Variant report

Variant	rs4947631
Chromosome Location	chr7:50603379-50603380
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr7:50601758..50604303-chr7:50604942..50607334,2	K562	blood:
2	chr7:50598241..50600922-chr7:50601073..50603965,2	K562	blood:
3	chr7:50601800..50604303-chr7:50605834..50607689,2	K562	blood:

Variant related genes	Relation type
ENSG00000226122	Chromatin interaction

Extended variants
information (count: 34 )
Associated
traits (count: 16 )

rSNPs within LD-proxies of this variant (count:30)

rs_ID	r²[population]
rs10228056	0.82[ASW][hapmap];1.00[CEU][hapmap];0.83[LWK][hapmap];1.00[TSI][hapmap];0.88[YRI][hapmap];0.86[EUR][1000 genomes]
rs11575351	0.86[EUR][1000 genomes]
rs11575383	1.00[CHB][hapmap]
rs11575387	1.00[CHB][hapmap]
rs11575388	1.00[CEU][hapmap];1.00[CHB][hapmap];0.85[GIH][hapmap]
rs11575450	1.00[CEU][hapmap];1.00[CHB][hapmap]
rs11763051	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][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]
rs11771860	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][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]
rs1304692	0.86[EUR][1000 genomes]
rs17133842	1.00[CEU][hapmap];1.00[CHB][hapmap]
rs17133853	1.00[CHB][hapmap]
rs17133877	0.83[TSI][hapmap]
rs17133881	1.00[CEU][hapmap];1.00[JPT][hapmap];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs17152014	1.00[CEU][hapmap];1.00[CHB][hapmap]
rs2122819	0.87[AFR][1000 genomes];0.85[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2167363	1.00[CHB][hapmap];1.00[JPT][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]
rs2329364	0.82[ASW][hapmap];1.00[CEU][hapmap];0.81[LWK][hapmap];1.00[TSI][hapmap];0.88[YRI][hapmap]
rs4245549	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.88[LWK][hapmap];1.00[MEX][hapmap];0.85[MKK][hapmap];1.00[TSI][hapmap];0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4455783	0.86[AFR][1000 genomes];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4947621	0.99[AFR][1000 genomes];0.86[AMR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4947625	0.86[AFR][1000 genomes];0.86[AMR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs57716050	0.86[EUR][1000 genomes]
rs58537381	0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs59221245	0.82[AMR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs61042486	0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6593011	1.00[CHD][hapmap]
rs73342836	0.82[AMR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs73342839	0.82[AMR][1000 genomes];0.92[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs73342848	0.82[AMR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7791875	1.00[CHB][hapmap];1.00[CHD][hapmap]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1016665	chr7:50452552-51404524	Enhancers Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Weak transcription ZNF genes & repeats Flanking Active TSS Genic enhancers Strong transcription Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	22 gene(s)	inside rSNPs	diseases
2	nsv888021	chr7:50538589-50610071	Enhancers Weak transcription Strong transcription Flanking Active TSS Bivalent Enhancer Genic enhancers ZNF genes & repeats Active TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
3	nsv1015758	chr7:50565404-50768153	Flanking Active TSS Genic enhancers Strong transcription Enhancers Weak transcription Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats Active TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	6 gene(s)	inside rSNPs	diseases
4	nsv1023228	chr7:50573214-50777634	Enhancers Flanking Active TSS Weak transcription Active TSS Strong transcription Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats 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:16)

SNP	Gene	Cis/trans	Tissue	Source
rs4947631	RNF11	trans	brain	seeQTL
rs4947631	SIPA1L3	trans	brain	seeQTL
rs4947631	CBWD1	trans	brain	seeQTL
rs4947631	SACS	trans	brain	seeQTL
rs4947631	CCDC82	trans	brain	seeQTL
rs4947631	GOLGA6L9	trans	brain	seeQTL
rs4947631	USH1G	trans	brain	seeQTL
rs4947631	MLLT1	trans	brain	seeQTL
rs4947631	ITFG1	trans	brain	seeQTL
rs4947631	ELMOD3	trans	brain	seeQTL
rs4947631	USP6	trans	brain	seeQTL
rs4947631	C2orf69	trans	brain	seeQTL
rs4947631	OLIG3	trans	brain	seeQTL
rs4947631	IDO2	trans	brain	seeQTL
rs4947631	FAM115A	trans	brain	seeQTL
rs4947631	WDR17	trans	brain	seeQTL

Chromatin state (count:43 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:50565200-50609000	Weak transcription	Rectal Mucosa Donor 29	rectum
2	chr7:50595200-50604600	Genic enhancers	Fetal Intestine Small	intestine
3	chr7:50597200-50603600	Weak transcription	Liver	Liver
4	chr7:50600200-50612600	Weak transcription	Small Intestine	intestine
5	chr7:50600600-50619400	Weak transcription	Pancreatic Islets	Pancreatic Islet
6	chr7:50601400-50603600	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
7	chr7:50601400-50603800	Enhancers	Placenta	Placenta
8	chr7:50601600-50603400	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
9	chr7:50601600-50603400	Flanking Active TSS	A549	lung
10	chr7:50601600-50603600	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
11	chr7:50601600-50603600	Enhancers	NHLF	lung
12	chr7:50601600-50631400	Weak transcription	Rectal Mucosa Donor 31	rectum
13	chr7:50601800-50603600	Enhancers	HMEC	breast
14	chr7:50602000-50603600	Enhancers	Muscle Satellite Cultured Cells	--
15	chr7:50602000-50603600	Enhancers	Fetal Adrenal Gland	Adrenal Gland
16	chr7:50602200-50603600	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
17	chr7:50602200-50603600	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
18	chr7:50602200-50603600	Enhancers	NH-A	brain
19	chr7:50602200-50603800	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
20	chr7:50602200-50603800	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
21	chr7:50602400-50603400	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
22	chr7:50602400-50603400	Enhancers	Fetal Muscle Trunk	muscle
23	chr7:50602400-50603400	Enhancers	Psoas Muscle	Psoas
24	chr7:50602400-50603400	Enhancers	Skeletal Muscle Female	skeletal muscle
25	chr7:50602400-50603400	Enhancers	HUVEC	blood vessel
26	chr7:50602400-50603400	Flanking Active TSS	K562	blood
27	chr7:50602400-50603600	Genic enhancers	Duodenum Mucosa	Duodenum
28	chr7:50602400-50603600	Enhancers	Osteobl	bone
29	chr7:50602400-50604200	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
30	chr7:50602400-50604200	Enhancers	NHDF-Ad	bronchial
31	chr7:50602600-50618200	Weak transcription	Pancreas	Pancrea
32	chr7:50602800-50603600	Enhancers	HSMM	muscle
33	chr7:50602800-50603600	Enhancers	HSMMtube	muscle
34	chr7:50602800-50603600	Enhancers	NHEK	skin
35	chr7:50602800-50604200	Enhancers	Skeletal Muscle Male	skeletal muscle
36	chr7:50602800-50604400	Enhancers	Hela-S3	cervix
37	chr7:50602800-50604400	Weak transcription	HepG2	liver
38	chr7:50602800-50606400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
39	chr7:50602800-50609600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
40	chr7:50602800-50610200	Weak transcription	Colonic Mucosa	Colon
41	chr7:50602800-50613800	Weak transcription	Sigmoid Colon	Sigmoid Colon
42	chr7:50603200-50604000	Genic enhancers	Fetal Intestine Large	intestine
43	chr7:50603200-50606000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived

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