Variant report

Variant	rs2175259
Chromosome Location	chr9:15421423-15421424
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:1)
CpG islands
(count:0)
Chromatin interactive
region (count:6)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

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

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr9:15421333-15423424	SK-N-MC	brain:	n/a	n/a

No data

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

No.	Distal block	Cell Line	Cell type
1	chr9:15421340..15424109-chr9:15510012..15511838,2	K562	blood:
2	chr9:15276373..15278004-chr9:15420785..15422574,2	MCF-7	breast:
3	chr9:15306135..15309581-chr9:15420818..15425516,6	MCF-7	breast:
4	chr9:15298942..15301605-chr9:15420446..15422025,2	MCF-7	breast:
5	chr9:15420595..15424773-chr9:15424796..15433036,11	MCF-7	breast:
6	chr9:15352501..15354066-chr9:15419261..15422025,2	MCF-7	breast:

No data

Variant related genes	Relation type
SNAPC3	TF binding region
ENSG00000251834	Chromatin interaction
ENSG00000164985	Chromatin interaction
ENSG00000155158	Chromatin interaction

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

rSNPs within LD-proxies of this variant (count:41)

rs_ID	r²[population]
rs10081655	1.00[CHB][hapmap];0.89[JPT][hapmap]
rs10115540	1.00[CHB][hapmap];0.89[JPT][hapmap]
rs10117968	0.94[CHB][hapmap];0.86[CHD][hapmap];0.90[JPT][hapmap];0.92[ASN][1000 genomes]
rs1033056	0.81[CHB][hapmap]
rs10733292	1.00[CHB][hapmap];0.89[JPT][hapmap]
rs10738392	1.00[CHB][hapmap];0.89[JPT][hapmap]
rs10738393	1.00[CHB][hapmap];0.85[CHD][hapmap];0.89[JPT][hapmap];0.86[ASN][1000 genomes]
rs10738395	0.94[CHB][hapmap];0.85[CHD][hapmap];0.89[JPT][hapmap];0.87[MKK][hapmap];0.84[ASN][1000 genomes]
rs10738397	0.94[CHB][hapmap];0.89[JPT][hapmap]
rs10756664	1.00[CHB][hapmap];0.89[JPT][hapmap]
rs10756666	0.94[CHB][hapmap];0.89[JPT][hapmap]
rs10962027	0.81[ASN][1000 genomes]
rs1123038	1.00[CHB][hapmap];0.89[JPT][hapmap]
rs12093	0.83[JPT][hapmap]
rs1397214	0.93[CHB][hapmap];1.00[JPT][hapmap];0.99[ASN][1000 genomes]
rs1397215	0.93[CHB][hapmap]
rs1567452	0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1976599	1.00[CHB][hapmap];0.89[JPT][hapmap]
rs2665504	0.80[CHB][hapmap];0.89[JPT][hapmap]
rs2737829	0.87[CHB][hapmap];0.84[JPT][hapmap]
rs2737842	0.87[CHB][hapmap];0.89[JPT][hapmap]
rs4741500	1.00[CHB][hapmap];0.83[JPT][hapmap]
rs4741501	0.87[JPT][hapmap]
rs4741504	0.92[CHB][hapmap];0.88[JPT][hapmap]
rs4741505	0.94[CHB][hapmap];0.89[JPT][hapmap]
rs4741506	0.93[CHB][hapmap];0.89[JPT][hapmap]
rs4741507	0.84[JPT][hapmap]
rs4741508	0.94[CHB][hapmap];0.84[JPT][hapmap]
rs6474915	0.83[CEU][hapmap];0.88[CHB][hapmap];0.93[GIH][hapmap];0.90[JPT][hapmap];0.88[TSI][hapmap];0.92[EUR][1000 genomes]
rs6474916	1.00[CHB][hapmap];0.84[JPT][hapmap];0.84[ASN][1000 genomes]
rs6474918	1.00[CHB][hapmap];0.89[JPT][hapmap]
rs6474923	0.92[CHB][hapmap];0.82[JPT][hapmap]
rs7021042	0.84[JPT][hapmap]
rs7026910	0.92[CHB][hapmap];0.87[JPT][hapmap]
rs7026970	0.94[CHB][hapmap];0.89[JPT][hapmap]
rs7042165	1.00[CHB][hapmap];0.89[JPT][hapmap]
rs7046713	0.94[CHB][hapmap];0.89[JPT][hapmap]
rs907075	0.94[CHB][hapmap];0.89[JPT][hapmap]
rs907076	0.94[CHB][hapmap];0.89[JPT][hapmap]
rs9650682	0.94[CHB][hapmap];0.89[JPT][hapmap]
rs9650683	0.94[CHB][hapmap];0.89[JPT][hapmap]

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	nsv517975	chr9:15286446-15534070	Weak transcription Genic enhancers Active TSS Flanking Active TSS Enhancers Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	23 gene(s)	inside rSNPs	diseases
2	nsv892625	chr9:15326251-16064850	Enhancers Active TSS Weak transcription Strong transcription Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	35 gene(s)	inside rSNPs	diseases
3	nsv1030287	chr9:15332709-15458001	Weak transcription Enhancers Strong transcription Active TSS Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases
4	nsv892626	chr9:15389610-15694690	Flanking Active TSS Active TSS Weak transcription Enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Strong transcription Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	27 gene(s)	inside rSNPs	diseases
5	nsv892627	chr9:15397969-15909450	Enhancers Flanking Active TSS Strong transcription Weak transcription Genic enhancers Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	28 gene(s)	inside rSNPs	diseases
6	nsv831520	chr9:15404866-15444447	Weak transcription Active TSS Strong transcription Genic enhancers Flanking Active TSS Enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region	15 gene(s)	inside rSNPs	diseases
7	nsv892628	chr9:15420805-15528290	Strong transcription Active TSS Weak transcription Enhancers Genic enhancers ZNF genes & repeats Flanking Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	21 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:20 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:15417000-15421800	Weak transcription	HepG2	liver
2	chr9:15417000-15422000	Weak transcription	H9 Cell Line	embryonic stem cell
3	chr9:15417000-15422000	Weak transcription	HUES64 Cell Line	embryonic stem cell
4	chr9:15417000-15422200	Weak transcription	Esophagus	oesophagus
5	chr9:15418000-15422000	Weak transcription	HUES48 Cell Line	embryonic stem cell
6	chr9:15418200-15422000	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
7	chr9:15418200-15422200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
8	chr9:15418400-15421600	Weak transcription	iPS-18 Cell Line	embryonic stem cell
9	chr9:15418400-15421800	Weak transcription	HUES6 Cell Line	embryonic stem cell
10	chr9:15418400-15421800	Weak transcription	iPS-15b Cell Line	embryonic stem cell
11	chr9:15420600-15422000	Weak transcription	Brain Cingulate Gyrus	brain
12	chr9:15420600-15422000	Enhancers	Osteobl	bone
13	chr9:15421200-15422000	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
14	chr9:15421400-15421600	Enhancers	Sigmoid Colon	Sigmoid Colon
15	chr9:15421400-15421800	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
16	chr9:15421400-15421800	Enhancers	Duodenum Mucosa	Duodenum
17	chr9:15421400-15422000	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
18	chr9:15421400-15422000	Enhancers	Rectal Mucosa Donor 31	rectum
19	chr9:15421400-15422200	Enhancers	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
20	chr9:15421400-15422200	Enhancers	Fetal Intestine Small	intestine

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