Variant report

Variant	rs4887166
Chromosome Location	chr15:74897598-74897599
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:3)
CpG islands
(count:0)
Chromatin interactive
region (count:3)
LncRNA
region (count:1)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:3 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr15:74897437-74897768	MCF10A-Er-Src	breast:	n/a	n/a
2	POLR2A	chr15:74897314-74898203	K562	blood:	n/a	n/a
3	POLR2A	chr15:74897156-74898954	PBDE	blood:	n/a	n/a

No data

(count:3 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr15:74881516..74883805-chr15:74896147..74898925,2	K562	blood:
2	chr15:74753117..74754905-chr15:74895780..74898493,2	MCF-7	breast:
3	chr15:74894451..74897620-chr15:74904865..74909062,6	K562	blood:

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

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-CLK3-1	chr15:74897274-74898074	NONHSAT047251

No data

Variant related genes	Relation type
CLK3	TF binding region
ENSG00000260919	Chromatin interaction
ENSG00000179335	Chromatin interaction
ENSG00000179361	Chromatin interaction
ENSG00000138629	Chromatin interaction
ENSG00000247240	Chromatin interaction

Extended variants
information (count: 99 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:89)

rs_ID	r²[population]
rs1030889	0.82[CHB][hapmap];0.91[JPT][hapmap]
rs10459648	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.88[AMR][1000 genomes];0.88[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs10851871	1.00[CEU][hapmap];0.95[CHB][hapmap];0.86[JPT][hapmap]
rs10851873	0.82[CHB][hapmap];0.91[JPT][hapmap]
rs11072490	0.81[EUR][1000 genomes]
rs11072492	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.85[AMR][1000 genomes];0.82[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs11072493	1.00[CEU][hapmap];1.00[CHB][hapmap];0.91[JPT][hapmap];0.87[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs11072494	1.00[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11072495	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11072496	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.91[AMR][1000 genomes];0.99[ASN][1000 genomes]
rs11072497	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs11072498	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs11629749	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.93[AMR][1000 genomes];0.99[ASN][1000 genomes]
rs11629946	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.89[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs11854461	0.90[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.90[YRI][hapmap]
rs11857328	0.82[EUR][1000 genomes]
rs12437519	0.87[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs12439113	1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];0.84[AMR][1000 genomes];0.86[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs12441932	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.93[AFR][1000 genomes];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12442013	0.88[AMR][1000 genomes];0.85[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs12442097	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.85[AMR][1000 genomes];0.86[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs12594447	0.83[AMR][1000 genomes];0.85[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs12909573	0.81[EUR][1000 genomes]
rs1456432	0.85[ASN][1000 genomes]
rs16969247	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];1.00[YRI][hapmap]
rs16969393	0.82[CHB][hapmap];0.91[JPT][hapmap]
rs16969612	0.81[EUR][1000 genomes]
rs1821847	0.81[EUR][1000 genomes]
rs1821848	0.85[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs1866113	0.90[CEU][hapmap];1.00[CHB][hapmap];0.91[JPT][hapmap];0.86[YRI][hapmap]
rs2068982	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[YRI][hapmap];0.90[AFR][1000 genomes];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2198843	1.00[CEU][hapmap];0.91[CHB][hapmap];0.95[JPT][hapmap];0.85[ASN][1000 genomes]
rs2289187	0.90[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap]
rs2289188	0.92[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.91[YRI][hapmap]
rs2415241	0.83[AMR][1000 genomes];0.83[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2415242	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.88[AMR][1000 genomes];0.86[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2415245	0.86[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs3985310	0.90[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap]
rs4886601	0.89[CEU][hapmap];1.00[CHB][hapmap];0.82[JPT][hapmap];0.93[AMR][1000 genomes];0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4887150	0.90[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.86[YRI][hapmap]
rs4887151	0.92[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap]
rs4887152	0.91[CEU][hapmap];0.90[YRI][hapmap]
rs4887154	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap]
rs4887155	0.81[EUR][1000 genomes]
rs4887159	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.88[AMR][1000 genomes];0.88[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs4887160	0.89[AMR][1000 genomes];0.89[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs4887162	0.90[AMR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4887163	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.90[AMR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4887165	0.85[ASN][1000 genomes]
rs58473469	0.94[AFR][1000 genomes];0.98[AMR][1000 genomes];0.88[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6495105	1.00[CEU][hapmap];1.00[CHB][hapmap];0.96[JPT][hapmap]
rs6495106	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap]
rs6495115	0.85[AMR][1000 genomes];0.87[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs6495116	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];1.00[YRI][hapmap];0.88[AFR][1000 genomes]
rs6495117	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6495118	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.87[AFR][1000 genomes];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6495121	1.00[CEU][hapmap];0.91[CHB][hapmap];0.95[JPT][hapmap];0.85[ASN][1000 genomes]
rs7161903	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs7163775	0.90[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap]
rs7166656	0.81[EUR][1000 genomes]
rs7166701	0.90[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap]
rs7167655	0.81[EUR][1000 genomes]
rs7171838	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.85[AMR][1000 genomes];0.88[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs7173006	0.81[EUR][1000 genomes]
rs7176095	0.94[AMR][1000 genomes];0.93[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7177407	0.85[AMR][1000 genomes];0.86[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs7178568	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.87[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs74025818	0.94[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs7497342	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs8023479	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.87[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs8023865	0.89[AFR][1000 genomes];0.90[AMR][1000 genomes];0.88[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs8026181	0.85[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs8026923	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.85[AMR][1000 genomes];0.86[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs8027066	1.00[CEU][hapmap];1.00[CHB][hapmap];0.91[JPT][hapmap];0.88[AMR][1000 genomes];0.86[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs8028163	0.85[AMR][1000 genomes];0.84[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs8028430	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.88[AMR][1000 genomes];0.86[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs8029116	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.85[AMR][1000 genomes];0.84[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs8029215	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.88[AMR][1000 genomes];0.83[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs8036030	0.86[CHB][hapmap];0.86[JPT][hapmap]
rs8037211	0.91[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.90[YRI][hapmap]
rs8037714	0.85[AMR][1000 genomes];0.83[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs8040745	0.87[AMR][1000 genomes];0.81[ASN][1000 genomes]
rs8041030	0.85[AMR][1000 genomes];0.84[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs8041807	0.85[AMR][1000 genomes];0.86[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs8042832	0.81[EUR][1000 genomes]
rs8043082	0.85[AMR][1000 genomes];0.86[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs9635320	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.94[AMR][1000 genomes];0.93[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9672559	1.00[CEU][hapmap];0.91[CHB][hapmap];0.95[JPT][hapmap];0.96[YRI][hapmap];0.86[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs9888684	0.81[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:10 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv1809847	chr15:74734500-74948063	Genic enhancers Flanking Active TSS Weak transcription Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Strong transcription Enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	70 gene(s)	inside rSNPs	diseases
2	esv1812223	chr15:74869438-74948063	Enhancers Strong transcription Active TSS Weak transcription Flanking Active TSS Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	40 gene(s)	inside rSNPs	diseases
3	nsv904379	chr15:74869438-75027880	Strong transcription Flanking Active TSS Active TSS Bivalent Enhancer Weak transcription Enhancers Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	54 gene(s)	inside rSNPs	diseases
4	nsv904380	chr15:74869438-75142761	Flanking Active TSS Weak transcription Active TSS Enhancers Strong transcription Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	69 gene(s)	inside rSNPs	diseases
5	esv1814078	chr15:74884447-74948063	Weak transcription Strong transcription Active TSS Genic enhancers Enhancers Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	40 gene(s)	inside rSNPs	diseases
6	nsv457204	chr15:74885091-74948063	Weak transcription Enhancers Flanking Active TSS Strong transcription Active TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	40 gene(s)	inside rSNPs	diseases
7	nsv569991	chr15:74885091-74948063	Strong transcription Enhancers Active TSS Weak transcription Genic enhancers Flanking Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	40 gene(s)	inside rSNPs	diseases
8	nsv542434	chr15:74885329-74929552	Flanking Active TSS Genic enhancers Enhancers Weak transcription Active TSS Strong transcription Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	39 gene(s)	inside rSNPs	diseases
9	nsv1047943	chr15:74885329-74940857	Enhancers Flanking Active TSS Weak transcription Strong transcription Active TSS Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	40 gene(s)	inside rSNPs	diseases
10	nsv817698	chr15:74889163-75019449	Genic enhancers Bivalent Enhancer Enhancers Flanking Bivalent TSS/Enh Active TSS Weak transcription Strong transcription Flanking Active TSS Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	54 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:38 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:74891200-74899200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
2	chr15:74891400-74898000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
3	chr15:74891400-74903400	Weak transcription	HMEC	breast
4	chr15:74891600-74907200	Weak transcription	Placenta Amnion	Placenta Amnion
5	chr15:74892000-74902400	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
6	chr15:74892200-74898200	Weak transcription	Fetal Kidney	kidney
7	chr15:74892200-74902600	Weak transcription	Right Atrium	heart
8	chr15:74892200-74906000	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
9	chr15:74892200-74906600	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
10	chr15:74892400-74898800	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
11	chr15:74892400-74902600	Weak transcription	Ovary	ovary
12	chr15:74892400-74906000	Weak transcription	Breast Myoepithelial Primary Cells	Breast
13	chr15:74892400-74906400	Weak transcription	Brain Inferior Temporal Lobe	brain
14	chr15:74892400-74906600	Weak transcription	Primary T cells from cord blood	blood
15	chr15:74892400-74906600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
16	chr15:74892600-74902600	Weak transcription	Spleen	Spleen
17	chr15:74892600-74902800	Weak transcription	Lung	lung
18	chr15:74893000-74906600	Weak transcription	Fetal Brain Female	brain
19	chr15:74893200-74906200	Weak transcription	Primary T cells fromperipheralblood	blood
20	chr15:74893400-74902400	Weak transcription	Left Ventricle	heart
21	chr15:74893800-74902600	Weak transcription	Pancreas	Pancrea
22	chr15:74894400-74906200	Weak transcription	Skeletal Muscle Male	skeletal muscle
23	chr15:74894800-74898000	Enhancers	Right Ventricle	heart
24	chr15:74895000-74898000	Enhancers	HepG2	liver
25	chr15:74895000-74901200	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
26	chr15:74895200-74901000	Weak transcription	Fetal Intestine Small	intestine
27	chr15:74895200-74906400	Weak transcription	Stomach Smooth Muscle	stomach
28	chr15:74895400-74897600	ZNF genes & repeats	iPS DF 19.11 Cell Line	embryonic stem cell
29	chr15:74895600-74897800	Weak transcription	Fetal Stomach	stomach
30	chr15:74895600-74902600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
31	chr15:74896400-74897600	Bivalent Enhancer	Foreskin Fibroblast Primary Cells skin02	Skin
32	chr15:74896800-74897600	Enhancers	Brain Germinal Matrix	brain
33	chr15:74896800-74897800	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
34	chr15:74896800-74898000	Bivalent Enhancer	Foreskin Fibroblast Primary Cells skin01	Skin
35	chr15:74897000-74900200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
36	chr15:74897200-74902400	Weak transcription	Primary hematopoietic stem cells short term culture	blood
37	chr15:74897400-74898000	Bivalent Enhancer	Cortex derived primary cultured neurospheres	brain
38	chr15:74897400-74898200	Enhancers	Brain Hippocampus Middle	brain

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