Variant report

Variant	rs3790612
Chromosome Location	chr1:113084146-113084147
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr1:113077855..113079726-chr1:113080031..113084166,3	K562	blood:

Extended variants
information (count: 89 )
Associated
traits (count: 10 )

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

rs_ID	r²[population]
rs10745331	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs10745332	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[ASN][1000 genomes]
rs10857969	0.85[ASN][1000 genomes]
rs11102494	0.87[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs11102508	0.84[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs11102510	0.86[EUR][1000 genomes]
rs12048528	0.90[ASW][hapmap];1.00[CEU][hapmap];0.93[CHB][hapmap];0.96[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.90[LWK][hapmap];0.91[MEX][hapmap];0.98[MKK][hapmap];0.92[TSI][hapmap];0.93[YRI][hapmap]
rs12118370	0.87[ASN][1000 genomes]
rs12119489	0.82[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12125361	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[YRI][hapmap];0.86[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs12136781	0.95[AFR][1000 genomes];0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12137107	0.81[AMR][1000 genomes];0.88[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12138335	1.00[CEU][hapmap];0.88[EUR][1000 genomes]
rs12143068	0.88[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1238	0.90[ASW][hapmap];1.00[CEU][hapmap];0.93[CHB][hapmap];0.96[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.90[LWK][hapmap];0.91[MEX][hapmap];0.98[MKK][hapmap];0.92[TSI][hapmap];0.85[YRI][hapmap]
rs12401734	1.00[CEU][hapmap];0.91[GIH][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.87[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs12402469	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[AFR][1000 genomes];0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12402929	1.00[CEU][hapmap];0.81[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs12406906	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap];0.83[MKK][hapmap];0.95[TSI][hapmap];0.82[YRI][hapmap];0.90[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12739994	1.00[CEU][hapmap];0.88[EUR][1000 genomes]
rs12750023	0.85[AFR][1000 genomes];0.81[AMR][1000 genomes];0.90[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12750621	1.00[CEU][hapmap]
rs12758377	0.81[AFR][1000 genomes];0.81[AMR][1000 genomes];0.88[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs17438324	0.97[AFR][1000 genomes];0.89[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2273369	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[AFR][1000 genomes];0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2279500	0.91[GIH][hapmap]
rs2932529	1.00[CEU][hapmap]
rs2932534	0.82[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.96[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.87[LWK][hapmap];0.91[MEX][hapmap];0.95[MKK][hapmap];0.92[TSI][hapmap];0.93[YRI][hapmap];0.86[ASN][1000 genomes]
rs2932535	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[YRI][hapmap];0.86[ASN][1000 genomes]
rs2932538	0.90[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.96[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.87[LWK][hapmap];0.91[MEX][hapmap];0.98[MKK][hapmap];0.92[TSI][hapmap];0.93[YRI][hapmap]
rs2932539	1.00[CEU][hapmap];0.93[CHB][hapmap];1.00[JPT][hapmap];0.91[YRI][hapmap]
rs3013441	0.90[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.92[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.90[LWK][hapmap];0.91[MEX][hapmap];0.98[MKK][hapmap];0.92[TSI][hapmap];0.93[YRI][hapmap];0.83[ASN][1000 genomes]
rs34531155	0.88[EUR][1000 genomes]
rs35482634	0.85[AMR][1000 genomes];0.90[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs36029940	0.83[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs3762335	0.97[AFR][1000 genomes];0.89[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs3790611	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.96[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.98[MKK][hapmap];1.00[TSI][hapmap];0.93[YRI][hapmap];0.86[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs3795820	1.00[CEU][hapmap];0.95[GIH][hapmap];0.91[MEX][hapmap];0.92[TSI][hapmap];0.84[EUR][1000 genomes]
rs4240534	0.81[AMR][1000 genomes];0.83[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs4838960	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.80[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs4838961	0.81[AMR][1000 genomes];0.83[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs4839257	1.00[CEU][hapmap];0.93[CHB][hapmap];0.96[CHD][hapmap];0.85[GIH][hapmap];1.00[JPT][hapmap];0.83[MEX][hapmap];0.92[TSI][hapmap]
rs61818772	0.83[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs61818800	0.91[ASN][1000 genomes]
rs6537740	1.00[CEU][hapmap];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs6537742	0.84[CEU][hapmap]
rs6537744	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[YRI][hapmap];0.85[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6537745	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs6537746	0.90[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.93[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.93[LWK][hapmap];0.91[MEX][hapmap];0.98[MKK][hapmap];0.92[TSI][hapmap];0.93[YRI][hapmap];0.81[AMR][1000 genomes];0.84[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs6537747	1.00[CEU][hapmap];1.00[CHB][hapmap];0.96[CHD][hapmap];0.85[GIH][hapmap];1.00[JPT][hapmap];0.83[MEX][hapmap];0.92[TSI][hapmap];0.88[ASN][1000 genomes]
rs6658555	1.00[CEU][hapmap];0.91[GIH][hapmap];0.91[MEX][hapmap];0.95[TSI][hapmap];0.83[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs6659677	0.97[AFR][1000 genomes];0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6661642	0.83[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6663922	0.93[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6668533	1.00[CEU][hapmap];0.91[GIH][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.87[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs6671645	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.85[GIH][hapmap];1.00[JPT][hapmap];0.83[MEX][hapmap];0.95[TSI][hapmap];0.84[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6672761	0.97[AFR][1000 genomes];0.89[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6673930	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[YRI][hapmap];0.82[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6674053	0.85[AFR][1000 genomes];0.81[AMR][1000 genomes];0.85[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs6674068	0.85[AFR][1000 genomes];0.81[AMR][1000 genomes];0.86[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs6681371	1.00[CEU][hapmap];0.91[GIH][hapmap];0.91[MEX][hapmap];0.81[MKK][hapmap];0.95[TSI][hapmap];0.83[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs6682678	0.90[ASW][hapmap];0.85[CEU][hapmap];0.82[CHB][hapmap];0.96[CHD][hapmap];0.92[GIH][hapmap];0.93[JPT][hapmap];0.90[LWK][hapmap];0.91[MEX][hapmap];0.98[MKK][hapmap];0.92[TSI][hapmap];0.93[YRI][hapmap]
rs6690169	0.89[AFR][1000 genomes];0.85[AMR][1000 genomes];0.90[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6690292	1.00[CEU][hapmap];0.85[ASN][1000 genomes]
rs6691025	0.81[AMR][1000 genomes];0.84[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs6691917	0.84[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6693880	0.97[AFR][1000 genomes];0.89[AMR][1000 genomes];0.91[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6696991	0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6698030	0.88[EUR][1000 genomes]
rs6701351	0.84[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7415988	1.00[CEU][hapmap];0.85[EUR][1000 genomes]
rs7516421	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7522110	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.92[AFR][1000 genomes];0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7527076	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.81[AMR][1000 genomes];0.85[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7535636	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.85[LWK][hapmap];0.91[MEX][hapmap];0.98[MKK][hapmap];0.95[TSI][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];0.89[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7537789	0.95[AFR][1000 genomes];0.91[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7540251	0.87[EUR][1000 genomes]
rs7542820	0.89[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7546203	0.81[AMR][1000 genomes];0.85[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7549547	0.97[AFR][1000 genomes];0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7551933	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.96[GIH][hapmap];1.00[JPT][hapmap];0.97[LWK][hapmap];0.91[MEX][hapmap];1.00[MKK][hapmap];0.95[TSI][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7552692	0.81[ASN][1000 genomes]
rs9429694	0.81[AMR][1000 genomes];0.85[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs999923	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.96[GIH][hapmap];1.00[JPT][hapmap];0.97[LWK][hapmap];0.91[MEX][hapmap];1.00[MKK][hapmap];0.95[TSI][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];0.89[AMR][1000 genomes];0.91[EUR][1000 genomes];0.95[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv13370	chr1:112693290-113246263	Flanking Active TSS Weak transcription Enhancers Active TSS Strong transcription Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	87 gene(s)	inside rSNPs	diseases
2	nsv1002971	chr1:112924725-113740584	Weak transcription Enhancers Active TSS Flanking Bivalent TSS/Enh Flanking Active TSS Strong transcription Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	166 gene(s)	inside rSNPs	diseases
3	nsv535059	chr1:112924725-113740584	Enhancers Weak transcription Strong transcription Flanking Active TSS Bivalent/Poised TSS Active TSS Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	166 gene(s)	inside rSNPs	diseases
4	nsv831081	chr1:112934920-113122640	Weak transcription Flanking Active TSS Active TSS Strong transcription Genic enhancers Enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	18 gene(s)	inside rSNPs	diseases
5	nsv432631	chr1:113071834-113200797	Weak transcription Strong transcription Enhancers Genic enhancers ZNF genes & repeats Active TSS Flanking Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	71 gene(s)	inside rSNPs	diseases

mRNA abundance (count:10)

SNP	Gene	Cis/trans	Tissue	Source
rs3790612	HBXIP	cis	parietal	SCAN
rs3790612	GSTM5	cis	parietal	SCAN
rs3790612	ST7L	cis	Lymphoblastoid	GTEx
rs3790612	CTTNBP2NL	cis	parietal	SCAN
rs3790612	ALX3	cis	parietal	SCAN
rs3790612	CAPZA1	Cis_1M	lymphoblastoid	RTeQTL
rs3790612	ST7L	cis	lung	GTEx
rs3790612	CAPZA1	cis	lymphoblastoid	seeQTL
rs3790612	ST7L	cis	lymphoblastoid	seeQTL
rs3790612	FAM102B	cis	cerebellum	SCAN

Chromatin state (count:112 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:113052200-113093200	Weak transcription	Brain Substantia Nigra	brain
2	chr1:113055800-113085200	Weak transcription	Thymus	Thymus
3	chr1:113058400-113086600	Weak transcription	A549	lung
4	chr1:113058800-113119400	Weak transcription	HepG2	liver
5	chr1:113060200-113132400	Weak transcription	Pancreas	Pancrea
6	chr1:113062400-113117400	Weak transcription	Psoas Muscle	Psoas
7	chr1:113063400-113092400	Weak transcription	Pancreatic Islets	Pancreatic Islet
8	chr1:113064400-113132200	Weak transcription	Primary hematopoietic stem cells short term culture	blood
9	chr1:113065000-113092400	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
10	chr1:113065200-113114800	Weak transcription	Small Intestine	intestine
11	chr1:113065400-113114600	Weak transcription	Fetal Brain Male	brain
12	chr1:113065800-113086200	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
13	chr1:113066000-113088800	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
14	chr1:113066000-113114600	Weak transcription	Primary T helper cells PMA-I stimulated	--
15	chr1:113066000-113132200	Weak transcription	Primary T helper naive cells from peripheral blood	blood
16	chr1:113066200-113114400	Weak transcription	Dnd41	blood
17	chr1:113067000-113117400	Weak transcription	Fetal Thymus	thymus
18	chr1:113067800-113090200	Weak transcription	H9 Cell Line	embryonic stem cell
19	chr1:113068000-113089600	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
20	chr1:113068000-113100200	Weak transcription	Fetal Heart	heart
21	chr1:113068600-113086400	Weak transcription	HUVEC	blood vessel
22	chr1:113068800-113087000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
23	chr1:113070400-113086000	Weak transcription	Spleen	Spleen
24	chr1:113070400-113095400	Weak transcription	Gastric	stomach
25	chr1:113070400-113120600	Weak transcription	Right Ventricle	heart
26	chr1:113070600-113088200	Weak transcription	H1 Cell Line	embryonic stem cell
27	chr1:113070600-113111600	Weak transcription	HUES48 Cell Line	embryonic stem cell
28	chr1:113070600-113112400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
29	chr1:113070600-113112400	Weak transcription	Primary hematopoietic stem cells	blood
30	chr1:113070600-113117800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
31	chr1:113070600-113120200	Weak transcription	Brain Inferior Temporal Lobe	brain
32	chr1:113070600-113132400	Weak transcription	Aorta	Aorta
33	chr1:113071200-113090600	Weak transcription	iPS-18 Cell Line	embryonic stem cell
34	chr1:113072000-113084400	Weak transcription	Skeletal Muscle Female	skeletal muscle
35	chr1:113072000-113114400	Weak transcription	Brain Anterior Caudate	brain
36	chr1:113072600-113087000	Weak transcription	Placenta Amnion	Placenta Amnion
37	chr1:113076400-113115200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
38	chr1:113078800-113090200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
39	chr1:113079400-113084800	Weak transcription	Primary T killer memory cells from peripheral blood	blood
40	chr1:113079600-113087000	Weak transcription	HSMMtube	muscle
41	chr1:113080000-113084600	Strong transcription	Liver	Liver
42	chr1:113080000-113085400	Strong transcription	Breast Myoepithelial Primary Cells	Breast
43	chr1:113080200-113084600	Strong transcription	Primary T cells from cord blood	blood
44	chr1:113080200-113085800	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
45	chr1:113080200-113117800	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
46	chr1:113080800-113084200	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
47	chr1:113080800-113084400	Strong transcription	Foreskin Fibroblast Primary Cells skin01	Skin
48	chr1:113080800-113085000	Strong transcription	Fetal Intestine Large	intestine
49	chr1:113080800-113085400	Strong transcription	Fetal Muscle Leg	muscle
50	chr1:113080800-113117400	Weak transcription	HUES6 Cell Line	embryonic stem cell

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links