113228800	Weak transcription	Cortex derived primary cultured neurospheres	brain
42	chr3:113209800-113232800	Weak transcription	Brain Inferior Temporal Lobe	brain
43	chr3:113210000-113224400	Weak transcription	Thymus	Thymus
44	chr3:113210000-113233000	Weak transcription	HSMM	muscle
45	chr3:113210200-113220600	Weak transcription	Fetal Lung	lung
46	chr3:113210200-113233200	Weak transcription	Colonic Mucosa	Colon
47	chr3:113210400-113231600	Weak transcription	Fetal Intestine Small	intestine
48	chr3:113210400-113232600	Weak transcription	NHLF	lung
49	chr3:113211800-113217800	Weak transcription	Primary B cells from cord blood	blood
50	chr3:113212200-113232800	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood

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