Variant report

Variant	rs2402871
Chromosome Location	chr7:127439519-127439520
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr7:127433199..127438037-chr7:127438962..127443082,8	K562	blood:
2	chr7:127436923..127439830-chr7:127443618..127447168,4	K562	blood:
3	chr7:127425728..127430973-chr7:127434300..127441103,9	K562	blood:
4	chr7:127439262..127442227-chr7:127516477..127518829,2	MCF-7	breast:

Extended variants
information (count: 73 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:68)

rs_ID	r²[population]
rs10954164	0.83[AFR][1000 genomes];0.86[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs11768841	0.87[AMR][1000 genomes];0.83[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs11772303	0.87[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs1193333	0.80[AMR][1000 genomes]
rs1193335	0.81[AMR][1000 genomes]
rs12539411	0.87[AFR][1000 genomes];0.93[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs12540484	0.92[AMR][1000 genomes];0.92[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12667197	0.95[AMR][1000 genomes];0.92[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12668077	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.86[MEX][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.87[AFR][1000 genomes];0.90[AMR][1000 genomes];0.90[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12672945	0.85[AMR][1000 genomes];0.84[ASN][1000 genomes]
rs12673293	0.87[AFR][1000 genomes];0.91[AMR][1000 genomes];0.88[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1345509	0.87[JPT][hapmap]
rs1419967	0.87[AFR][1000 genomes];0.95[AMR][1000 genomes];0.91[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1419968	0.80[CHB][hapmap];0.93[JPT][hapmap]
rs16871926	0.87[AFR][1000 genomes];0.93[AMR][1000 genomes];0.88[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs17151229	0.83[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs17151377	0.87[AFR][1000 genomes];0.96[AMR][1000 genomes];0.91[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs17151470	0.87[AFR][1000 genomes];0.95[AMR][1000 genomes];0.88[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2058457	0.87[AFR][1000 genomes];0.93[AMR][1000 genomes];0.90[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2241291	0.82[ASW][hapmap];0.92[CEU][hapmap];0.95[CHB][hapmap];0.97[CHD][hapmap];0.86[GIH][hapmap];0.94[JPT][hapmap];0.81[MEX][hapmap];0.87[TSI][hapmap];0.82[YRI][hapmap]
rs2582717	1.00[CHB][hapmap];0.86[GIH][hapmap]
rs327510	0.85[CHB][hapmap]
rs327512	0.85[CHB][hapmap]
rs327516	0.85[CHB][hapmap]
rs3757763	0.92[CEU][hapmap];0.95[CHB][hapmap];0.97[CHD][hapmap];0.88[GIH][hapmap];0.94[JPT][hapmap];1.00[MEX][hapmap];0.87[TSI][hapmap];0.81[AMR][1000 genomes]
rs3757771	0.82[AMR][1000 genomes];0.80[ASN][1000 genomes]
rs3757778	0.87[AFR][1000 genomes];0.99[AMR][1000 genomes];0.91[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs3757780	0.91[AFR][1000 genomes];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs3779526	0.87[JPT][hapmap]
rs3808077	0.94[JPT][hapmap]
rs3808078	0.88[AMR][1000 genomes];0.86[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs3808086	0.87[AMR][1000 genomes];0.87[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs3808088	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.86[MEX][hapmap];0.87[MKK][hapmap];0.92[TSI][hapmap];1.00[YRI][hapmap];0.87[AFR][1000 genomes];0.89[AMR][1000 genomes];0.87[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs3824003	0.87[AFR][1000 genomes];0.96[AMR][1000 genomes];0.91[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4728079	0.87[AFR][1000 genomes];0.91[AMR][1000 genomes];0.91[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4731377	0.83[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs56185520	0.90[AMR][1000 genomes];0.89[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs58106688	0.87[AFR][1000 genomes];0.91[AMR][1000 genomes];0.91[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs59140894	0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs62481385	0.91[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs62481416	0.87[AFR][1000 genomes];0.91[AMR][1000 genomes];0.91[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs62481419	0.91[AMR][1000 genomes];0.90[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs62481443	0.87[AFR][1000 genomes];0.91[AMR][1000 genomes];0.87[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs62481447	0.91[AMR][1000 genomes];0.87[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs62481450	0.88[AMR][1000 genomes];0.86[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs67338333	0.94[AMR][1000 genomes];0.91[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs698406	0.90[CHB][hapmap]
rs698408	0.83[AMR][1000 genomes];0.80[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs712697	0.90[CHB][hapmap]
rs712700	0.90[CHB][hapmap]
rs712701	0.90[CHB][hapmap]
rs712703	0.90[CHB][hapmap]
rs712704	0.90[CHB][hapmap]
rs712707	0.95[CEU][hapmap];1.00[CHB][hapmap];0.88[JPT][hapmap];0.86[AMR][1000 genomes];0.86[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs712715	0.85[AMR][1000 genomes];0.87[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs712718	0.92[AMR][1000 genomes];0.88[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs712719	0.96[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];0.93[GIH][hapmap];0.88[JPT][hapmap];0.90[MEX][hapmap];0.87[MKK][hapmap];0.87[TSI][hapmap];0.93[AMR][1000 genomes];0.91[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs765971	0.91[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs806166	0.88[AMR][1000 genomes];0.85[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs806169	0.82[AMR][1000 genomes];0.85[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs806172	1.00[ASW][hapmap];0.96[CEU][hapmap];1.00[CHB][hapmap];0.87[CHD][hapmap];0.93[GIH][hapmap];0.88[JPT][hapmap];0.90[MEX][hapmap];0.90[MKK][hapmap];0.87[TSI][hapmap];0.88[AMR][1000 genomes];0.85[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs806174	0.90[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs806175	0.95[CHB][hapmap]
rs806180	0.86[CHB][hapmap];0.88[JPT][hapmap]
rs806188	0.95[CHB][hapmap];0.88[JPT][hapmap];0.82[AMR][1000 genomes]
rs806193	0.93[CHB][hapmap]
rs882694	0.87[AFR][1000 genomes];0.93[AMR][1000 genomes];0.90[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs9791922	0.89[AMR][1000 genomes];0.87[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	nsv1030387	chr7:127348973-127455890	Weak transcription Enhancers Strong transcription Genic enhancers ZNF genes & repeats Flanking Active TSS Bivalent Enhancer Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs2402871	GPR37	cis	cerebellum	SCAN
rs2402871	GCC1	cis	lymphoblastoid	seeQTL

Chromatin state (count:106 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:127382000-127473000	Weak transcription	Hela-S3	cervix
2	chr7:127401000-127447600	Weak transcription	Fetal Intestine Large	intestine
3	chr7:127401000-127447800	Weak transcription	Fetal Intestine Small	intestine
4	chr7:127407400-127447600	Weak transcription	Dnd41	blood
5	chr7:127422400-127445400	Weak transcription	Aorta	Aorta
6	chr7:127423000-127449200	Weak transcription	Small Intestine	intestine
7	chr7:127423200-127440000	Weak transcription	Sigmoid Colon	Sigmoid Colon
8	chr7:127423200-127447600	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
9	chr7:127423400-127449000	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
10	chr7:127423600-127447400	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
11	chr7:127427600-127447600	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
12	chr7:127427600-127447600	Weak transcription	Thymus	Thymus
13	chr7:127429800-127447600	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
14	chr7:127429800-127448200	Weak transcription	A549	lung
15	chr7:127430800-127444400	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
16	chr7:127431000-127447600	Weak transcription	Fetal Thymus	thymus
17	chr7:127431000-127449000	Weak transcription	Placenta Amnion	Placenta Amnion
18	chr7:127431400-127447600	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
19	chr7:127431600-127449400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
20	chr7:127432000-127442800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
21	chr7:127432000-127447600	Weak transcription	NHLF	lung
22	chr7:127432000-127448800	Weak transcription	NHDF-Ad	bronchial
23	chr7:127432400-127444400	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
24	chr7:127432400-127446800	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
25	chr7:127432400-127447600	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
26	chr7:127432600-127447400	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
27	chr7:127432600-127447600	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
28	chr7:127433800-127442400	Weak transcription	GM12878-XiMat	blood
29	chr7:127434000-127439800	Weak transcription	HepG2	liver
30	chr7:127434400-127447200	Weak transcription	Primary hematopoietic stem cells	blood
31	chr7:127435000-127439800	Weak transcription	Brain Angular Gyrus	brain
32	chr7:127435000-127447400	Weak transcription	Primary B cells from peripheral blood	blood
33	chr7:127435000-127447600	Weak transcription	Primary B cells from cord blood	blood
34	chr7:127435000-127448800	Weak transcription	Muscle Satellite Cultured Cells	--
35	chr7:127435000-127459800	Weak transcription	Primary neutrophils fromperipheralblood	blood
36	chr7:127435400-127440200	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
37	chr7:127435600-127447200	Weak transcription	Osteobl	bone
38	chr7:127437200-127440200	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
39	chr7:127437200-127440400	Enhancers	HUES64 Cell Line	embryonic stem cell
40	chr7:127437200-127440400	Enhancers	iPS-18 Cell Line	embryonic stem cell
41	chr7:127437200-127440600	Enhancers	HUES48 Cell Line	embryonic stem cell
42	chr7:127437200-127455400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
43	chr7:127437400-127440000	Enhancers	iPS DF 6.9 Cell Line	embryonic stem cell
44	chr7:127437400-127440200	Enhancers	iPS-15b Cell Line	embryonic stem cell
45	chr7:127437400-127440200	Enhancers	iPS-20b Cell Line	embryonic stem cell
46	chr7:127437400-127440400	Enhancers	Skeletal Muscle Male	skeletal muscle
47	chr7:127437400-127441200	Enhancers	Cortex derived primary cultured neurospheres	brain
48	chr7:127437400-127447600	Weak transcription	Placenta	Placenta
49	chr7:127437400-127447800	Weak transcription	Lung	lung
50	chr7:127437600-127440600	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain

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