Variant report

Variant	rs7862428
Chromosome Location	chr9:15482976-15482977
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr6:27832881..27833609-chr9:15482471..15483085,2	NB4	blood:

Variant related genes	Relation type
ENSG00000198374	Chromatin interaction

Extended variants
information (count: 56 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:51)

rs_ID	r²[population]
rs10283923	1.00[CEU][hapmap];0.89[JPT][hapmap];0.83[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs10283927	0.92[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs1033056	0.82[AMR][1000 genomes]
rs1046388	0.84[AFR][1000 genomes];0.94[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs10738393	0.93[YRI][hapmap];0.83[AFR][1000 genomes]
rs10738395	0.89[YRI][hapmap]
rs10738397	0.93[YRI][hapmap];0.89[AFR][1000 genomes]
rs10738398	0.93[AFR][1000 genomes]
rs10756666	0.89[YRI][hapmap];0.87[AFR][1000 genomes]
rs10962036	0.85[AFR][1000 genomes]
rs10962048	1.00[JPT][hapmap]
rs12336503	0.92[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs12336509	0.93[CEU][hapmap];0.89[JPT][hapmap];0.92[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs12339417	0.92[CEU][hapmap];1.00[JPT][hapmap];0.92[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs12685082	1.00[JPT][hapmap]
rs13248	0.89[JPT][hapmap]
rs1397214	0.93[YRI][hapmap]
rs16933311	0.89[JPT][hapmap]
rs16933316	1.00[JPT][hapmap];0.93[ASN][1000 genomes]
rs16933320	0.89[JPT][hapmap]
rs1828383	0.88[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs2175257	0.80[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs2382530	0.87[AFR][1000 genomes]
rs2777949	1.00[CEU][hapmap];0.85[EUR][1000 genomes]
rs2777950	0.84[CEU][hapmap];0.92[YRI][hapmap];0.87[AFR][1000 genomes];0.97[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs28515581	0.86[AMR][1000 genomes]
rs28537229	0.88[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs4741501	0.83[AFR][1000 genomes]
rs4741502	0.89[AFR][1000 genomes]
rs4741505	0.93[YRI][hapmap];0.89[AFR][1000 genomes]
rs4741507	0.93[YRI][hapmap];0.86[AFR][1000 genomes];0.85[AMR][1000 genomes]
rs4741508	0.92[YRI][hapmap];0.89[AFR][1000 genomes];0.85[AMR][1000 genomes]
rs57191285	0.85[ASN][1000 genomes]
rs57849124	0.87[ASN][1000 genomes]
rs58607272	0.88[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs62571010	0.89[EUR][1000 genomes]
rs62571021	0.85[ASN][1000 genomes]
rs62571030	0.88[EUR][1000 genomes]
rs6474915	0.89[YRI][hapmap]
rs6474927	0.86[EUR][1000 genomes]
rs7018658	0.91[AFR][1000 genomes];0.97[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs7021042	0.96[YRI][hapmap];0.98[AFR][1000 genomes];0.85[AMR][1000 genomes]
rs7021778	0.90[JPT][hapmap]
rs7026910	0.87[AFR][1000 genomes]
rs73408340	0.87[ASN][1000 genomes]
rs73644655	0.88[ASN][1000 genomes]
rs7856318	0.84[CEU][hapmap];0.89[JPT][hapmap]
rs7857933	1.00[JPT][hapmap]
rs907075	0.90[YRI][hapmap];0.87[AFR][1000 genomes]
rs907076	0.82[AFR][1000 genomes]
rs9650682	0.93[YRI][hapmap]

Variant overlapped rSNPs/rCNVs (count:5 , 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	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
4	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
5	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:120 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:15433400-15492400	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
2	chr9:15439000-15492200	Strong transcription	Primary hematopoietic stem cells short term culture	blood
3	chr9:15442800-15508400	Strong transcription	Fetal Thymus	thymus
4	chr9:15443200-15490400	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
5	chr9:15443200-15492400	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
6	chr9:15443800-15492200	Strong transcription	HUES64 Cell Line	embryonic stem cell
7	chr9:15444000-15487600	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
8	chr9:15444000-15492400	Strong transcription	HUES48 Cell Line	embryonic stem cell
9	chr9:15444400-15495200	Weak transcription	Fetal Heart	heart
10	chr9:15444600-15491200	Strong transcription	HUES6 Cell Line	embryonic stem cell
11	chr9:15447000-15509800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
12	chr9:15449000-15492200	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
13	chr9:15449800-15509000	Weak transcription	Small Intestine	intestine
14	chr9:15452200-15492400	Weak transcription	Right Ventricle	heart
15	chr9:15454600-15508600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
16	chr9:15457000-15492400	Weak transcription	Lung	lung
17	chr9:15459000-15492200	Strong transcription	H1 Cell Line	embryonic stem cell
18	chr9:15460800-15510000	Weak transcription	Esophagus	oesophagus
19	chr9:15461000-15492200	Strong transcription	iPS-18 Cell Line	embryonic stem cell
20	chr9:15461600-15483800	Weak transcription	Fetal Intestine Small	intestine
21	chr9:15461600-15492400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
22	chr9:15461600-15492800	Weak transcription	Pancreas	Pancrea
23	chr9:15462800-15505200	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
24	chr9:15466200-15492400	Weak transcription	Gastric	stomach
25	chr9:15466600-15492400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
26	chr9:15467200-15501000	Weak transcription	Colon Smooth Muscle	Colon
27	chr9:15467400-15505600	Weak transcription	Skeletal Muscle Male	skeletal muscle
28	chr9:15468800-15483800	Weak transcription	Fetal Stomach	stomach
29	chr9:15468800-15484400	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
30	chr9:15468800-15484600	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
31	chr9:15468800-15492400	Weak transcription	Colonic Mucosa	Colon
32	chr9:15468800-15492400	Weak transcription	Spleen	Spleen
33	chr9:15469200-15491800	Weak transcription	Stomach Smooth Muscle	stomach
34	chr9:15469200-15505600	Weak transcription	NHLF	lung
35	chr9:15469800-15486400	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
36	chr9:15470400-15485200	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
37	chr9:15471000-15492600	Strong transcription	Primary B cells from peripheral blood	blood
38	chr9:15472200-15509000	Weak transcription	HMEC	breast
39	chr9:15473000-15486000	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
40	chr9:15473800-15486000	Weak transcription	Muscle Satellite Cultured Cells	--
41	chr9:15473800-15492200	Weak transcription	Liver	Liver
42	chr9:15475000-15485200	Weak transcription	Brain Inferior Temporal Lobe	brain
43	chr9:15476400-15485200	Weak transcription	Rectal Mucosa Donor 31	rectum
44	chr9:15476400-15504000	Weak transcription	Skeletal Muscle Female	skeletal muscle
45	chr9:15476600-15483600	Strong transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
46	chr9:15476600-15484800	Weak transcription	Osteobl	bone
47	chr9:15476600-15492200	Weak transcription	Left Ventricle	heart
48	chr9:15476600-15508800	Weak transcription	Rectal Smooth Muscle	rectum
49	chr9:15476600-15510000	Weak transcription	Sigmoid Colon	Sigmoid Colon
50	chr9:15477000-15485400	Weak transcription	K562	blood

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links