Variant report

Variant	rs10878597
Chromosome Location	chr12:40840325-40840326
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:123)
CpG islands
(count:0)
Chromatin interactive
region (count:1)
LncRNA
region (count:1)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

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

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	CTCF	chr12:40840275-40840508	HUVEC	blood vessel:	n/a	n/a
2	CTCF	chr12:40840280-40840430	HEEpiC	esophagus:	n/a	n/a
3	CTCF	chr12:40840320-40840470	NHEK	skin:	n/a	n/a
4	CTCF	chr12:40840320-40840470	AoAF	blood vessel:	n/a	n/a
5	CTCF	chr12:40840300-40840450	AG09309	skin:	n/a	n/a
6	CTCF	chr12:40840280-40840430	BE2_C	brain:	n/a	n/a
7	CTCF	chr12:40840260-40840410	WERI-Rb-1	eye:	n/a	n/a
8	CTCF	chr12:40840300-40840450	HL-60	blood:	n/a	n/a
9	SMC3	chr12:40840183-40840574	GM12878	blood:	n/a	n/a
10	CTCF	chr12:40840211-40840478	HepG2	liver:	n/a	n/a
11	CTCF	chr12:40840281-40840451	MCF-7	breast:	n/a	n/a
12	CTCF	chr12:40840260-40840410	GM12865	blood:	n/a	n/a
13	CTCF	chr12:40840295-40840472	GM20000	blood:	n/a	n/a
14	RAD21	chr12:40840236-40840548	H1-hESC	embryonic stem cell:	n/a	n/a
15	CTCF	chr12:40840286-40840484	LNCaP	prostate:	n/a	n/a
16	CTCF	chr12:40840320-40840470	GM12866	blood:	n/a	n/a
17	CTCF	chr12:40840211-40840461	A549	lung:	n/a	n/a
18	CTCF	chr12:40840202-40840518	SK-N-SH_RA	brain:	n/a	n/a
19	RAD21	chr12:40840235-40840485	GM12878	blood:	n/a	n/a
20	CTCF	chr12:40840291-40840476	K562	blood:	n/a	n/a
21	RAD21	chr12:40840236-40840541	GM12878	blood:	n/a	n/a
22	CTCF	chr12:40840280-40840430	GM12868	blood:	n/a	n/a
23	CTCF	chr12:40840320-40840470	HEK293	kidney:	n/a	n/a
24	ARID3A	chr12:40840290-40840374	K562	blood:	n/a	n/a
25	CTCF	chr12:40840300-40840450	WERI-Rb-1	eye:	n/a	n/a
26	CTCF	chr12:40840101-40840731	SK-N-SH	brain:	n/a	n/a
27	CTCF	chr12:40840240-40840390	GM12867	blood:	n/a	n/a
28	CTCF	chr12:40840251-40840451	K562	blood:	n/a	n/a
29	CTCF	chr12:40840280-40840430	AG04449	skin:	n/a	n/a
30	CTCF	chr12:40840300-40840450	HEK293	kidney:	n/a	n/a
31	CTCF	chr12:40840300-40840450	HMEC	breast:	n/a	n/a
32	SMC3	chr12:40840220-40840523	Hela-S3	cervix:	n/a	n/a
33	CTCF	chr12:40840291-40840465	HepG2	liver:	n/a	n/a
34	CTCF	chr12:40840323-40840452	Pancreas_OC	pancreas:	n/a	n/a
35	CTCF	chr12:40840300-40840450	NHDF-neo	bronchial:	n/a	n/a
36	CTCF	chr12:40840320-40840470	GM12865	blood:	n/a	n/a
37	CTCF	chr12:40840300-40840450	GM12873	blood:	n/a	n/a
38	CTCF	chr12:40840274-40840445	A549	lung:	n/a	n/a
39	ZNF143	chr12:40840247-40840557	GM12878	blood:	n/a	chr12:40840261-40840276
40	CTCF	chr12:40840320-40840470	GM12874	blood:	n/a	n/a
41	CTCF	chr12:40840312-40840386	GM19239	blood:	n/a	n/a
42	RAD21	chr12:40840243-40840534	GM12878	blood:	n/a	n/a
43	CTCF	chr12:40840260-40840410	NHEK	skin:	n/a	n/a
44	CTCF	chr12:40840280-40840430	MCF-7	breast:	n/a	n/a
45	CTCF	chr12:40840300-40840450	BJ	skin:	n/a	n/a
46	CTCF	chr12:40840300-40840450	GM12872	blood:	n/a	n/a
47	JUN	chr12:40840228-40840490	HepG2	liver:	n/a	chr12:40840376-40840389
48	CTCF	chr12:40840180-40840330	A549	lung:	n/a	n/a
49	CTCF	chr12:40840320-40840470	Caco-2	colon:	n/a	n/a
50	RAD21	chr12:40840280-40840443	SK-N-SH_RA	brain:	n/a	n/a

No data

(count:1 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr12:40719158..40719845-chr12:40839913..40840458,2	MCF-7	breast:

(count:1 , 50 per page) page: 1

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-MUC19-1	chr12:40840290-40840431	NONHSAT027728

No data

Variant related genes	Relation type
ENSG00000258167	TF binding region

Extended variants
information (count: 30 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:26)

rs_ID	r²[population]
rs10784618	0.99[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10784620	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.99[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10784621	1.00[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];1.00[MEX][hapmap];0.99[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.99[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10784622	0.99[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10878584	0.96[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10878589	0.95[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10878590	0.99[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10878591	0.99[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10878592	0.99[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10878594	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.99[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10878595	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.99[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11176635	0.96[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11176644	0.99[AFR][1000 genomes];0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11176665	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.99[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11176696	0.97[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11176697	0.97[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11564227	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.99[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1346307	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.99[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1346308	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.99[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1346309	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.99[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7295553	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7301939	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.99[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7954676	0.96[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7966110	0.99[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7966877	0.96[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7972395	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.99[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]

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	nsv832377	chr12:40704881-40855223	Weak transcription Enhancers ZNF genes & repeats Strong transcription Active TSS Flanking Active TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	8 gene(s)	inside rSNPs	diseases
2	nsv899033	chr12:40758652-41122288	Bivalent/Poised TSS Enhancers Strong transcription Flanking Active TSS Weak transcription Transcr. at gene 5' and 3' ZNF genes & repeats Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	23 gene(s)	inside rSNPs	diseases
3	nsv1039272	chr12:40817585-40841318	Enhancers	TF binding region Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
4	nsv558606	chr12:40837331-40863052	Enhancers	TF binding region Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases

No data

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:40839000-40841000	Enhancers	Fetal Heart	heart

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