Variant report

Variant	rs4073149
Chromosome Location	chr15:74898419-74898420
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:4)
CpG islands
(count:0)
Chromatin interactive
region (count:3)
LncRNA
region (count:1)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:4 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr15:74898296-74898736	K562	blood:	n/a	n/a
2	POLR2A	chr15:74897992-74898553	MCF10A-Er-Src	breast:	n/a	n/a
3	POLR2A	chr15:74897156-74898954	PBDE	blood:	n/a	n/a
4	ZNF143	chr15:74898134-74898480	K562	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	chr15:74832872..74835682-chr15:74898201..74900978,2	K562	blood:

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

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-CLK3-1	chr15:74898298-74898436	NONHSAT047256

No data

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

Extended variants
information (count: 93 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:83)

rs_ID	r²[population]
rs1030888	1.00[CEU][hapmap];0.90[CHB][hapmap];0.86[JPT][hapmap];0.83[AMR][1000 genomes]
rs10459601	1.00[CEU][hapmap];0.91[CHB][hapmap];0.86[CHD][hapmap];1.00[GIH][hapmap];0.86[JPT][hapmap];0.95[MEX][hapmap];1.00[TSI][hapmap];0.84[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs10459648	0.87[CHD][hapmap];0.92[GIH][hapmap];0.91[MEX][hapmap];0.84[TSI][hapmap];0.83[YRI][hapmap]
rs11072489	0.92[ASW][hapmap];0.81[LWK][hapmap];0.96[YRI][hapmap]
rs11072492	0.92[ASW][hapmap];0.87[CHD][hapmap];0.92[GIH][hapmap];0.86[LWK][hapmap];0.91[MEX][hapmap];0.84[TSI][hapmap];1.00[YRI][hapmap];0.82[AFR][1000 genomes]
rs11072494	0.92[ASW][hapmap];0.87[CHD][hapmap];0.92[GIH][hapmap];0.84[LWK][hapmap];0.91[MEX][hapmap];0.84[TSI][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];0.82[AMR][1000 genomes]
rs11072495	0.92[ASW][hapmap];0.87[CHD][hapmap];0.92[GIH][hapmap];0.91[LWK][hapmap];0.91[MEX][hapmap];0.84[TSI][hapmap];0.96[YRI][hapmap];0.95[AFR][1000 genomes];0.82[AMR][1000 genomes]
rs11072496	0.84[CHD][hapmap];0.86[GIH][hapmap]
rs11072497	0.84[CHD][hapmap];0.82[GIH][hapmap]
rs11072498	0.84[CHD][hapmap];0.82[GIH][hapmap]
rs11072499	1.00[CEU][hapmap];0.91[CHB][hapmap];0.84[CHD][hapmap];0.94[GIH][hapmap];0.90[JPT][hapmap];0.86[MEX][hapmap];1.00[TSI][hapmap];0.84[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs1128628	0.90[JPT][hapmap];0.91[ASN][1000 genomes]
rs11629749	0.87[CHD][hapmap];0.83[GIH][hapmap]
rs11629946	0.87[CHD][hapmap];0.87[GIH][hapmap];0.83[MEX][hapmap]
rs11854461	0.87[CHD][hapmap];0.92[GIH][hapmap];0.86[MEX][hapmap];0.84[TSI][hapmap]
rs11857192	0.84[AMR][1000 genomes]
rs12439054	0.82[AMR][1000 genomes]
rs12439113	0.92[YRI][hapmap];0.81[AFR][1000 genomes]
rs12441932	0.84[TSI][hapmap]
rs12594447	0.89[AFR][1000 genomes]
rs1821848	0.81[AFR][1000 genomes]
rs1866113	0.87[CHD][hapmap];0.92[GIH][hapmap];0.91[MEX][hapmap];0.84[TSI][hapmap]
rs1866114	0.87[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.85[YRI][hapmap]
rs1992145	0.85[JPT][hapmap]
rs2068982	0.84[CHD][hapmap];0.89[GIH][hapmap];0.91[MEX][hapmap];0.84[TSI][hapmap]
rs2099593	0.81[EUR][1000 genomes]
rs2289187	0.92[ASW][hapmap];0.87[CHD][hapmap];0.92[GIH][hapmap];0.84[LWK][hapmap];0.91[MEX][hapmap];0.89[TSI][hapmap];0.89[YRI][hapmap]
rs2415241	0.86[AFR][1000 genomes]
rs2415242	0.85[CHD][hapmap];0.92[GIH][hapmap];0.91[MEX][hapmap];0.84[TSI][hapmap];0.83[YRI][hapmap]
rs2899826	0.85[ASW][hapmap];0.87[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.81[LWK][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap]
rs3985310	0.87[CHD][hapmap];0.92[GIH][hapmap];0.91[MEX][hapmap];0.84[TSI][hapmap]
rs4646421	1.00[CEU][hapmap];0.91[CHB][hapmap];0.86[JPT][hapmap]
rs4886601	0.92[ASW][hapmap];0.87[CHD][hapmap];0.92[GIH][hapmap];0.86[LWK][hapmap];0.91[MEX][hapmap];0.84[TSI][hapmap];0.96[YRI][hapmap];0.92[AFR][1000 genomes];0.81[AMR][1000 genomes]
rs4887150	0.87[CHD][hapmap];0.92[GIH][hapmap];0.91[MEX][hapmap];0.84[TSI][hapmap]
rs4887154	1.00[YRI][hapmap]
rs4887156	0.84[AMR][1000 genomes]
rs4887158	0.84[AMR][1000 genomes]
rs4887159	0.87[CHD][hapmap];0.92[GIH][hapmap];0.91[MEX][hapmap];0.84[TSI][hapmap];0.83[YRI][hapmap]
rs4887162	0.92[AFR][1000 genomes]
rs4887163	0.92[ASW][hapmap];0.87[CHD][hapmap];0.92[GIH][hapmap];0.89[LWK][hapmap];0.91[MEX][hapmap];0.84[TSI][hapmap];1.00[YRI][hapmap];0.92[AFR][1000 genomes]
rs56291837	0.86[AMR][1000 genomes];0.84[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs59665282	0.84[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs6495104	1.00[CEU][hapmap];0.91[CHB][hapmap];0.86[CHD][hapmap];0.97[GIH][hapmap];0.86[JPT][hapmap];0.95[MEX][hapmap];1.00[TSI][hapmap]
rs6495105	1.00[YRI][hapmap]
rs6495112	1.00[CEU][hapmap];0.90[CHB][hapmap];0.84[CHD][hapmap];1.00[GIH][hapmap];0.81[JPT][hapmap];0.95[MEX][hapmap];1.00[TSI][hapmap];0.84[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs6495115	0.88[AFR][1000 genomes]
rs6495116	0.87[CHD][hapmap];0.92[GIH][hapmap];0.91[MEX][hapmap];0.84[TSI][hapmap]
rs6495117	0.87[CHD][hapmap];0.92[GIH][hapmap];0.91[MEX][hapmap];0.84[TSI][hapmap]
rs6495118	0.87[CHD][hapmap];0.92[GIH][hapmap];0.86[MEX][hapmap];0.84[TSI][hapmap]
rs6495119	1.00[CEU][hapmap];0.91[CHB][hapmap];0.84[CHD][hapmap];0.94[GIH][hapmap];0.90[JPT][hapmap];0.86[MEX][hapmap];1.00[TSI][hapmap];0.89[AMR][1000 genomes];0.90[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs6495121	0.82[GIH][hapmap]
rs7161903	0.84[CHD][hapmap];0.82[GIH][hapmap]
rs7161990	0.85[ASW][hapmap];0.87[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.95[JPT][hapmap];0.89[LWK][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.85[YRI][hapmap]
rs7163775	0.85[ASW][hapmap];0.87[CHD][hapmap];0.92[GIH][hapmap];0.84[LWK][hapmap];0.91[MEX][hapmap];0.84[TSI][hapmap];0.83[YRI][hapmap]
rs7166701	0.92[ASW][hapmap];0.84[CHD][hapmap];0.92[GIH][hapmap];0.84[LWK][hapmap];0.91[MEX][hapmap];0.84[TSI][hapmap];0.89[YRI][hapmap]
rs7170734	0.81[AMR][1000 genomes];0.81[ASN][1000 genomes]
rs7171838	0.92[ASW][hapmap];0.86[CHD][hapmap];0.92[GIH][hapmap];0.84[LWK][hapmap];0.91[MEX][hapmap];0.84[TSI][hapmap];1.00[YRI][hapmap];0.85[AFR][1000 genomes]
rs7175512	1.00[CEU][hapmap];0.91[CHB][hapmap];0.81[JPT][hapmap];0.84[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs7176095	0.96[AFR][1000 genomes];0.82[AMR][1000 genomes]
rs7177407	0.89[AFR][1000 genomes]
rs7178568	0.86[CHD][hapmap];0.87[GIH][hapmap];0.83[MEX][hapmap]
rs7497036	1.00[CEU][hapmap];0.91[CHB][hapmap];0.86[CHD][hapmap];1.00[GIH][hapmap];0.86[JPT][hapmap];0.95[MEX][hapmap];1.00[TSI][hapmap];0.88[AMR][1000 genomes];0.90[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs7497342	0.84[CHD][hapmap];0.82[GIH][hapmap]
rs7497906	0.86[AMR][1000 genomes];0.84[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs750608	0.87[CEU][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];0.92[GIH][hapmap];0.81[JPT][hapmap];0.91[LWK][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap]
rs8023786	1.00[CEU][hapmap];0.91[CHB][hapmap];0.86[JPT][hapmap];0.84[AMR][1000 genomes]
rs8026923	1.00[YRI][hapmap];0.87[AFR][1000 genomes]
rs8027066	0.82[YRI][hapmap]
rs8028163	0.82[AFR][1000 genomes]
rs8028430	0.87[CHD][hapmap];0.92[GIH][hapmap];0.91[MEX][hapmap];0.84[TSI][hapmap];0.83[YRI][hapmap]
rs8028893	0.84[AMR][1000 genomes]
rs8029116	0.92[ASW][hapmap];0.86[CHD][hapmap];0.92[GIH][hapmap];0.91[LWK][hapmap];0.91[MEX][hapmap];0.84[TSI][hapmap];1.00[YRI][hapmap];0.82[AFR][1000 genomes]
rs8029215	0.87[CHD][hapmap];0.92[GIH][hapmap];0.91[MEX][hapmap];0.84[TSI][hapmap];0.82[YRI][hapmap]
rs8037714	0.83[AFR][1000 genomes]
rs8040120	0.87[CEU][hapmap];0.91[CHB][hapmap];0.86[CHD][hapmap];1.00[GIH][hapmap];0.91[MEX][hapmap]
rs8040674	0.90[AMR][1000 genomes];0.80[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs8041030	0.82[AFR][1000 genomes]
rs8041807	0.84[AFR][1000 genomes]
rs8043082	0.85[AFR][1000 genomes]
rs950323	0.84[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs9635320	0.92[ASW][hapmap];0.87[CHD][hapmap];0.92[GIH][hapmap];0.86[LWK][hapmap];0.91[MEX][hapmap];0.84[TSI][hapmap];0.96[YRI][hapmap];0.91[AFR][1000 genomes];0.82[AMR][1000 genomes]
rs9672559	0.86[GIH][hapmap];0.84[TSI][hapmap]
rs9788672	0.89[AMR][1000 genomes];0.90[EUR][1000 genomes];0.87[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:32 , 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	chr15:74891400-74903400	Weak transcription	HMEC	breast
3	chr15:74891600-74907200	Weak transcription	Placenta Amnion	Placenta Amnion
4	chr15:74892000-74902400	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
5	chr15:74892200-74902600	Weak transcription	Right Atrium	heart
6	chr15:74892200-74906000	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
7	chr15:74892200-74906600	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
8	chr15:74892400-74898800	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
9	chr15:74892400-74902600	Weak transcription	Ovary	ovary
10	chr15:74892400-74906000	Weak transcription	Breast Myoepithelial Primary Cells	Breast
11	chr15:74892400-74906400	Weak transcription	Brain Inferior Temporal Lobe	brain
12	chr15:74892400-74906600	Weak transcription	Primary T cells from cord blood	blood
13	chr15:74892400-74906600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
14	chr15:74892600-74902600	Weak transcription	Spleen	Spleen
15	chr15:74892600-74902800	Weak transcription	Lung	lung
16	chr15:74893000-74906600	Weak transcription	Fetal Brain Female	brain
17	chr15:74893200-74906200	Weak transcription	Primary T cells fromperipheralblood	blood
18	chr15:74893400-74902400	Weak transcription	Left Ventricle	heart
19	chr15:74893800-74902600	Weak transcription	Pancreas	Pancrea
20	chr15:74894400-74906200	Weak transcription	Skeletal Muscle Male	skeletal muscle
21	chr15:74895000-74901200	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
22	chr15:74895200-74901000	Weak transcription	Fetal Intestine Small	intestine
23	chr15:74895200-74906400	Weak transcription	Stomach Smooth Muscle	stomach
24	chr15:74895600-74902600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
25	chr15:74897000-74900200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
26	chr15:74897200-74902400	Weak transcription	Primary hematopoietic stem cells short term culture	blood
27	chr15:74897600-74902000	Weak transcription	Brain Germinal Matrix	brain
28	chr15:74898000-74898600	Bivalent/Poised TSS	Foreskin Fibroblast Primary Cells skin02	Skin
29	chr15:74898000-74901400	Weak transcription	Right Ventricle	heart
30	chr15:74898200-74898800	Bivalent Enhancer	Foreskin Fibroblast Primary Cells skin01	Skin
31	chr15:74898200-74902200	Weak transcription	Brain Hippocampus Middle	brain
32	chr15:74898400-74898600	Bivalent Enhancer	Fetal Muscle Trunk	muscle

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