Variant report

Variant	rs10269684
Chromosome Location	chr7:116789768-116789769
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr7:116789339-116789796	K562	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr7:116785354..116788256-chr7:116788814..116790892,2	K562	blood:

Variant related genes	Relation type
ST7-AS2	TF binding region
ENSG00000226367	Chromatin interaction

Extended variants
information (count: 101 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:100)

rs_ID	r²[population]
rs10224047	0.98[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10224800	0.98[AFR][1000 genomes];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10228205	1.00[CHB][hapmap];1.00[CHD][hapmap];0.88[GIH][hapmap];0.93[JPT][hapmap];1.00[ASN][1000 genomes]
rs10235357	1.00[ASN][1000 genomes]
rs10253112	1.00[ASN][1000 genomes]
rs10260273	0.99[ASN][1000 genomes]
rs10260934	1.00[CHB][hapmap];1.00[CHD][hapmap];0.88[GIH][hapmap];0.93[JPT][hapmap];1.00[ASN][1000 genomes]
rs10262380	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs10270156	0.88[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10270160	1.00[ASN][1000 genomes]
rs10278192	0.93[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10280789	0.88[GIH][hapmap];1.00[ASN][1000 genomes]
rs10487358	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.96[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];0.96[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12333554	1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[ASN][1000 genomes]
rs12333994	1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[ASN][1000 genomes]
rs12670227	0.90[ASN][1000 genomes]
rs12671521	1.00[ASN][1000 genomes]
rs153015	1.00[CHB][hapmap];0.92[JPT][hapmap];0.91[ASN][1000 genomes]
rs153016	1.00[CHB][hapmap];0.96[CHD][hapmap];0.88[GIH][hapmap];0.93[JPT][hapmap];0.91[ASN][1000 genomes]
rs17139387	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs17139390	1.00[CHB][hapmap];1.00[CHD][hapmap];0.83[GIH][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs171552	0.97[ASN][1000 genomes]
rs171553	0.90[ASN][1000 genomes]
rs173496	1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[ASN][1000 genomes]
rs185187	1.00[CHB][hapmap];0.96[CHD][hapmap];0.88[GIH][hapmap];1.00[JPT][hapmap];0.91[ASN][1000 genomes]
rs192238	1.00[CHB][hapmap];0.93[JPT][hapmap];0.91[ASN][1000 genomes]
rs193555	1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[ASN][1000 genomes]
rs193556	0.89[ASN][1000 genomes]
rs193557	0.90[ASN][1000 genomes]
rs193559	0.90[ASN][1000 genomes]
rs193560	1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[ASN][1000 genomes]
rs193561	1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[ASN][1000 genomes]
rs193562	0.82[ASW][hapmap];0.89[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];0.89[GIH][hapmap];0.93[JPT][hapmap];1.00[MEX][hapmap];0.82[MKK][hapmap];0.93[TSI][hapmap];0.94[AMR][1000 genomes];0.87[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs193563	1.00[CHB][hapmap];0.96[CHD][hapmap];0.88[GIH][hapmap];0.93[JPT][hapmap];0.90[ASN][1000 genomes]
rs193564	1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[ASN][1000 genomes]
rs193565	1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[ASN][1000 genomes]
rs193566	0.90[ASN][1000 genomes]
rs193567	1.00[CHB][hapmap];0.96[CHD][hapmap];0.83[GIH][hapmap];0.84[JPT][hapmap];0.91[ASN][1000 genomes]
rs193568	1.00[CHB][hapmap];0.96[CHD][hapmap];0.88[GIH][hapmap];0.93[JPT][hapmap];0.91[ASN][1000 genomes]
rs193569	1.00[CHB][hapmap];0.96[CHD][hapmap];0.88[GIH][hapmap];0.93[JPT][hapmap];0.91[ASN][1000 genomes]
rs193570	1.00[CHB][hapmap];0.86[CHD][hapmap];0.88[GIH][hapmap];0.86[JPT][hapmap];0.91[ASN][1000 genomes]
rs2188692	1.00[CHB][hapmap];1.00[JPT][hapmap];0.99[ASN][1000 genomes]
rs2214167	0.81[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.94[MEX][hapmap];0.92[MKK][hapmap];0.96[TSI][hapmap];0.96[YRI][hapmap];0.96[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2402154	0.99[ASN][1000 genomes]
rs2402155	1.00[CHB][hapmap];1.00[JPT][hapmap];0.99[ASN][1000 genomes]
rs2402156	1.00[CHB][hapmap];1.00[JPT][hapmap];0.99[ASN][1000 genomes]
rs2402157	1.00[CHB][hapmap];1.00[CHD][hapmap];0.88[GIH][hapmap];1.00[JPT][hapmap];0.99[ASN][1000 genomes]
rs2402158	1.00[CHB][hapmap];1.00[CHD][hapmap];0.88[GIH][hapmap];0.85[JPT][hapmap];0.99[ASN][1000 genomes]
rs2402159	1.00[CHB][hapmap];1.00[CHD][hapmap];0.88[GIH][hapmap];0.93[JPT][hapmap];0.99[ASN][1000 genomes]
rs28481622	0.90[ASN][1000 genomes]
rs28626669	0.90[ASN][1000 genomes]
rs34656305	0.81[EUR][1000 genomes]
rs3808215	1.00[CHB][hapmap];0.93[JPT][hapmap];0.99[ASN][1000 genomes]
rs3824031	0.91[ASN][1000 genomes]
rs38861	1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[ASN][1000 genomes]
rs38862	1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[ASN][1000 genomes]
rs38863	0.91[ASN][1000 genomes]
rs38864	0.91[ASN][1000 genomes]
rs38865	0.91[ASN][1000 genomes]
rs38866	1.00[CHB][hapmap];0.92[JPT][hapmap];0.91[ASN][1000 genomes]
rs38867	1.00[CHB][hapmap];0.93[JPT][hapmap];0.91[ASN][1000 genomes]
rs38868	1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[ASN][1000 genomes]
rs38869	1.00[CHB][hapmap];0.91[JPT][hapmap];0.91[ASN][1000 genomes]
rs38870	1.00[CHB][hapmap];0.96[CHD][hapmap];0.88[GIH][hapmap];0.93[JPT][hapmap];0.91[ASN][1000 genomes]
rs38871	1.00[CHB][hapmap];0.93[JPT][hapmap];0.91[ASN][1000 genomes]
rs38872	1.00[CHB][hapmap];0.93[JPT][hapmap];0.91[ASN][1000 genomes]
rs38873	0.91[ASN][1000 genomes]
rs38874	0.89[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[AMR][1000 genomes];0.86[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs38875	0.83[CEU][hapmap];1.00[CHB][hapmap];0.96[CHD][hapmap];0.89[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.90[TSI][hapmap];0.93[AMR][1000 genomes];0.86[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs38876	0.91[ASN][1000 genomes]
rs38877	0.91[ASN][1000 genomes]
rs38878	1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[ASN][1000 genomes]
rs38879	0.94[AMR][1000 genomes];0.87[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs38880	1.00[CHB][hapmap];0.96[CHD][hapmap];0.88[GIH][hapmap];0.93[JPT][hapmap];0.91[ASN][1000 genomes]
rs38881	1.00[CHB][hapmap];0.93[JPT][hapmap];0.91[ASN][1000 genomes]
rs38882	1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[ASN][1000 genomes]
rs38883	1.00[CHB][hapmap];0.96[CHD][hapmap];0.88[GIH][hapmap];1.00[JPT][hapmap];0.91[ASN][1000 genomes]
rs38884	0.91[ASN][1000 genomes]
rs38885	1.00[CHB][hapmap];0.93[JPT][hapmap];0.91[ASN][1000 genomes]
rs38886	1.00[CHB][hapmap];0.93[JPT][hapmap];0.91[ASN][1000 genomes]
rs38887	1.00[CHB][hapmap];0.92[CHD][hapmap];0.88[GIH][hapmap];0.93[JPT][hapmap];0.91[ASN][1000 genomes]
rs38888	0.89[CEU][hapmap];1.00[CHB][hapmap];0.93[JPT][hapmap];0.87[AMR][1000 genomes];0.83[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs38889	1.00[CHB][hapmap];0.93[JPT][hapmap];0.89[ASN][1000 genomes]
rs467	1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[ASN][1000 genomes]
rs56680066	0.81[EUR][1000 genomes]
rs57238791	0.99[ASN][1000 genomes]
rs57518803	0.98[AFR][1000 genomes];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs57609520	0.97[ASN][1000 genomes]
rs57778199	0.97[ASN][1000 genomes]
rs60653618	0.91[ASN][1000 genomes]
rs66535855	0.97[ASN][1000 genomes]
rs66668879	1.00[ASN][1000 genomes]
rs67039230	1.00[ASN][1000 genomes]
rs67452319	0.99[ASN][1000 genomes]
rs68189831	0.99[ASN][1000 genomes]
rs6966117	0.98[AFR][1000 genomes];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6976661	0.93[AMR][1000 genomes];0.88[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs739556	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs9784960	0.99[ASN][1000 genomes]
rs9785047	0.99[ASN][1000 genomes]

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

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv831108	chr7:116749534-116952011	Enhancers Weak transcription Strong transcription Active TSS Genic enhancers Flanking Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	25 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs10269684	GPR85	cis	cerebellum	SCAN

Chromatin state (count:85 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:116754200-116797400	Weak transcription	Fetal Stomach	stomach
2	chr7:116765000-116790200	Weak transcription	Psoas Muscle	Psoas
3	chr7:116765000-116792400	Weak transcription	Fetal Kidney	kidney
4	chr7:116765000-116797200	Weak transcription	Pancreas	Pancrea
5	chr7:116765400-116791800	Weak transcription	Skeletal Muscle Male	skeletal muscle
6	chr7:116765400-116798000	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
7	chr7:116767000-116797400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
8	chr7:116767200-116797200	Weak transcription	Brain Cingulate Gyrus	brain
9	chr7:116767600-116797200	Weak transcription	Cortex derived primary cultured neurospheres	brain
10	chr7:116773000-116791600	Weak transcription	Colon Smooth Muscle	Colon
11	chr7:116773600-116797000	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
12	chr7:116775200-116790800	Weak transcription	Fetal Brain Male	brain
13	chr7:116775200-116791800	Weak transcription	Small Intestine	intestine
14	chr7:116775800-116798000	Weak transcription	Hela-S3	cervix
15	chr7:116776200-116797000	Weak transcription	Brain Hippocampus Middle	brain
16	chr7:116776200-116797200	Weak transcription	Gastric	stomach
17	chr7:116776400-116797200	Weak transcription	NHLF	lung
18	chr7:116776400-116830200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
19	chr7:116776600-116792400	Weak transcription	Duodenum Smooth Muscle	Duodenum
20	chr7:116776600-116792600	Weak transcription	Brain Angular Gyrus	brain
21	chr7:116776600-116797000	Weak transcription	HSMM	muscle
22	chr7:116776600-116797400	Weak transcription	Brain Inferior Temporal Lobe	brain
23	chr7:116778800-116790400	Weak transcription	Aorta	Aorta
24	chr7:116778800-116791400	Weak transcription	Skeletal Muscle Female	skeletal muscle
25	chr7:116778800-116791800	Weak transcription	Sigmoid Colon	Sigmoid Colon
26	chr7:116778800-116794200	Weak transcription	Right Ventricle	heart
27	chr7:116779200-116797400	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
28	chr7:116779600-116811200	Weak transcription	Fetal Brain Female	brain
29	chr7:116779800-116797000	Weak transcription	Brain Germinal Matrix	brain
30	chr7:116781200-116797000	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
31	chr7:116781400-116792400	Weak transcription	Liver	Liver
32	chr7:116782400-116792600	Weak transcription	HSMMtube	muscle
33	chr7:116782600-116795000	Weak transcription	Breast Myoepithelial Primary Cells	Breast
34	chr7:116783200-116794400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
35	chr7:116783400-116791800	Weak transcription	Left Ventricle	heart
36	chr7:116783400-116792400	Weak transcription	Fetal Muscle Leg	muscle
37	chr7:116783400-116794200	Weak transcription	Stomach Smooth Muscle	stomach
38	chr7:116783400-116797200	Weak transcription	Lung	lung
39	chr7:116783400-116811000	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
40	chr7:116783600-116793000	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
41	chr7:116783800-116792400	Weak transcription	Fetal Lung	lung
42	chr7:116783800-116794400	Weak transcription	Placenta	Placenta
43	chr7:116783800-116796600	Weak transcription	Osteobl	bone
44	chr7:116783800-116797200	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
45	chr7:116783800-116797200	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
46	chr7:116783800-116797200	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
47	chr7:116783800-116797200	Weak transcription	NH-A	brain
48	chr7:116784000-116789800	Weak transcription	K562	blood
49	chr7:116784000-116791400	Weak transcription	Fetal Heart	heart
50	chr7:116784000-116797600	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin

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