Variant report

Variant	rs3808078
Chromosome Location	chr7:127581677-127581678
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 87 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:82)

rs_ID	r²[population]
rs1024910	0.88[AMR][1000 genomes];0.88[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs10954164	0.84[AFR][1000 genomes];0.98[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs11768841	0.96[AFR][1000 genomes];0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs11772303	0.87[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs1193331	0.88[ASN][1000 genomes]
rs1193333	0.84[AFR][1000 genomes];0.91[AMR][1000 genomes];0.89[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1193335	0.92[AMR][1000 genomes];0.89[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs124756	0.85[CHB][hapmap];0.83[JPT][hapmap];1.00[YRI][hapmap];0.80[AMR][1000 genomes]
rs12539411	0.88[AFR][1000 genomes];0.90[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs12540484	0.81[AMR][1000 genomes]
rs12667197	0.83[AMR][1000 genomes]
rs12668077	1.00[ASW][hapmap];1.00[CEU][hapmap];0.95[CHB][hapmap];0.97[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.85[MEX][hapmap];0.91[MKK][hapmap];0.95[TSI][hapmap];0.82[YRI][hapmap];0.88[AFR][1000 genomes];0.89[AMR][1000 genomes];0.93[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs12672945	0.83[AMR][1000 genomes]
rs12673293	0.88[AFR][1000 genomes];0.90[AMR][1000 genomes];0.98[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs1345509	0.87[JPT][hapmap]
rs1419967	0.88[AFR][1000 genomes];0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs1419968	0.93[JPT][hapmap]
rs16871926	0.88[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs17151229	0.88[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs17151377	0.88[AFR][1000 genomes];0.92[AMR][1000 genomes];0.94[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs17151470	0.88[AFR][1000 genomes];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs17732677	0.80[ASN][1000 genomes]
rs2058457	0.88[AFR][1000 genomes];0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2241291	0.82[ASW][hapmap];0.92[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];0.91[GIH][hapmap];0.94[JPT][hapmap];1.00[LWK][hapmap];0.85[MEX][hapmap];0.87[MKK][hapmap];0.92[TSI][hapmap];1.00[YRI][hapmap];0.87[AMR][1000 genomes];0.88[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2402871	0.88[AMR][1000 genomes];0.86[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs2543477	0.81[AMR][1000 genomes];0.86[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs322813	0.85[CHB][hapmap];0.83[JPT][hapmap];1.00[YRI][hapmap]
rs322819	0.85[CHB][hapmap];0.82[GIH][hapmap];0.83[JPT][hapmap];0.85[MEX][hapmap]
rs322820	0.81[CHB][hapmap];0.82[GIH][hapmap];0.83[JPT][hapmap];0.85[MEX][hapmap]
rs322821	0.81[CHB][hapmap];0.82[GIH][hapmap];0.83[JPT][hapmap];1.00[LWK][hapmap];0.85[MEX][hapmap];1.00[YRI][hapmap];0.80[AMR][1000 genomes]
rs322822	0.80[AMR][1000 genomes]
rs322823	0.85[CHB][hapmap];0.83[JPT][hapmap];0.81[MEX][hapmap]
rs322824	0.80[AMR][1000 genomes]
rs322825	0.85[CHB][hapmap];0.81[GIH][hapmap];0.81[MEX][hapmap];1.00[YRI][hapmap];0.80[AMR][1000 genomes]
rs322826	0.80[CHB][hapmap];0.83[JPT][hapmap]
rs322827	0.81[JPT][hapmap]
rs322828	0.81[JPT][hapmap]
rs322829	0.80[AMR][1000 genomes]
rs322830	0.80[AMR][1000 genomes]
rs322837	0.80[AMR][1000 genomes]
rs322840	0.85[CHB][hapmap];0.82[GIH][hapmap];0.83[JPT][hapmap];0.85[MEX][hapmap];0.82[YRI][hapmap]
rs3757754	0.80[AMR][1000 genomes]
rs3757759	0.80[AMR][1000 genomes]
rs3757760	0.82[ASW][hapmap];0.92[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];0.91[GIH][hapmap];0.94[JPT][hapmap];1.00[LWK][hapmap];0.85[MEX][hapmap];0.87[MKK][hapmap];0.92[TSI][hapmap];1.00[YRI][hapmap];0.86[AMR][1000 genomes];0.87[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs3757763	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.93[GIH][hapmap];0.94[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.83[MKK][hapmap];0.92[TSI][hapmap];0.92[AMR][1000 genomes];0.90[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs3757771	0.84[AFR][1000 genomes];0.88[AMR][1000 genomes];0.82[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs3757778	0.88[AFR][1000 genomes];0.90[AMR][1000 genomes];0.94[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs3757780	0.82[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs3779522	0.80[AMR][1000 genomes]
rs3779523	0.85[CHB][hapmap];0.83[JPT][hapmap];0.80[AMR][1000 genomes]
rs3779526	0.87[JPT][hapmap]
rs3779527	0.86[AMR][1000 genomes];0.87[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs3808056	0.81[CEU][hapmap];0.80[CHB][hapmap];0.82[GIH][hapmap];0.81[JPT][hapmap];0.85[TSI][hapmap];0.81[EUR][1000 genomes]
rs3808077	0.81[CHB][hapmap];0.94[JPT][hapmap]
rs3808082	0.83[ASN][1000 genomes]
rs3808086	0.96[AFR][1000 genomes];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs3808088	1.00[ASW][hapmap];1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];0.85[MEX][hapmap];1.00[MKK][hapmap];0.97[TSI][hapmap];0.82[YRI][hapmap];0.88[AFR][1000 genomes];0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs3823995	0.87[JPT][hapmap]
rs3824003	0.88[AFR][1000 genomes];0.92[AMR][1000 genomes];0.94[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs4728079	0.88[AFR][1000 genomes];0.90[AMR][1000 genomes];0.94[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs4731377	0.87[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs4731386	0.83[ASN][1000 genomes]
rs58106688	0.88[AFR][1000 genomes];0.90[AMR][1000 genomes];0.94[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs59140894	0.82[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs62481385	0.86[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs62481416	0.88[AFR][1000 genomes];0.90[AMR][1000 genomes];0.94[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs62481419	0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs62481443	0.88[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs62481447	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs62481450	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6467155	0.89[AMR][1000 genomes];0.88[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6467156	0.89[AMR][1000 genomes];0.88[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs67338333	0.80[AFR][1000 genomes];0.90[AMR][1000 genomes];0.94[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs6944446	0.81[JPT][hapmap]
rs6969233	0.80[AMR][1000 genomes]
rs6973092	0.87[JPT][hapmap]
rs712718	0.81[AMR][1000 genomes]
rs712719	0.82[AMR][1000 genomes]
rs765971	0.85[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs7789322	0.88[AMR][1000 genomes];0.87[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs882694	0.88[AFR][1000 genomes];0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs9791922	0.88[AFR][1000 genomes];0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[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	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
5	nsv1024743	chr7:127498695-127670004	Genic enhancers Strong transcription Weak transcription Enhancers Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Active TSS Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	6 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs3808078	COPG2	cis	cerebellum	SCAN
rs3808078	GPR37	cis	cerebellum	SCAN
rs3808078	GCC1	cis	lymphoblastoid	seeQTL

Chromatin state (count:123 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:127562200-127589800	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
2	chr7:127568200-127583400	Weak transcription	Fetal Heart	heart
3	chr7:127568200-127594000	Weak transcription	Rectal Smooth Muscle	rectum
4	chr7:127569800-127615600	Weak transcription	Colonic Mucosa	Colon
5	chr7:127570000-127583800	Weak transcription	Psoas Muscle	Psoas
6	chr7:127570000-127585800	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
7	chr7:127570000-127591400	Weak transcription	Primary neutrophils fromperipheralblood	blood
8	chr7:127570600-127584600	Weak transcription	Skeletal Muscle Female	skeletal muscle
9	chr7:127570600-127615600	Weak transcription	Small Intestine	intestine
10	chr7:127570600-127615800	Weak transcription	Esophagus	oesophagus
11	chr7:127570600-127616400	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
12	chr7:127570800-127583600	Weak transcription	Lung	lung
13	chr7:127570800-127589200	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
14	chr7:127570800-127599600	Weak transcription	Stomach Smooth Muscle	stomach
15	chr7:127570800-127618200	Weak transcription	Rectal Mucosa Donor 29	rectum
16	chr7:127571000-127615600	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
17	chr7:127571000-127615800	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
18	chr7:127571400-127583600	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
19	chr7:127571400-127589800	Weak transcription	Fetal Stomach	stomach
20	chr7:127571400-127617800	Weak transcription	Primary T killer memory cells from peripheral blood	blood
21	chr7:127571600-127582000	Weak transcription	Hela-S3	cervix
22	chr7:127571600-127582600	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
23	chr7:127571600-127583600	Weak transcription	Right Ventricle	heart
24	chr7:127571600-127584800	Weak transcription	Primary T helper naive cells from peripheral blood	blood
25	chr7:127571600-127594400	Weak transcription	Duodenum Smooth Muscle	Duodenum
26	chr7:127571600-127618000	Weak transcription	Rectal Mucosa Donor 31	rectum
27	chr7:127571800-127583000	Weak transcription	Thymus	Thymus
28	chr7:127571800-127583600	Weak transcription	Brain Substantia Nigra	brain
29	chr7:127571800-127584000	Weak transcription	H1 Cell Line	embryonic stem cell
30	chr7:127571800-127602800	Weak transcription	Aorta	Aorta
31	chr7:127572000-127582800	Weak transcription	Adipose Nuclei	Adipose
32	chr7:127572000-127583600	Weak transcription	Placenta	Placenta
33	chr7:127572000-127584200	Weak transcription	Left Ventricle	heart
34	chr7:127572200-127583600	Weak transcription	Fetal Lung	lung
35	chr7:127572400-127582400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
36	chr7:127573000-127582400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
37	chr7:127573200-127588600	Weak transcription	Ovary	ovary
38	chr7:127573800-127583800	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
39	chr7:127574400-127582400	Weak transcription	HUVEC	blood vessel
40	chr7:127574400-127587600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
41	chr7:127576400-127582400	Weak transcription	Duodenum Mucosa	Duodenum
42	chr7:127576400-127583600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
43	chr7:127576400-127584200	Weak transcription	Right Atrium	heart
44	chr7:127576400-127589000	Weak transcription	Fetal Kidney	kidney
45	chr7:127576400-127607000	Weak transcription	Spleen	Spleen
46	chr7:127576400-127615800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
47	chr7:127577400-127588000	Weak transcription	HUES6 Cell Line	embryonic stem cell
48	chr7:127577600-127582000	Weak transcription	Brain Inferior Temporal Lobe	brain
49	chr7:127577600-127583600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
50	chr7:127577600-127583600	Weak transcription	Pancreas	Pancrea

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