Variant report

Variant	rs1004488
Chromosome Location	chr2:9884673-9884674
allele	C/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	NFIC	chr2:9884345-9885033	SK-N-SH	brain:	n/a	chr2:9884639-9884655
2	PBX3	chr2:9884412-9885035	SK-N-SH	brain:	n/a	n/a
3	PBX3	chr2:9884412-9885011	SK-N-SH	brain:	n/a	n/a
4	TCF12	chr2:9884320-9885171	SK-N-SH	brain:	n/a	chr2:9885052-9885059

No.	Distal block	Cell Line	Cell type
1	chr2:9883472..9885352-chr2:9885421..9887800,2	MCF-7	breast:
2	chr2:9877830..9880619-chr2:9884575..9886353,2	MCF-7	breast:
3	chr2:9881645..9885042-chr2:9886477..9889282,3	K562	blood:
4	chr2:9877832..9879861-chr2:9884355..9886742,3	K562	blood:

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

Extended variants
information (count: 41 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:34)

rs_ID	r²[population]
rs10172624	1.00[AMR][1000 genomes]
rs10185303	1.00[EUR][1000 genomes]
rs10188428	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs10190680	1.00[AMR][1000 genomes]
rs10200454	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs10208526	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs10469619	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs11685143	1.00[EUR][1000 genomes]
rs11900302	1.00[EUR][1000 genomes]
rs11901478	1.00[EUR][1000 genomes]
rs13392859	1.00[EUR][1000 genomes]
rs13392861	1.00[EUR][1000 genomes]
rs13417294	1.00[EUR][1000 genomes]
rs13420034	1.00[EUR][1000 genomes]
rs16867063	1.00[EUR][1000 genomes]
rs16867103	1.00[EUR][1000 genomes]
rs16867145	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs4327210	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs56832685	1.00[EUR][1000 genomes]
rs57119165	1.00[EUR][1000 genomes]
rs58377484	1.00[EUR][1000 genomes]
rs59042599	1.00[EUR][1000 genomes]
rs59457002	1.00[EUR][1000 genomes]
rs60115192	1.00[EUR][1000 genomes]
rs6723929	1.00[AMR][1000 genomes]
rs6728922	1.00[AMR][1000 genomes]
rs73155171	1.00[EUR][1000 genomes]
rs73164230	1.00[EUR][1000 genomes]
rs73164231	1.00[EUR][1000 genomes]
rs73164234	1.00[EUR][1000 genomes]
rs73164238	1.00[EUR][1000 genomes]
rs73164239	1.00[EUR][1000 genomes]
rs73164242	1.00[EUR][1000 genomes]
rs73913171	1.00[AMR][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:34 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:9877400-9885000	Weak transcription	HMEC	breast
2	chr2:9880000-9885000	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
3	chr2:9880200-9885200	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
4	chr2:9880200-9892800	Weak transcription	Thymus	Thymus
5	chr2:9880200-9893200	Weak transcription	Right Atrium	heart
6	chr2:9880800-9885200	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
7	chr2:9881600-9885200	Weak transcription	Psoas Muscle	Psoas
8	chr2:9882200-9885000	Weak transcription	Hela-S3	cervix
9	chr2:9883600-9885400	Enhancers	Fetal Muscle Leg	muscle
10	chr2:9883800-9885400	Enhancers	Fetal Muscle Trunk	muscle
11	chr2:9884000-9885200	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
12	chr2:9884000-9885200	Enhancers	Fetal Heart	heart
13	chr2:9884000-9885800	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
14	chr2:9884000-9886000	Enhancers	NHDF-Ad	bronchial
15	chr2:9884200-9885000	Enhancers	Duodenum Mucosa	Duodenum
16	chr2:9884200-9885200	Enhancers	Fetal Intestine Small	intestine
17	chr2:9884200-9885400	Enhancers	Skeletal Muscle Male	skeletal muscle
18	chr2:9884200-9885600	Enhancers	Fetal Intestine Large	intestine
19	chr2:9884200-9885600	Enhancers	A549	lung
20	chr2:9884200-9886400	Enhancers	Pancreas	Pancrea
21	chr2:9884400-9884800	Enhancers	Foreskin Melanocyte Primary Cells skin01	Skin
22	chr2:9884400-9884800	Weak transcription	Sigmoid Colon	Sigmoid Colon
23	chr2:9884400-9885200	Enhancers	Colonic Mucosa	Colon
24	chr2:9884400-9885200	Enhancers	Rectal Mucosa Donor 29	rectum
25	chr2:9884400-9885200	Enhancers	Right Ventricle	heart
26	chr2:9884400-9885400	Bivalent Enhancer	Fetal Adrenal Gland	Adrenal Gland
27	chr2:9884400-9885400	Enhancers	Left Ventricle	heart
28	chr2:9884400-9885600	Enhancers	Lung	lung
29	chr2:9884400-9885600	Enhancers	Rectal Mucosa Donor 31	rectum
30	chr2:9884600-9884800	Enhancers	Skeletal Muscle Female	skeletal muscle
31	chr2:9884600-9885400	Bivalent Enhancer	HepG2	liver
32	chr2:9884600-9885600	Enhancers	HSMM	muscle
33	chr2:9884600-9885800	Bivalent Enhancer	Foreskin Fibroblast Primary Cells skin01	Skin
34	chr2:9884600-9886600	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin

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