Variant report

Variant	rs3738197
Chromosome Location	chr1:211971587-211971588
allele	C/T
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	STAT3	chr1:211971559-211971658	MCF10A-Er-Src	breast:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr1:211969318..211974006-chr1:211975194..211979282,5	K562	blood:
2	chr1:211969318..211971729-chr1:211976490..211978991,3	K562	blood:

Variant related genes	Relation type
ENSG00000212205	TF binding region
LPGAT1	TF binding region
ENSG00000212205	Chromatin interaction

Extended variants
information (count: 42 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:42)

rs_ID	r²[population]
rs10863929	0.81[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs11119807	0.91[ASN][1000 genomes]
rs11119813	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];1.00[TSI][hapmap];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11487823	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1157168	0.89[CHD][hapmap];1.00[JPT][hapmap];0.85[ASN][1000 genomes]
rs12059988	0.82[AFR][1000 genomes];0.87[AMR][1000 genomes];0.90[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12076991	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12077561	0.85[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12084756	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[AMR][1000 genomes];0.86[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs12085235	0.83[ASN][1000 genomes]
rs12085288	0.83[ASN][1000 genomes]
rs12088743	0.85[AFR][1000 genomes];0.91[ASN][1000 genomes]
rs12090490	0.86[AFR][1000 genomes];0.81[AMR][1000 genomes];0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12095938	0.85[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[YRI][hapmap];0.91[ASN][1000 genomes]
rs12410970	0.91[ASN][1000 genomes]
rs28768080	0.81[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs28800280	0.83[AMR][1000 genomes];0.90[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs28862981	0.90[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2970578	0.88[CHD][hapmap];0.86[JPT][hapmap]
rs3862952	0.93[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.89[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.92[MKK][hapmap];1.00[TSI][hapmap];0.83[YRI][hapmap];0.89[AMR][1000 genomes];0.84[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs4447046	0.83[AMR][1000 genomes];0.90[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4537651	0.89[ASN][1000 genomes]
rs4562685	0.91[ASN][1000 genomes]
rs4623773	0.81[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs56132364	0.83[AMR][1000 genomes];0.90[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs61828246	0.80[ASN][1000 genomes]
rs61828259	0.91[ASN][1000 genomes]
rs61828491	1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61828492	0.82[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs61828510	0.91[ASN][1000 genomes]
rs6540709	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];0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6662067	0.91[ASN][1000 genomes]
rs6664082	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[AMR][1000 genomes];0.86[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs6678582	0.81[AMR][1000 genomes];0.89[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6684049	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.91[AFR][1000 genomes];0.88[AMR][1000 genomes];0.86[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs6704043	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.91[AFR][1000 genomes];0.89[AMR][1000 genomes];0.84[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs72747039	0.80[ASN][1000 genomes]
rs72747051	0.85[ASN][1000 genomes]
rs7518896	0.93[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];1.00[TSI][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7524009	1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.93[TSI][hapmap];0.91[ASN][1000 genomes]
rs7534335	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.88[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];0.98[TSI][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7547097	0.86[JPT][hapmap]

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs3738197	INTS7	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:100 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:211914000-211973600	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
2	chr1:211915800-211991800	Weak transcription	Muscle Satellite Cultured Cells	--
3	chr1:211916800-211994200	Weak transcription	Fetal Brain Male	brain
4	chr1:211919200-212001200	Weak transcription	Gastric	stomach
5	chr1:211923000-211991800	Weak transcription	HSMM	muscle
6	chr1:211924000-212002400	Weak transcription	NHLF	lung
7	chr1:211938200-211999400	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
8	chr1:211939600-211978200	Weak transcription	Pancreatic Islets	Pancreatic Islet
9	chr1:211939600-211992600	Weak transcription	Esophagus	oesophagus
10	chr1:211939800-212002400	Weak transcription	HSMMtube	muscle
11	chr1:211940000-212000600	Weak transcription	Rectal Smooth Muscle	rectum
12	chr1:211943400-211972000	Weak transcription	HUES48 Cell Line	embryonic stem cell
13	chr1:211945800-211979000	Weak transcription	Colon Smooth Muscle	Colon
14	chr1:211946200-211984200	Weak transcription	NH-A	brain
15	chr1:211947400-212002400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
16	chr1:211950000-211987000	Weak transcription	Fetal Thymus	thymus
17	chr1:211950600-211971800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
18	chr1:211951400-211978800	Weak transcription	Fetal Lung	lung
19	chr1:211951400-211992600	Weak transcription	Ovary	ovary
20	chr1:211952200-212003000	Weak transcription	Placenta Amnion	Placenta Amnion
21	chr1:211957600-211985200	Weak transcription	Brain Germinal Matrix	brain
22	chr1:211957600-211998800	Weak transcription	NHDF-Ad	bronchial
23	chr1:211957600-212000800	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
24	chr1:211957800-211973600	Weak transcription	K562	blood
25	chr1:211958000-211984200	Weak transcription	HUVEC	blood vessel
26	chr1:211960800-211982200	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
27	chr1:211960800-211987600	Weak transcription	Pancreas	Pancrea
28	chr1:211961200-212002200	Weak transcription	Primary T helper cells PMA-I stimulated	--
29	chr1:211962400-211978600	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
30	chr1:211962600-211983000	Weak transcription	Primary T helper cells fromperipheralblood	blood
31	chr1:211963600-211985800	Weak transcription	Hela-S3	cervix
32	chr1:211964800-211972000	Strong transcription	Fetal Intestine Small	intestine
33	chr1:211965600-211974600	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
34	chr1:211965800-211971800	Weak transcription	Left Ventricle	heart
35	chr1:211965800-211972800	Weak transcription	Right Ventricle	heart
36	chr1:211965800-211974200	Weak transcription	NHEK	skin
37	chr1:211965800-211976400	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
38	chr1:211965800-211976600	Weak transcription	Fetal Kidney	kidney
39	chr1:211965800-211978800	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
40	chr1:211965800-211985400	Weak transcription	Skeletal Muscle Male	skeletal muscle
41	chr1:211965800-211992600	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
42	chr1:211965800-212002200	Weak transcription	Primary T cells from cord blood	blood
43	chr1:211966000-211972200	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
44	chr1:211966000-211979000	Weak transcription	Fetal Brain Female	brain
45	chr1:211966400-211972800	Weak transcription	HepG2	liver
46	chr1:211966400-211974400	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
47	chr1:211966400-211983000	Weak transcription	Duodenum Smooth Muscle	Duodenum
48	chr1:211966400-211997400	Weak transcription	Sigmoid Colon	Sigmoid Colon
49	chr1:211966400-212002400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
50	chr1:211966600-211974600	Weak transcription	Fetal Adrenal Gland	Adrenal Gland

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