Variant report

Variant	rs12668077
Chromosome Location	chr7:127476253-127476254
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr7:127473878..127476646-chr7:127477198..127480540,3	K562	blood:
2	chr7:127306135..127308740-chr7:127475843..127478656,2	K562	blood:
3	chr7:127031985..127033507-chr7:127475912..127478469,2	K562	blood:
4	chr7:127471216..127474145-chr7:127474684..127476389,2	K562	blood:
5	chr7:127473878..127476756-chr7:127477234..127480540,3	K562	blood:

Variant related genes	Relation type
ENSG00000048405	Chromatin interaction

Extended variants
information (count: 71 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:66)

rs_ID	r²[population]
rs1024910	0.84[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs10954164	0.96[AFR][1000 genomes];0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs11768841	0.92[AFR][1000 genomes];0.95[AMR][1000 genomes];0.91[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs11772303	0.82[AFR][1000 genomes];0.89[AMR][1000 genomes];0.88[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs1193333	0.80[AFR][1000 genomes];0.80[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs1193335	0.81[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs12539411	1.00[AFR][1000 genomes];0.89[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs12540484	0.83[AMR][1000 genomes];0.82[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs12667197	0.85[AMR][1000 genomes];0.82[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs12672945	0.92[AMR][1000 genomes];0.81[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs12673293	1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1345509	0.87[JPT][hapmap]
rs1419967	1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1419968	0.80[CHB][hapmap];0.93[JPT][hapmap];0.84[ASN][1000 genomes]
rs16871926	1.00[AFR][1000 genomes];0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs17151229	0.90[AMR][1000 genomes];0.88[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs17151377	1.00[AFR][1000 genomes];0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs17151470	1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2058457	1.00[AFR][1000 genomes];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[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];0.95[MEX][hapmap];0.95[MKK][hapmap];0.87[TSI][hapmap];0.82[YRI][hapmap];0.84[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs2402871	0.87[AFR][1000 genomes];0.90[AMR][1000 genomes];0.90[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2582717	1.00[CHB][hapmap];0.86[GIH][hapmap]
rs3757760	0.82[ASW][hapmap];0.92[CEU][hapmap];0.95[CHB][hapmap];0.97[CHD][hapmap];0.86[GIH][hapmap];0.94[JPT][hapmap];0.95[MEX][hapmap];0.95[MKK][hapmap];0.87[TSI][hapmap];0.82[YRI][hapmap];0.83[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs3757763	0.92[CEU][hapmap];0.95[CHB][hapmap];0.97[CHD][hapmap];0.88[GIH][hapmap];0.94[JPT][hapmap];0.86[MEX][hapmap];0.91[MKK][hapmap];0.87[TSI][hapmap];0.81[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs3757771	0.90[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs3757778	1.00[AFR][1000 genomes];0.89[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs3757780	0.87[AFR][1000 genomes];0.91[AMR][1000 genomes];0.89[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs3779526	0.87[JPT][hapmap]
rs3779527	0.83[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs3808077	0.94[JPT][hapmap]
rs3808078	0.88[AFR][1000 genomes];0.89[AMR][1000 genomes];0.93[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs3808086	0.92[AFR][1000 genomes];0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];0.90[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[MEX][hapmap];0.91[MKK][hapmap];0.92[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs3823995	0.87[JPT][hapmap]
rs3824003	1.00[AFR][1000 genomes];0.91[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4728079	1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4731377	0.89[AMR][1000 genomes];0.88[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs56185520	0.80[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs58106688	1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs59140894	0.91[AMR][1000 genomes];0.90[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs62481385	0.87[AFR][1000 genomes];0.87[AMR][1000 genomes];0.89[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs62481416	1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62481419	0.84[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62481443	1.00[AFR][1000 genomes];0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs62481447	0.88[AFR][1000 genomes];0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs62481450	0.88[AFR][1000 genomes];0.89[AMR][1000 genomes];0.94[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs6467155	0.85[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs6467156	0.85[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs67338333	0.92[AFR][1000 genomes];0.89[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6944446	0.81[JPT][hapmap]
rs6973092	0.87[JPT][hapmap]
rs698408	0.82[ASN][1000 genomes]
rs712707	0.95[CEU][hapmap];1.00[CHB][hapmap];0.88[JPT][hapmap];0.82[ASN][1000 genomes]
rs712715	0.83[ASN][1000 genomes]
rs712718	0.83[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs712719	0.96[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];0.93[GIH][hapmap];0.88[JPT][hapmap];0.87[TSI][hapmap];0.84[AMR][1000 genomes];0.81[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs765971	0.87[AFR][1000 genomes];0.94[AMR][1000 genomes];0.89[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7789322	0.84[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs806166	0.82[ASN][1000 genomes]
rs806169	0.81[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];0.86[MKK][hapmap];0.87[TSI][hapmap];0.81[ASN][1000 genomes]
rs806174	0.80[AMR][1000 genomes]
rs806175	0.95[CHB][hapmap]
rs806180	0.86[CHB][hapmap];0.88[JPT][hapmap]
rs882694	1.00[AFR][1000 genomes];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9791922	0.84[AFR][1000 genomes];0.96[AMR][1000 genomes];0.94[EUR][1000 genomes];0.88[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
rs12668077	GCC1	cis	lymphoblastoid	seeQTL
rs12668077	GPR37	cis	cerebellum	SCAN

Chromatin state (count:72 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:127448400-127484800	Weak transcription	Aorta	Aorta
2	chr7:127449000-127484200	Weak transcription	Primary T cells fromperipheralblood	blood
3	chr7:127456400-127476800	Weak transcription	Esophagus	oesophagus
4	chr7:127457000-127477600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
5	chr7:127457000-127497800	Weak transcription	Gastric	stomach
6	chr7:127460800-127477200	Weak transcription	Primary T helper cells fromperipheralblood	blood
7	chr7:127461000-127484400	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
8	chr7:127461000-127495600	Weak transcription	Primary T helper naive cells from peripheral blood	blood
9	chr7:127461000-127497600	Weak transcription	Fetal Stomach	stomach
10	chr7:127461400-127476800	Weak transcription	HSMM	muscle
11	chr7:127461400-127477000	Weak transcription	Primary T cells from cord blood	blood
12	chr7:127461400-127477200	Weak transcription	Primary T helper cells PMA-I stimulated	--
13	chr7:127461400-127477200	Weak transcription	Duodenum Mucosa	Duodenum
14	chr7:127461400-127477400	Weak transcription	NH-A	brain
15	chr7:127461400-127477600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
16	chr7:127461600-127485600	Weak transcription	HSMMtube	muscle
17	chr7:127463200-127477200	Weak transcription	Rectal Mucosa Donor 31	rectum
18	chr7:127463400-127477600	Weak transcription	Fetal Intestine Small	intestine
19	chr7:127463400-127479000	Weak transcription	Fetal Lung	lung
20	chr7:127463600-127477600	Weak transcription	HMEC	breast
21	chr7:127463600-127482800	Weak transcription	Small Intestine	intestine
22	chr7:127463800-127477200	Weak transcription	NHEK	skin
23	chr7:127465000-127483200	Weak transcription	HepG2	liver
24	chr7:127469400-127488800	Weak transcription	Thymus	Thymus
25	chr7:127469800-127477200	Weak transcription	Primary B cells from cord blood	blood
26	chr7:127470200-127484400	Weak transcription	Fetal Heart	heart
27	chr7:127471800-127477200	Weak transcription	Fetal Kidney	kidney
28	chr7:127471800-127478000	Weak transcription	Right Ventricle	heart
29	chr7:127471800-127484200	Weak transcription	Left Ventricle	heart
30	chr7:127471800-127495600	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
31	chr7:127472200-127484000	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
32	chr7:127472600-127476600	Enhancers	Primary monocytes fromperipheralblood	blood
33	chr7:127472600-127477600	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
34	chr7:127472800-127477200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
35	chr7:127472800-127483800	Weak transcription	Brain Substantia Nigra	brain
36	chr7:127473600-127477600	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
37	chr7:127473800-127477200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
38	chr7:127473800-127477600	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
39	chr7:127473800-127477600	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
40	chr7:127473800-127479000	Weak transcription	Pancreas	Pancrea
41	chr7:127473800-127479000	Weak transcription	Right Atrium	heart
42	chr7:127473800-127479000	Weak transcription	Osteobl	bone
43	chr7:127473800-127482800	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
44	chr7:127473800-127482800	Weak transcription	Muscle Satellite Cultured Cells	--
45	chr7:127474000-127484400	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
46	chr7:127474000-127495800	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
47	chr7:127474200-127485200	Weak transcription	Hela-S3	cervix
48	chr7:127474200-127490400	Weak transcription	NHLF	lung
49	chr7:127474400-127477400	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
50	chr7:127474400-127479200	ZNF genes & repeats	GM12878-XiMat	blood

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