Variant report

Variant	rs12470409
Chromosome Location	chr2:9883082-9883083
allele	A/G
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	CTCF	chr2:9882940-9883090	GM12869	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr2:9881645..9885042-chr2:9886477..9889282,3	K562	blood:
2	chr2:9761639..9764568-chr2:9881456..9883138,2	K562	blood:
3	chr2:9881091..9883145-chr2:9887782..9890192,2	K562	blood:
4	chr2:9881447..9883906-chr2:9890191..9892636,2	MCF-7	breast:

Variant related genes	Relation type
RNU4-73P	TF binding region
ENSG00000240960	TF binding region
ENSG00000240960	Chromatin interaction

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	0.86[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs11674024	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11676286	0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11678697	0.91[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]
rs12472594	0.82[ASN][1000 genomes]
rs12475853	0.87[ASN][1000 genomes]
rs12476199	0.82[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];0.86[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	0.90[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[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:25 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:9877400-9885000	Weak transcription	HMEC	breast
2	chr2:9880000-9883200	Enhancers	Fetal Muscle Leg	muscle
3	chr2:9880000-9884000	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
4	chr2:9880000-9884200	Weak transcription	Fetal Intestine Large	intestine
5	chr2:9880000-9884400	Weak transcription	Lung	lung
6	chr2:9880000-9885000	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
7	chr2:9880200-9884200	Weak transcription	Sigmoid Colon	Sigmoid Colon
8	chr2:9880200-9884400	Weak transcription	Colonic Mucosa	Colon
9	chr2:9880200-9884400	Weak transcription	Rectal Mucosa Donor 29	rectum
10	chr2:9880200-9884400	Weak transcription	Rectal Mucosa Donor 31	rectum
11	chr2:9880200-9885200	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
12	chr2:9880200-9892800	Weak transcription	Thymus	Thymus
13	chr2:9880200-9893200	Weak transcription	Right Atrium	heart
14	chr2:9880800-9885200	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
15	chr2:9881400-9884000	Weak transcription	NHDF-Ad	bronchial
16	chr2:9881400-9884200	Weak transcription	Duodenum Mucosa	Duodenum
17	chr2:9881400-9884200	Weak transcription	A549	lung
18	chr2:9881400-9884400	Weak transcription	Left Ventricle	heart
19	chr2:9881400-9884400	Weak transcription	Right Ventricle	heart
20	chr2:9881400-9884600	Weak transcription	HSMM	muscle
21	chr2:9881600-9884000	Weak transcription	Fetal Heart	heart
22	chr2:9881600-9885200	Weak transcription	Psoas Muscle	Psoas
23	chr2:9882000-9884200	Weak transcription	Skeletal Muscle Male	skeletal muscle
24	chr2:9882000-9884600	Weak transcription	Skeletal Muscle Female	skeletal muscle
25	chr2:9882200-9885000	Weak transcription	Hela-S3	cervix

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