Variant report

Variant	rs3731586
Chromosome Location	chr2:31749028-31749029
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:105)
CpG islands
(count:0)
Chromatin interactive
region (count:3)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:105 , 50 per page) page: 1 2 3

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	SMC3	chr2:31748935-31749354	HepG2	liver:	n/a	n/a
2	CTCF	chr2:31749000-31749150	HRE	kidney:	n/a	n/a
3	CTCF	chr2:31748895-31749456	GM12878	blood:	n/a	n/a
4	ZNF143	chr2:31748977-31749256	H1-hESC	embryonic stem cell:	n/a	n/a
5	CTCF	chr2:31749020-31749170	HEEpiC	esophagus:	n/a	n/a
6	YY1	chr2:31748961-31749240	H1-hESC	embryonic stem cell:	n/a	n/a
7	CTCF	chr2:31749000-31749150	HCT-116	colon:	n/a	n/a
8	RUNX3	chr2:31748937-31749333	GM12878	blood:	n/a	n/a
9	YY1	chr2:31748961-31749163	GM12878	blood:	n/a	n/a
10	SMC3	chr2:31748918-31749342	GM12878	blood:	n/a	n/a
11	ZNF143	chr2:31748965-31749280	K562	blood:	n/a	n/a
12	RAD21	chr2:31748895-31749423	MCF-7	breast:	n/a	n/a
13	YY1	chr2:31749027-31749205	HCT-116	colon:	n/a	n/a
14	CTCF	chr2:31748980-31749130	A549	lung:	n/a	n/a
15	CTCF	chr2:31748949-31749243	ECC-1	luminal epithelium:	n/a	n/a
16	MYC	chr2:31748887-31749191	MCF10A-Er-Src	breast:	n/a	n/a
17	MAFF	chr2:31749001-31749325	HepG2	liver:	n/a	n/a
18	CTCF	chr2:31749021-31749250	HepG2	liver:	n/a	n/a
19	RAD21	chr2:31748897-31749385	ECC-1	luminal epithelium:	n/a	n/a
20	CTCF	chr2:31748980-31749130	HMEC	breast:	n/a	n/a
21	CTCF	chr2:31749020-31749248	GM10248	blood:	n/a	n/a
22	CTCF	chr2:31748868-31749281	HepG2	liver:	n/a	n/a
23	YY1	chr2:31749022-31749226	K562	blood:	n/a	n/a
24	RAD21	chr2:31748694-31749518	SK-N-SH	brain:	n/a	n/a
25	RAD21	chr2:31748901-31749331	H1-hESC	embryonic stem cell:	n/a	n/a
26	RAD21	chr2:31749006-31749196	K562	blood:	n/a	n/a
27	CTCF	chr2:31749000-31749150	GM12873	blood:	n/a	n/a
28	CTCF	chr2:31749020-31749170	GM06990	blood:	n/a	n/a
29	RAD21	chr2:31748942-31749301	HepG2	liver:	n/a	n/a
30	RAD21	chr2:31748972-31749394	A549	lung:	n/a	n/a
31	CTCF	chr2:31749000-31749150	HFF-Myc	foreskin:	n/a	n/a
32	ARID3A	chr2:31748989-31749197	HepG2	liver:	n/a	n/a
33	CTCF	chr2:31748885-31749762	SK-N-SH	brain:	n/a	n/a
34	RAD21	chr2:31748945-31749297	SK-N-SH_RA	brain:	n/a	n/a
35	CTCF	chr2:31748880-31749030	A549	lung:	n/a	n/a
36	CTCF	chr2:31748885-31749314	A549	lung:	n/a	n/a
37	CTCF	chr2:31748956-31749288	K562	blood:	n/a	n/a
38	CTCF	chr2:31749000-31749270	A549	lung:	n/a	n/a
39	RAD21	chr2:31748805-31749337	IMR90	lung:	n/a	n/a
40	CTCF	chr2:31748904-31749234	H1-hESC	embryonic stem cell:	n/a	n/a
41	RAD21	chr2:31748974-31749335	H1-hESC	embryonic stem cell:	n/a	n/a
42	YY1	chr2:31748988-31749222	GM12892	blood:	n/a	n/a
43	CTCF	chr2:31749020-31749170	NHLF	lung:	n/a	n/a
44	CTCF	chr2:31749016-31749262	LNCaP	prostate:	n/a	n/a
45	RAD21	chr2:31748778-31749440	A549	lung:	n/a	n/a
46	CTCF	chr2:31749027-31749212	A549	lung:	n/a	n/a
47	CTCF	chr2:31748833-31749269	GM13977	blood:	n/a	n/a
48	CTCF	chr2:31748974-31749283	HUVEC	blood vessel:	n/a	n/a
49	CTCF	chr2:31748993-31749280	Gliobla	brain:	n/a	n/a
50	CTCF	chr2:31749000-31749150	HCM	heart:	n/a	n/a

No data

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

No.	Distal block	Cell Line	Cell type
1	chr2:31636673..31637179-chr2:31748776..31749495,2	MCF-7	breast:
2	chr2:31742379..31744112-chr2:31748051..31749878,2	K562	blood:
3	chr2:31636647..31637404-chr2:31748707..31749593,5	MCF-7	breast:

No data

Variant related genes	Relation type
ENSG00000228563	TF binding region

Extended variants
information (count: 48 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:37)

rs_ID	r²[population]
rs10204002	0.83[EUR][1000 genomes]
rs1042578	0.86[CHB][hapmap];1.00[JPT][hapmap]
rs11690596	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs11889731	1.00[CHB][hapmap];0.93[YRI][hapmap];0.93[AFR][1000 genomes];0.94[ASN][1000 genomes]
rs11892064	0.86[CHB][hapmap];0.93[ASN][1000 genomes]
rs12691180	0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12712320	0.82[AMR][1000 genomes];0.92[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12997020	0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12997024	0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs13016636	0.80[EUR][1000 genomes]
rs13395648	0.82[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs13432696	0.84[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs17011453	1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[ASN][1000 genomes]
rs1884722	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs206804	0.83[JPT][hapmap]
rs206805	0.83[JPT][hapmap]
rs206841	0.80[EUR][1000 genomes]
rs206844	0.80[EUR][1000 genomes]
rs2268794	1.00[CHB][hapmap];0.90[ASN][1000 genomes]
rs2281546	1.00[CHB][hapmap];0.94[ASN][1000 genomes]
rs28383032	0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs28383050	0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35702549	0.97[AFR][1000 genomes];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3754838	1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[EUR][1000 genomes]
rs3819844	0.82[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs4141419	0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs472445	0.83[EUR][1000 genomes]
rs479847	0.82[EUR][1000 genomes]
rs533833	0.83[EUR][1000 genomes]
rs6543632	0.85[AMR][1000 genomes];0.91[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6543633	0.87[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6543634	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs7562326	1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[EUR][1000 genomes]
rs7571644	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];0.85[AMR][1000 genomes];0.91[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7594951	1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[EUR][1000 genomes]
rs7599086	0.82[CEU][hapmap];0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs9332975	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:11 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv532648	chr2:31591498-32312698	Weak transcription Enhancers Active TSS Flanking Active TSS Strong transcription ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	39 gene(s)	inside rSNPs	diseases
2	nsv456030	chr2:31598823-31820256	Enhancers Active TSS ZNF genes & repeats Bivalent/Poised TSS Flanking Active TSS Weak transcription Genic enhancers Bivalent Enhancer Strong transcription Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
3	nsv456041	chr2:31598823-31820256	Weak transcription Enhancers Bivalent Enhancer Flanking Active TSS Active TSS Genic enhancers ZNF genes & repeats Strong transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
4	nsv581269	chr2:31598823-31820256	Weak transcription Strong transcription Bivalent Enhancer Enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Genic enhancers Active TSS Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
5	nsv998853	chr2:31601455-31858961	Enhancers Weak transcription Genic enhancers Active TSS Flanking Active TSS ZNF genes & repeats Strong transcription Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
6	nsv1005565	chr2:31603134-31868877	Genic enhancers Active TSS Bivalent Enhancer Enhancers Strong transcription Weak transcription Flanking Active TSS Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
7	nsv1007179	chr2:31616112-31835410	Enhancers Flanking Active TSS Bivalent Enhancer Weak transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS Active TSS ZNF genes & repeats Strong transcription Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
8	nsv1005032	chr2:31616112-31867450	Bivalent Enhancer Enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Weak transcription Flanking Active TSS Active TSS Bivalent/Poised TSS Genic enhancers Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
9	nsv1013891	chr2:31629179-31854283	Flanking Active TSS Enhancers Weak transcription Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats Genic enhancers Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
10	nsv535612	chr2:31629179-31854283	Enhancers Active TSS Weak transcription Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS Strong transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
11	nsv999815	chr2:31654667-31777296	Enhancers Weak transcription Active TSS Flanking Active TSS Genic enhancers Strong transcription ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases

No data

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:31748200-31750400	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
2	chr2:31748800-31749200	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
3	chr2:31748800-31749600	Enhancers	Fetal Intestine Small	intestine
4	chr2:31748800-31749800	Weak transcription	Liver	Liver
5	chr2:31748800-31750600	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell

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