Variant report

Variant	rs961233
Chromosome Location	chr15:93473624-93473625
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:0)
CpG islands
(count:0)
Chromatin interactive
region (count:11)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:11 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr15:93463483..93466768-chr15:93471204..93475396,3	MCF-7	breast:
2	chr15:93466975..93470280-chr15:93472259..93475491,4	MCF-7	breast:
3	chr15:93471074..93473914-chr15:93495809..93497722,2	K562	blood:
4	chr15:93446137..93449802-chr15:93471461..93474569,3	K562	blood:
5	chr15:93352610..93354229-chr15:93472657..93474218,2	MCF-7	breast:
6	chr15:93459389..93462852-chr15:93472444..93474181,3	K562	blood:
7	chr15:93459389..93460980-chr15:93471786..93474181,2	K562	blood:
8	chr15:93466503..93469874-chr15:93472083..93475098,4	K562	blood:
9	chr15:93345772..93348684-chr15:93471870..93473819,2	K562	blood:
10	chr15:93472774..93474766-chr15:93477734..93480112,2	K562	blood:
11	chr15:93443271..93444821-chr15:93472288..93474451,2	K562	blood:

No data

Variant related genes	Relation type
ENSG00000173575	Chromatin interaction
ENSG00000264173	Chromatin interaction
ENSG00000185442	Chromatin interaction

Extended variants
information (count: 52 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:45)

rs_ID	r²[population]
rs10520716	0.85[CHB][hapmap];0.83[CHD][hapmap];0.86[GIH][hapmap];1.00[JPT][hapmap];0.86[MEX][hapmap]
rs10520719	0.86[JPT][hapmap]
rs11074120	0.81[JPT][hapmap]
rs11630582	0.86[JPT][hapmap]
rs11634207	0.86[JPT][hapmap]
rs12437674	0.84[GIH][hapmap];0.93[JPT][hapmap];0.86[MEX][hapmap]
rs12443243	0.85[CHB][hapmap];1.00[JPT][hapmap];0.94[ASN][1000 genomes]
rs12901950	0.92[JPT][hapmap]
rs12904680	0.92[JPT][hapmap]
rs12906132	0.86[JPT][hapmap]
rs12907579	0.86[JPT][hapmap]
rs12908494	0.90[ASN][1000 genomes]
rs12916015	0.92[JPT][hapmap]
rs1318689	1.00[CEU][hapmap];0.92[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1320819	0.85[CHB][hapmap];1.00[JPT][hapmap]
rs1406714	0.92[CEU][hapmap];0.92[CHB][hapmap];0.95[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.93[TSI][hapmap];0.85[AMR][1000 genomes];0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1534779	0.86[JPT][hapmap]
rs17525800	0.86[JPT][hapmap]
rs1881835	0.84[CHB][hapmap];0.92[JPT][hapmap]
rs2033844	0.86[JPT][hapmap]
rs2272457	0.86[JPT][hapmap]
rs28573213	0.86[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs35865218	0.80[AMR][1000 genomes];0.92[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs3743469	0.88[ASN][1000 genomes]
rs3784786	0.86[JPT][hapmap]
rs3817597	0.81[JPT][hapmap]
rs3826035	0.81[JPT][hapmap]
rs3826036	0.85[CHB][hapmap];0.93[JPT][hapmap];0.92[ASN][1000 genomes]
rs4327000	0.93[JPT][hapmap]
rs4778052	0.92[JPT][hapmap]
rs4778065	0.85[JPT][hapmap]
rs6497009	0.89[ASN][1000 genomes]
rs6497010	0.86[JPT][hapmap];0.88[ASN][1000 genomes]
rs7164668	0.93[JPT][hapmap];0.90[ASN][1000 genomes]
rs7167194	0.91[JPT][hapmap]
rs7168780	0.86[ASN][1000 genomes]
rs7173103	0.85[CHB][hapmap];1.00[JPT][hapmap];0.91[ASN][1000 genomes]
rs7175134	0.91[ASN][1000 genomes]
rs7176652	0.86[JPT][hapmap]
rs8024528	0.92[CHB][hapmap];0.80[JPT][hapmap];0.90[ASN][1000 genomes]
rs8026695	1.00[CEU][hapmap];0.92[CHB][hapmap];0.95[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.95[TSI][hapmap];0.86[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs8035739	0.85[CHB][hapmap];0.87[CHD][hapmap];0.84[GIH][hapmap];1.00[JPT][hapmap];0.90[ASN][1000 genomes]
rs8042395	0.81[JPT][hapmap]
rs8042632	0.81[JPT][hapmap]
rs920389	0.92[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	nsv948738	chr15:93070742-93728147	Strong transcription Weak transcription Flanking Active TSS Enhancers Genic enhancers Active TSS Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	169 gene(s)	inside rSNPs	diseases
2	nsv1049490	chr15:93134405-93591660	Enhancers Genic enhancers Weak transcription Strong transcription Active TSS ZNF genes & repeats Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	151 gene(s)	inside rSNPs	diseases
3	nsv530846	chr15:93323949-94030462	Active TSS Strong transcription Flanking Active TSS Enhancers Weak transcription Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	153 gene(s)	inside rSNPs	diseases
4	nsv948881	chr15:93383740-93603608	Genic enhancers Strong transcription Weak transcription Transcr. at gene 5' and 3' Enhancers Flanking Active TSS Active TSS ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	91 gene(s)	inside rSNPs	diseases
5	nsv1047496	chr15:93412778-93475878	Enhancers Flanking Active TSS Active TSS Strong transcription Transcr. at gene 5' and 3' Genic enhancers Weak transcription ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA	87 gene(s)	inside rSNPs	diseases
6	nsv530847	chr15:93444024-93555676	Strong transcription Weak transcription Enhancers Genic enhancers Active TSS Flanking Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA	40 gene(s)	inside rSNPs	diseases
7	nsv917347	chr15:93444094-93586814	Enhancers Flanking Active TSS Weak transcription Transcr. at gene 5' and 3' Genic enhancers Strong transcription Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA	39 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs961233	CHD2	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:127 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:93457000-93489800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
2	chr15:93461600-93486800	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
3	chr15:93461600-93489200	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
4	chr15:93462000-93474800	Genic enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
5	chr15:93463200-93486800	Strong transcription	Dnd41	blood
6	chr15:93464200-93475000	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
7	chr15:93465400-93488400	Strong transcription	iPS-20b Cell Line	embryonic stem cell
8	chr15:93466000-93476200	Strong transcription	Placenta	Placenta
9	chr15:93466200-93475000	Strong transcription	HUVEC	blood vessel
10	chr15:93466200-93477000	Strong transcription	Primary hematopoietic stem cells short term culture	blood
11	chr15:93466200-93479200	Strong transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
12	chr15:93466200-93480800	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
13	chr15:93466200-93488200	Strong transcription	HUES6 Cell Line	embryonic stem cell
14	chr15:93466200-93488200	Strong transcription	Thymus	Thymus
15	chr15:93466200-93489400	Strong transcription	K562	blood
16	chr15:93466400-93475800	Strong transcription	Liver	Liver
17	chr15:93466400-93476400	Weak transcription	Fetal Heart	heart
18	chr15:93466400-93476800	Strong transcription	Primary hematopoietic stem cells	blood
19	chr15:93466400-93480800	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
20	chr15:93466400-93489000	Strong transcription	HUES64 Cell Line	embryonic stem cell
21	chr15:93466600-93474200	Strong transcription	HepG2	liver
22	chr15:93466600-93476400	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
23	chr15:93466600-93490600	Strong transcription	Fetal Lung	lung
24	chr15:93466800-93479600	Strong transcription	Primary B cells from peripheral blood	blood
25	chr15:93466800-93490200	Strong transcription	HUES48 Cell Line	embryonic stem cell
26	chr15:93467200-93476200	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
27	chr15:93467200-93490200	Strong transcription	iPS-18 Cell Line	embryonic stem cell
28	chr15:93467200-93490600	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
29	chr15:93467400-93476400	Strong transcription	Primary neutrophils fromperipheralblood	blood
30	chr15:93467400-93477000	Strong transcription	Stomach Smooth Muscle	stomach
31	chr15:93467400-93489200	Strong transcription	Primary B cells from cord blood	blood
32	chr15:93467400-93490000	Strong transcription	H1 Cell Line	embryonic stem cell
33	chr15:93467600-93474800	Strong transcription	iPS-15b Cell Line	embryonic stem cell
34	chr15:93467600-93490400	Strong transcription	H9 Cell Line	embryonic stem cell
35	chr15:93467600-93490600	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
36	chr15:93467800-93478600	Strong transcription	Primary T cells from cord blood	blood
37	chr15:93467800-93480000	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
38	chr15:93468000-93473800	Strong transcription	Brain Hippocampus Middle	brain
39	chr15:93468000-93475800	Strong transcription	Primary monocytes fromperipheralblood	blood
40	chr15:93468000-93476200	Strong transcription	Monocytes-CD14+_RO01746	blood
41	chr15:93468600-93490400	Strong transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
42	chr15:93468800-93474200	Genic enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
43	chr15:93469000-93489800	Strong transcription	Fetal Thymus	thymus
44	chr15:93469600-93474600	Strong transcription	Primary T cells fromperipheralblood	blood
45	chr15:93469600-93484600	Strong transcription	Left Ventricle	heart
46	chr15:93469800-93475400	Strong transcription	Colonic Mucosa	Colon
47	chr15:93470000-93474800	Genic enhancers	Osteobl	bone
48	chr15:93470000-93479800	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
49	chr15:93470000-93488200	Strong transcription	GM12878-XiMat	blood
50	chr15:93470200-93476600	Strong transcription	Fetal Intestine Large	intestine

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links