Variant report

Variant	rs3757778
Chromosome Location	chr7:127456607-127456608
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 72 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:67)

rs_ID	r²[population]
rs1024910	0.83[EUR][1000 genomes]
rs10954164	0.96[AFR][1000 genomes];0.95[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs11768841	0.92[AFR][1000 genomes];0.88[AMR][1000 genomes];0.92[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs11772303	0.82[AFR][1000 genomes];0.97[AMR][1000 genomes];0.89[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs1193333	0.80[AFR][1000 genomes];0.81[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs1193335	0.82[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs12539411	1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs12540484	0.91[AMR][1000 genomes];0.83[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12667197	0.93[AMR][1000 genomes];0.83[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12668077	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];0.98[GIH][hapmap];0.88[JPT][hapmap];0.82[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.89[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12672945	0.83[AMR][1000 genomes];0.82[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs12673293	1.00[AFR][1000 genomes];0.90[AMR][1000 genomes];0.97[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs1419967	1.00[AFR][1000 genomes];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1419968	0.80[CHB][hapmap];0.82[JPT][hapmap]
rs16871926	1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs17151229	0.99[AMR][1000 genomes];0.89[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs17151377	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs17151470	1.00[AFR][1000 genomes];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2058457	1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2241291	0.82[ASW][hapmap];0.92[CEU][hapmap];0.95[CHB][hapmap];0.95[CHD][hapmap];0.88[GIH][hapmap];0.82[JPT][hapmap];0.85[MEX][hapmap];0.95[MKK][hapmap];0.87[TSI][hapmap];0.82[YRI][hapmap];0.83[EUR][1000 genomes]
rs2402871	0.87[AFR][1000 genomes];0.99[AMR][1000 genomes];0.91[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2543477	0.81[EUR][1000 genomes]
rs2582717	1.00[CHB][hapmap];0.84[GIH][hapmap];0.89[JPT][hapmap]
rs327510	0.85[CHB][hapmap]
rs327512	0.85[CHB][hapmap]
rs3757760	0.82[EUR][1000 genomes]
rs3757763	0.92[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];0.91[GIH][hapmap];0.82[JPT][hapmap];0.95[MEX][hapmap];0.91[MKK][hapmap];0.87[TSI][hapmap];0.82[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs3757771	0.83[AMR][1000 genomes]
rs3757780	0.87[AFR][1000 genomes];0.92[AMR][1000 genomes];0.90[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs3779527	0.82[EUR][1000 genomes]
rs3808077	0.82[JPT][hapmap]
rs3808078	0.88[AFR][1000 genomes];0.90[AMR][1000 genomes];0.94[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs3808086	0.92[AFR][1000 genomes];0.88[AMR][1000 genomes];0.95[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs3808088	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.95[GIH][hapmap];0.88[JPT][hapmap];1.00[LWK][hapmap];0.82[MEX][hapmap];0.91[MKK][hapmap];0.92[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.87[AMR][1000 genomes];0.95[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs3824003	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4728079	1.00[AFR][1000 genomes];0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4731377	0.97[AMR][1000 genomes];0.89[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs56185520	0.88[AMR][1000 genomes];0.80[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs58106688	1.00[AFR][1000 genomes];0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs59140894	0.92[AMR][1000 genomes];0.91[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs62481385	0.87[AFR][1000 genomes];0.96[AMR][1000 genomes];0.90[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs62481416	1.00[AFR][1000 genomes];0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs62481419	0.84[AFR][1000 genomes];0.90[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs62481443	1.00[AFR][1000 genomes];0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs62481447	0.88[AFR][1000 genomes];0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs62481450	0.88[AFR][1000 genomes];0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs6467155	0.83[EUR][1000 genomes]
rs6467156	0.83[EUR][1000 genomes]
rs67338333	0.92[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs698408	0.82[AMR][1000 genomes];0.80[ASN][1000 genomes]
rs712703	0.90[CHB][hapmap]
rs712704	0.90[CHB][hapmap]
rs712707	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[AMR][1000 genomes];0.80[ASN][1000 genomes]
rs712715	0.83[AMR][1000 genomes];0.81[ASN][1000 genomes]
rs712718	0.91[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs712719	0.96[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];0.90[GIH][hapmap];1.00[JPT][hapmap];0.85[MEX][hapmap];0.87[TSI][hapmap];0.92[AMR][1000 genomes];0.82[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs765971	0.87[AFR][1000 genomes];0.95[AMR][1000 genomes];0.90[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7789322	0.82[EUR][1000 genomes]
rs806166	0.87[AMR][1000 genomes];0.80[ASN][1000 genomes]
rs806169	0.81[AMR][1000 genomes];0.80[ASN][1000 genomes]
rs806172	1.00[ASW][hapmap];0.96[CEU][hapmap];1.00[CHB][hapmap];0.85[CHD][hapmap];0.90[GIH][hapmap];1.00[JPT][hapmap];0.85[MEX][hapmap];0.86[MKK][hapmap];0.87[TSI][hapmap];0.87[AMR][1000 genomes];0.80[ASN][1000 genomes]
rs806174	0.88[AMR][1000 genomes]
rs806175	0.95[CHB][hapmap];0.81[GIH][hapmap];0.84[JPT][hapmap]
rs806180	0.86[CHB][hapmap];1.00[JPT][hapmap]
rs806188	0.95[CHB][hapmap];1.00[JPT][hapmap];0.81[AMR][1000 genomes]
rs882694	1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs9791922	0.84[AFR][1000 genomes];0.87[AMR][1000 genomes];0.95[EUR][1000 genomes];0.83[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	nsv1022385	chr7:127246656-127971194	Weak transcription Bivalent Enhancer Enhancers Active TSS Bivalent/Poised TSS Strong transcription Genic enhancers Flanking Bivalent TSS/Enh Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	37 gene(s)	inside rSNPs	diseases
2	nsv539120	chr7:127246656-127971194	Enhancers Weak transcription Active TSS Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Strong transcription Flanking Active TSS 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	37 gene(s)	inside rSNPs	diseases
3	nsv1016143	chr7:127251359-127726762	Strong transcription Enhancers Bivalent Enhancer Weak transcription Flanking Active TSS Genic enhancers Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	27 gene(s)	inside rSNPs	diseases
4	nsv831123	chr7:127289511-127510396	Flanking Active TSS Enhancers Weak transcription Strong transcription Genic enhancers ZNF genes & repeats Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	21 gene(s)	inside rSNPs	diseases
5	nsv526535	chr7:127445594-127623840	Enhancers Weak transcription Flanking Active TSS Genic enhancers Strong transcription ZNF genes & repeats Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs3757778	GCC1	cis	lymphoblastoid	seeQTL
rs3757778	GPR37	cis	cerebellum	SCAN

Chromatin state (count:97 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:127382000-127473000	Weak transcription	Hela-S3	cervix
2	chr7:127435000-127459800	Weak transcription	Primary neutrophils fromperipheralblood	blood
3	chr7:127440200-127460800	Weak transcription	Duodenum Smooth Muscle	Duodenum
4	chr7:127441200-127460000	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
5	chr7:127441400-127458200	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
6	chr7:127443200-127460200	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
7	chr7:127448000-127459600	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
8	chr7:127448400-127484800	Weak transcription	Aorta	Aorta
9	chr7:127448600-127459600	Weak transcription	Fetal Intestine Small	intestine
10	chr7:127449000-127484200	Weak transcription	Primary T cells fromperipheralblood	blood
11	chr7:127449200-127459600	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
12	chr7:127449200-127460000	Weak transcription	NH-A	brain
13	chr7:127449200-127460400	Weak transcription	Placenta	Placenta
14	chr7:127449400-127458600	Weak transcription	Primary T helper cells PMA-I stimulated	--
15	chr7:127449400-127460000	Weak transcription	Primary B cells from peripheral blood	blood
16	chr7:127449600-127459400	Weak transcription	Primary monocytes fromperipheralblood	blood
17	chr7:127449600-127459600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
18	chr7:127449600-127459800	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
19	chr7:127449600-127460200	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
20	chr7:127449600-127460800	Weak transcription	Sigmoid Colon	Sigmoid Colon
21	chr7:127449600-127461200	Weak transcription	Right Atrium	heart
22	chr7:127449600-127472600	Weak transcription	Lung	lung
23	chr7:127449800-127456800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
24	chr7:127449800-127459600	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
25	chr7:127449800-127459800	Weak transcription	Primary T helper cells fromperipheralblood	blood
26	chr7:127449800-127460000	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
27	chr7:127449800-127460000	Weak transcription	Fetal Intestine Large	intestine
28	chr7:127449800-127460000	Weak transcription	Rectal Mucosa Donor 29	rectum
29	chr7:127449800-127460000	Weak transcription	Small Intestine	intestine
30	chr7:127449800-127460200	Weak transcription	Fetal Stomach	stomach
31	chr7:127449800-127460200	Weak transcription	NHEK	skin
32	chr7:127449800-127460800	Weak transcription	Brain Substantia Nigra	brain
33	chr7:127449800-127460800	Weak transcription	Fetal Thymus	thymus
34	chr7:127449800-127469200	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
35	chr7:127450000-127459600	Weak transcription	Primary hematopoietic stem cells	blood
36	chr7:127450000-127459600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
37	chr7:127450000-127460800	Weak transcription	Liver	Liver
38	chr7:127450200-127458600	Weak transcription	Primary hematopoietic stem cells short term culture	blood
39	chr7:127450400-127457800	Weak transcription	Adipose Nuclei	Adipose
40	chr7:127450400-127459600	Weak transcription	Placenta Amnion	Placenta Amnion
41	chr7:127450400-127460200	Weak transcription	Duodenum Mucosa	Duodenum
42	chr7:127450400-127460200	Weak transcription	HMEC	breast
43	chr7:127450600-127460000	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
44	chr7:127450800-127471200	Weak transcription	Dnd41	blood
45	chr7:127451200-127460000	Weak transcription	Primary B cells from cord blood	blood
46	chr7:127452600-127460000	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
47	chr7:127452800-127460000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
48	chr7:127452800-127460400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
49	chr7:127452800-127462600	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
50	chr7:127453000-127459600	Weak transcription	Psoas Muscle	Psoas

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