Variant report

Variant	rs11676286
Chromosome Location	chr2:9880937-9880938
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	SMC3	chr2:9880681-9881458	Hela-S3	cervix:	n/a	chr2:9881363-9881371
2	BRCA1	chr2:9880701-9881166	Hela-S3	cervix:	n/a	n/a
3	NFIC	chr2:9880490-9881124	ECC-1	luminal epithelium:	n/a	chr2:9880709-9880725 chr2:9880708-9880725
4	JUND	chr2:9880706-9881440	Hela-S3	cervix:	n/a	chr2:9880967-9880978 chr2:9880969-9880981 chr2:9880971-9880979
5	GTF2F1	chr2:9880638-9881572	Hela-S3	cervix:	n/a	n/a
6	RFX5	chr2:9880717-9881191	Hela-S3	cervix:	n/a	n/a
7	NFYB	chr2:9880684-9881047	Hela-S3	cervix:	n/a	chr2:9880878-9880893
8	TCF7L2	chr2:9880872-9881479	Hela-S3	cervix:	n/a	n/a
9	RCOR1	chr2:9880591-9881455	Hela-S3	cervix:	n/a	n/a
10	USF2	chr2:9880775-9881119	Hela-S3	cervix:	n/a	n/a
11	STAT3	chr2:9880765-9881442	Hela-S3	cervix:	n/a	n/a
12	JUN	chr2:9880725-9881649	Hela-S3	cervix:	n/a	chr2:9880967-9880978 chr2:9880969-9880981 chr2:9880971-9880979
13	CHD2	chr2:9880729-9881172	Hela-S3	cervix:	n/a	n/a
14	EP300	chr2:9880720-9881197	Hela-S3	cervix:	n/a	n/a
15	RAD21	chr2:9880738-9881228	Hela-S3	cervix:	n/a	n/a
16	NFIC	chr2:9880461-9881068	ECC-1	luminal epithelium:	n/a	chr2:9880709-9880725 chr2:9880708-9880725
17	E2F4	chr2:9880911-9880957	MCF10A-Er-Src	breast:	n/a	n/a
18	TBP	chr2:9880710-9881289	Hela-S3	cervix:	n/a	n/a
19	MAX	chr2:9880769-9881532	Hela-S3	cervix:	n/a	n/a
20	MAFK	chr2:9880751-9881197	Hela-S3	cervix:	n/a	n/a
21	ZNF143	chr2:9880880-9881436	Hela-S3	cervix:	n/a	n/a
22	FOS	chr2:9880772-9881190	Hela-S3	cervix:	n/a	chr2:9880967-9880978 chr2:9880969-9880981 chr2:9880971-9880979
23	CEBPB	chr2:9880740-9881525	Hela-S3	cervix:	n/a	n/a
24	ZKSCAN1	chr2:9880517-9881114	Hela-S3	cervix:	n/a	n/a
25	MAZ	chr2:9880799-9881575	Hela-S3	cervix:	n/a	n/a

Variant related genes	Relation type
RNU4-73P	TF binding region

Extended variants
information (count: 98 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:91)

rs_ID	r²[population]
rs10171491	0.89[ASN][1000 genomes]
rs10173057	0.84[ASN][1000 genomes]
rs10176382	0.92[ASN][1000 genomes]
rs10178017	0.86[ASN][1000 genomes]
rs10180724	0.92[ASN][1000 genomes]
rs10200779	0.86[ASN][1000 genomes]
rs10200869	0.87[ASN][1000 genomes]
rs10202283	0.85[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs10202938	0.82[ASN][1000 genomes]
rs10929596	0.80[ASN][1000 genomes]
rs10929597	0.80[ASN][1000 genomes]
rs10929598	0.80[ASN][1000 genomes]
rs10929600	0.82[ASN][1000 genomes]
rs10929602	0.82[ASN][1000 genomes]
rs10929605	0.82[ASN][1000 genomes]
rs10929607	0.92[ASN][1000 genomes]
rs10929608	0.92[ASN][1000 genomes]
rs10929609	0.92[ASN][1000 genomes]
rs1110317	0.80[ASN][1000 genomes]
rs1123269	0.82[AMR][1000 genomes];0.86[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs11674024	0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11678697	0.86[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11695437	0.82[ASN][1000 genomes]
rs11892176	0.82[ASN][1000 genomes]
rs11901380	0.80[ASN][1000 genomes]
rs11902412	0.82[ASN][1000 genomes]
rs12470409	0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12472594	0.82[ASN][1000 genomes]
rs12475853	0.87[ASN][1000 genomes]
rs12476199	0.81[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12476232	0.86[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12692393	0.93[ASN][1000 genomes]
rs12692394	0.93[ASN][1000 genomes]
rs12991432	0.81[ASN][1000 genomes]
rs12996417	0.81[AMR][1000 genomes];0.87[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs13018695	0.92[ASN][1000 genomes]
rs13023725	0.85[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs13024852	0.81[ASN][1000 genomes]
rs13028425	0.92[ASN][1000 genomes]
rs13395171	0.92[ASN][1000 genomes]
rs13398163	0.92[ASN][1000 genomes]
rs13398193	0.92[ASN][1000 genomes]
rs13398304	0.92[ASN][1000 genomes]
rs1554107	0.86[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1877949	0.80[ASN][1000 genomes]
rs1877950	0.82[ASN][1000 genomes]
rs1877951	0.82[ASN][1000 genomes]
rs1877953	0.82[ASN][1000 genomes]
rs2357264	0.81[ASN][1000 genomes]
rs2357265	0.81[ASN][1000 genomes]
rs4459704	0.81[ASN][1000 genomes]
rs4668638	0.82[ASN][1000 genomes]
rs4668639	0.82[ASN][1000 genomes]
rs4668640	0.82[ASN][1000 genomes]
rs4668642	0.82[ASN][1000 genomes]
rs4668643	0.82[ASN][1000 genomes]
rs4668644	0.85[ASN][1000 genomes]
rs4669428	0.80[ASN][1000 genomes]
rs4669429	0.80[ASN][1000 genomes]
rs4669430	0.80[ASN][1000 genomes]
rs4669432	0.82[ASN][1000 genomes]
rs4669433	0.82[ASN][1000 genomes]
rs4669435	0.82[ASN][1000 genomes]
rs4669437	0.81[ASN][1000 genomes]
rs4669441	0.82[ASN][1000 genomes]
rs4669445	0.82[ASN][1000 genomes]
rs4669446	0.82[ASN][1000 genomes]
rs4669447	0.92[ASN][1000 genomes]
rs4669448	0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs5020306	0.80[ASN][1000 genomes]
rs58961346	0.82[ASN][1000 genomes]
rs6432033	0.80[ASN][1000 genomes]
rs6713497	0.91[ASN][1000 genomes]
rs6724483	0.81[ASN][1000 genomes]
rs6727688	0.81[ASN][1000 genomes]
rs6732548	0.81[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs6736421	0.82[ASN][1000 genomes]
rs6740013	0.91[ASN][1000 genomes]
rs6742929	0.91[ASN][1000 genomes]
rs6743152	0.90[ASN][1000 genomes]
rs6752842	0.82[ASN][1000 genomes]
rs6754662	0.90[ASN][1000 genomes]
rs6756567	0.85[ASN][1000 genomes]
rs6760150	0.86[ASN][1000 genomes]
rs6761286	0.90[ASN][1000 genomes]
rs6761920	0.85[ASN][1000 genomes]
rs7423455	0.85[ASN][1000 genomes]
rs7423458	0.86[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7592044	0.80[ASN][1000 genomes]
rs868442	0.83[ASN][1000 genomes]
rs885572	0.82[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:7 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv469405	chr2:9814374-9964947	Enhancers Weak transcription Flanking Active TSS Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	26 gene(s)	inside rSNPs	diseases
2	nsv580930	chr2:9814374-9964947	Enhancers Flanking Bivalent TSS/Enh Active TSS Flanking Active TSS Weak transcription Bivalent Enhancer Genic enhancers Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	26 gene(s)	inside rSNPs	diseases
3	nsv1003026	chr2:9854939-10012516	Enhancers Bivalent Enhancer Flanking Active TSS Weak transcription Active TSS Strong transcription ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	34 gene(s)	inside rSNPs	diseases
4	nsv470443	chr2:9857018-9975557	Enhancers Flanking Bivalent TSS/Enh Weak transcription Active TSS Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	23 gene(s)	inside rSNPs	diseases
5	nsv1014911	chr2:9863969-9905959	Enhancers Weak transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Flanking Active TSS Active TSS Bivalent/Poised TSS ZNF genes & repeats Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
6	nsv873618	chr2:9870631-9919759	Enhancers Weak transcription Flanking Active TSS Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	15 gene(s)	inside rSNPs	diseases
7	nsv873619	chr2:9870631-9956981	Weak transcription Flanking Bivalent TSS/Enh Enhancers Bivalent Enhancer Active TSS Flanking Active TSS Bivalent/Poised TSS ZNF genes & repeats Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	21 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:30 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:9877400-9885000	Weak transcription	HMEC	breast
2	chr2:9878400-9881400	Enhancers	Left Ventricle	heart
3	chr2:9879000-9881000	Weak transcription	A549	lung
4	chr2:9879600-9882200	Enhancers	HSMMtube	muscle
5	chr2:9880000-9881200	Enhancers	Muscle Satellite Cultured Cells	--
6	chr2:9880000-9881400	Enhancers	HSMM	muscle
7	chr2:9880000-9881600	Enhancers	Psoas Muscle	Psoas
8	chr2:9880000-9883200	Enhancers	Fetal Muscle Leg	muscle
9	chr2:9880000-9884000	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
10	chr2:9880000-9884200	Weak transcription	Fetal Intestine Large	intestine
11	chr2:9880000-9884400	Weak transcription	Lung	lung
12	chr2:9880000-9885000	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
13	chr2:9880200-9881000	Weak transcription	Fetal Muscle Trunk	muscle
14	chr2:9880200-9881000	Enhancers	Skeletal Muscle Female	skeletal muscle
15	chr2:9880200-9881400	Enhancers	Duodenum Mucosa	Duodenum
16	chr2:9880200-9884200	Weak transcription	Sigmoid Colon	Sigmoid Colon
17	chr2:9880200-9884400	Weak transcription	Colonic Mucosa	Colon
18	chr2:9880200-9884400	Weak transcription	Rectal Mucosa Donor 29	rectum
19	chr2:9880200-9884400	Weak transcription	Rectal Mucosa Donor 31	rectum
20	chr2:9880200-9885200	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
21	chr2:9880200-9892800	Weak transcription	Thymus	Thymus
22	chr2:9880200-9893200	Weak transcription	Right Atrium	heart
23	chr2:9880600-9881600	Enhancers	Fetal Heart	heart
24	chr2:9880600-9881600	Flanking Active TSS	Hela-S3	cervix
25	chr2:9880800-9881000	Enhancers	Skeletal Muscle Male	skeletal muscle
26	chr2:9880800-9881000	Enhancers	Small Intestine	intestine
27	chr2:9880800-9881400	Enhancers	Right Ventricle	heart
28	chr2:9880800-9881400	Enhancers	NH-A	brain
29	chr2:9880800-9881400	Enhancers	NHDF-Ad	bronchial
30	chr2:9880800-9885200	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin

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