Variant report

Variant	rs6963925
Chromosome Location	chr7:12531180-12531181
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr7:12326033..12327864-chr7:12530775..12532531,2	K562	blood:
2	chr7:12528914..12532541-chr7:12534824..12536655,4	K562	blood:

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-SCIN-4	chr7:12530721-12531630	NONHSAT119228

Variant related genes	Relation type
ENSG00000226690	Chromatin interaction

Extended variants
information (count: 67 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:41)

rs_ID	r²[population]
rs10046485	0.90[ASN][1000 genomes]
rs10046487	0.90[ASN][1000 genomes]
rs10046491	0.91[ASN][1000 genomes]
rs10215269	0.99[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10215656	0.91[ASN][1000 genomes]
rs10249671	0.83[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs10488155	0.91[ASN][1000 genomes]
rs11977668	0.91[ASN][1000 genomes]
rs11981273	0.91[ASN][1000 genomes]
rs1440014	0.85[AFR][1000 genomes]
rs1440017	0.91[ASN][1000 genomes]
rs16877494	0.96[ASN][1000 genomes]
rs28551764	0.91[ASN][1000 genomes]
rs34965005	0.91[ASN][1000 genomes]
rs3735183	0.90[ASN][1000 genomes]
rs4719312	0.91[ASN][1000 genomes]
rs4719316	0.97[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4721099	0.84[ASN][1000 genomes]
rs4721104	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs57076782	0.91[ASN][1000 genomes]
rs57347805	0.84[ASN][1000 genomes]
rs57835825	0.91[ASN][1000 genomes]
rs58280274	0.84[ASN][1000 genomes]
rs59060587	0.91[ASN][1000 genomes]
rs59301534	0.91[ASN][1000 genomes]
rs60043259	0.91[ASN][1000 genomes]
rs61112361	0.90[ASN][1000 genomes]
rs66889911	0.85[AFR][1000 genomes]
rs6954423	0.91[ASN][1000 genomes]
rs6975302	0.91[ASN][1000 genomes]
rs6975517	0.91[ASN][1000 genomes]
rs6976074	0.91[ASN][1000 genomes]
rs73056737	0.91[ASN][1000 genomes]
rs73056743	0.91[ASN][1000 genomes]
rs73056757	0.91[ASN][1000 genomes]
rs734083	0.91[ASN][1000 genomes]
rs758282	0.91[ASN][1000 genomes]
rs7785791	0.85[AFR][1000 genomes];0.99[ASN][1000 genomes]
rs7794551	0.84[AFR][1000 genomes];0.99[ASN][1000 genomes]
rs7795767	0.91[ASN][1000 genomes]
rs847914	0.86[AFR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:26 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv534432	chr7:12148960-12693032	Enhancers Weak transcription Active TSS Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS Strong transcription Flanking Active TSS Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	23 gene(s)	inside rSNPs	diseases
2	nsv1024554	chr7:12214722-12967418	Active TSS Flanking Active TSS ZNF genes & repeats Weak transcription Enhancers Strong transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Genic enhancers Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	58 gene(s)	inside rSNPs	diseases
3	nsv538735	chr7:12214722-12967418	Bivalent/Poised TSS Enhancers Weak transcription Active TSS Flanking Active TSS Bivalent Enhancer Strong transcription Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	58 gene(s)	inside rSNPs	diseases
4	nsv464373	chr7:12406826-12536336	Enhancers Active TSS Weak transcription Bivalent/Poised TSS Bivalent Enhancer Flanking Active TSS Flanking Bivalent TSS/Enh Strong transcription ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
5	nsv606224	chr7:12406826-12536336	Enhancers Flanking Active TSS Weak transcription Strong transcription Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
6	esv2757212	chr7:12505613-12596535	Enhancers Active TSS Weak transcription ZNF genes & repeats Flanking Active TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
7	esv2759511	chr7:12505613-12596535	Weak transcription Active TSS Enhancers Flanking Active TSS ZNF genes & repeats Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
8	nsv1017055	chr7:12509227-12553217	Enhancers Active TSS ZNF genes & repeats Flanking Active TSS Weak transcription	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
9	nsv464377	chr7:12512802-12564128	Enhancers Active TSS Flanking Active TSS Weak transcription	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
10	nsv606228	chr7:12512802-12564128	Enhancers Weak transcription Active TSS Flanking Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
11	nsv8048	chr7:12514460-12564736	Active TSS Flanking Active TSS Enhancers Weak transcription	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
12	esv3692921	chr7:12515906-12564128	Enhancers Weak transcription Active TSS Flanking Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
13	nsv464378	chr7:12516170-12562500	Enhancers Active TSS Weak transcription Flanking Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
14	nsv606229	chr7:12516170-12562500	Enhancers Weak transcription Active TSS Flanking Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
15	nsv519965	chr7:12516170-12564128	Active TSS Enhancers Weak transcription Flanking Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
16	nsv470055	chr7:12516170-12564128	Weak transcription Enhancers Active TSS Flanking Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
17	nsv606230	chr7:12516170-12564128	Active TSS Enhancers Weak transcription Flanking Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
18	nsv818482	chr7:12516170-12564128	Enhancers Active TSS Weak transcription Flanking Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
19	nsv1028361	chr7:12517477-12548420	Enhancers Active TSS Weak transcription Flanking Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
20	nsv1027185	chr7:12517477-12549015	Active TSS Enhancers Weak transcription Flanking Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
21	nsv1022047	chr7:12517477-12552147	Enhancers Weak transcription Active TSS Flanking Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
22	nsv1027708	chr7:12517477-12558257	Enhancers Active TSS Weak transcription Flanking Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
23	esv2761074	chr7:12517477-12566200	Active TSS Enhancers Weak transcription Flanking Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
24	nsv887640	chr7:12519212-12543794	Enhancers Active TSS Weak transcription Flanking Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
25	nsv1021371	chr7:12530491-12710429	Bivalent Enhancer Weak transcription Enhancers Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Active TSS Flanking Active TSS ZNF genes & repeats Strong transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
26	nsv1017577	chr7:12530491-12722947	Weak transcription Bivalent Enhancer Enhancers Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent/Poised TSS Genic enhancers Active TSS Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs6963925	VWDE	cis	Thyroid	GTEx

Chromatin state (count:5 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:12529600-12536600	Weak transcription	K562	blood
2	chr7:12530400-12536600	Weak transcription	HUES64 Cell Line	embryonic stem cell
3	chr7:12530600-12536600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
4	chr7:12530800-12536600	Weak transcription	HUES48 Cell Line	embryonic stem cell
5	chr7:12531000-12536200	Weak transcription	iPS-15b Cell Line	embryonic stem cell

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