Variant report

Variant	rs9462466
Chromosome Location	chr6:38901358-38901359
allele	A/G
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:6)
LncRNA
region (count:0)
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	chr6:38901300-38901450	Hela-S3	cervix:	n/a	n/a
2	CTCF	chr6:38901320-38901470	Caco-2	colon:	n/a	n/a
3	CTCF	chr6:38901131-38901751	A549	lung:	n/a	n/a
4	RAD21	chr6:38901255-38901530	SK-N-SH_RA	brain:	n/a	n/a
5	CTCF	chr6:38901240-38901390	NHDF-neo	bronchial:	n/a	n/a
6	CTCF	chr6:38901326-38901503	Pancreas_OC	pancreas:	n/a	n/a
7	CTCF	chr6:38901340-38901490	GM12872	blood:	n/a	n/a
8	RAD21	chr6:38901176-38901666	MCF-7	breast:	n/a	n/a
9	CTCF	chr6:38901320-38901470	NHEK	skin:	n/a	n/a
10	CTCF	chr6:38901320-38901470	HMF	breast:	n/a	n/a
11	CTCF	chr6:38901340-38901490	GM12865	blood:	n/a	n/a
12	CTCF	chr6:38901300-38901450	HMEC	breast:	n/a	n/a
13	CTCF	chr6:38901280-38901430	GM12865	blood:	n/a	n/a
14	CTCF	chr6:38901324-38901508	HepG2	liver:	n/a	n/a
15	CUX1	chr6:38901291-38901400	K562	blood:	n/a	n/a
16	CTCF	chr6:38901320-38901470	GM12872	blood:	n/a	n/a
17	SMC3	chr6:38901283-38901564	Hela-S3	cervix:	n/a	n/a
18	RAD21	chr6:38901258-38901496	IMR90	lung:	n/a	n/a
19	ARID3A	chr6:38901263-38901545	K562	blood:	n/a	n/a
20	CTCF	chr6:38901304-38901519	Hela-S3	cervix:	n/a	n/a
21	ZNF143	chr6:38901299-38901537	K562	blood:	n/a	n/a
22	CTCF	chr6:38901320-38901470	SK-N-SH_RA	brain:	n/a	n/a
23	RAD21	chr6:38901240-38901555	HepG2	liver:	n/a	n/a
24	CTCF	chr6:38901287-38901520	Lung_OC	lung:	n/a	n/a
25	RAD21	chr6:38901319-38901480	A549	lung:	n/a	n/a
26	GATA3	chr6:38901276-38901697	T-47D	breast:	n/a	n/a
27	CTCF	chr6:38901340-38901490	HMF	breast:	n/a	n/a
28	CTCF	chr6:38901262-38901537	HUVEC	blood vessel:	n/a	n/a
29	CTCF	chr6:38901300-38901450	HRPEpiC	eye:	n/a	n/a
30	CTCF	chr6:38901320-38901470	BJ	skin:	n/a	n/a
31	CTCF	chr6:38901280-38901430	HRE	kidney:	n/a	n/a
32	CTCF	chr6:38901340-38901490	HUVEC	blood vessel:	n/a	n/a
33	GATA3	chr6:38901242-38901597	T-47D	breast:	n/a	chr6:38901274-38901281
34	CTCF	chr6:38901280-38901430	HL-60	blood:	n/a	n/a
35	CTCF	chr6:38901340-38901490	GM12869	blood:	n/a	n/a
36	CTCF	chr6:38901205-38901593	GM12878	blood:	n/a	n/a
37	CTCF	chr6:38901340-38901490	GM12864	blood:	n/a	n/a
38	CTCF	chr6:38901300-38901450	SAEC	small airway:	n/a	n/a
39	CTCF	chr6:38901340-38901490	HRPEpiC	eye:	n/a	n/a
40	CTCF	chr6:38901320-38901470	AG09319	gingival:	n/a	n/a
41	SMC3	chr6:38901195-38901507	HepG2	liver:	n/a	n/a
42	RAD21	chr6:38901239-38901566	Hela-S3	cervix:	n/a	n/a
43	CTCF	chr6:38901237-38901520	K562	blood:	n/a	n/a
44	CTCF	chr6:38901210-38901593	K562	blood:	n/a	n/a
45	CTCF	chr6:38901300-38901450	HFF	foreskin:	n/a	n/a
46	ZNF143	chr6:38901330-38901533	GM12878	blood:	n/a	n/a
47	CTCF	chr6:38901300-38901450	HA-sp	spinal cord:	n/a	n/a
48	CTCF	chr6:38901320-38901470	BE2_C	brain:	n/a	n/a
49	RAD21	chr6:38901111-38901628	HCT-116	colon:	n/a	n/a
50	CTCF	chr6:38901340-38901490	Hela-S3	cervix:	n/a	n/a

No data

(count:6 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr6:38773740..38774704-chr6:38901124..38901864,4	MCF-7	breast:
2	chr6:38896535..38899367-chr6:38900906..38902876,2	MCF-7	breast:
3	chr6:38901008..38902530-chr6:38905671..38907488,2	K562	blood:
4	chr6:38763255..38763863-chr6:38901115..38901700,2	MCF-7	breast:
5	chr6:38839518..38840375-chr6:38900813..38901849,3	MCF-7	breast:
6	chr6:38839463..38840459-chr6:38901033..38901837,4	MCF-7	breast:

No data

Variant related genes	Relation type
ENSG00000231150	TF binding region
ENSG00000231150	Chromatin interaction

Extended variants
information (count: 26 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:21)

rs_ID	r²[population]
rs11753074	1.00[CEU][hapmap];0.82[JPT][hapmap];0.88[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs11753138	1.00[CEU][hapmap];0.88[CHB][hapmap];0.92[JPT][hapmap]
rs1332012	1.00[CEU][hapmap]
rs1537231	0.81[CEU][hapmap]
rs2235871	0.81[CEU][hapmap]
rs2273093	0.81[CEU][hapmap]
rs3734611	1.00[CHB][hapmap]
rs3857575	1.00[CEU][hapmap];0.92[JPT][hapmap]
rs4714202	0.90[CEU][hapmap]
rs4714203	0.90[CEU][hapmap]
rs4714208	0.81[CEU][hapmap]
rs62398577	0.92[ASN][1000 genomes]
rs7766930	0.81[CEU][hapmap]
rs9296270	0.85[YRI][hapmap]
rs9380817	0.81[CEU][hapmap]
rs9462460	1.00[CEU][hapmap]
rs9462464	1.00[CEU][hapmap];0.88[CHB][hapmap];0.92[JPT][hapmap];0.88[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs9462467	0.85[YRI][hapmap]
rs9462469	0.81[CEU][hapmap]
rs9470949	1.00[CEU][hapmap];0.88[CHB][hapmap];0.83[JPT][hapmap]
rs9470950	1.00[CEU][hapmap]

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	nsv885817	chr6:38036420-39019503	Enhancers Weak transcription Flanking Active TSS Bivalent/Poised TSS Strong transcription Active TSS Genic enhancers ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	26 gene(s)	inside rSNPs	diseases
2	nsv830643	chr6:38726675-38905589	Enhancers Flanking Active TSS Weak transcription Active TSS Genic enhancers Bivalent Enhancer ZNF genes & repeats Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
3	nsv1028088	chr6:38821047-39163549	Weak transcription Active TSS Enhancers Flanking Active TSS Strong transcription Bivalent Enhancer Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	10 gene(s)	inside rSNPs	diseases
4	nsv538205	chr6:38821047-39163549	Flanking Active TSS Weak transcription Enhancers Active TSS Strong transcription Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	10 gene(s)	inside rSNPs	diseases
5	nsv885821	chr6:38843970-39039503	Bivalent Enhancer Weak transcription Enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Flanking Active TSS Strong transcription Active TSS ZNF genes & repeats Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:3 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:38900800-38901600	Enhancers	Fetal Intestine Large	intestine
2	chr6:38900800-38901600	Enhancers	Fetal Intestine Small	intestine
3	chr6:38901200-38901400	Enhancers	Primary T regulatory cells fromperipheralblood	blood

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