Variant report

Variant	rs10024002
Chromosome Location	chr4:20711031-20711032
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr4:20705332..20707768-chr4:20710083..20712545,3	K562	blood:
2	chr4:20700439..20703043-chr4:20709421..20711457,2	MCF-7	breast:
3	chr4:20702272..20703966-chr4:20709575..20711144,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000163138	Chromatin interaction

Extended variants
information (count: 83 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:77)

rs_ID	r²[population]
rs10011908	0.87[AMR][1000 genomes]
rs10017693	0.90[CEU][hapmap];1.00[CHB][hapmap];0.84[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10018931	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs10022322	0.94[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.88[JPT][hapmap];0.98[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];0.98[TSI][hapmap];0.96[YRI][hapmap];0.99[AFR][1000 genomes];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10025286	0.96[AFR][1000 genomes];0.99[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10034054	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs10084802	0.94[ASW][hapmap];0.91[GIH][hapmap];0.98[LWK][hapmap];0.98[MKK][hapmap];0.86[TSI][hapmap];0.96[YRI][hapmap];0.90[AFR][1000 genomes]
rs10805219	0.85[AFR][1000 genomes];0.85[EUR][1000 genomes]
rs10938801	0.83[ASW][hapmap];0.84[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.82[MEX][hapmap];0.81[MKK][hapmap];0.84[AFR][1000 genomes];0.89[ASN][1000 genomes]
rs11941041	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11944886	0.99[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs12152652	0.82[AFR][1000 genomes];0.86[EUR][1000 genomes]
rs12331966	1.00[CEU][hapmap];0.81[CHB][hapmap];0.88[JPT][hapmap];0.96[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs12640448	1.00[CHB][hapmap];0.95[CHD][hapmap];0.88[JPT][hapmap]
rs12641186	1.00[CHB][hapmap];0.89[ASN][1000 genomes]
rs12644782	0.95[CEU][hapmap];0.88[JPT][hapmap];0.96[YRI][hapmap];0.94[AFR][1000 genomes];0.84[AMR][1000 genomes];0.93[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs12650007	0.90[AFR][1000 genomes];0.82[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs16869851	0.89[ASN][1000 genomes]
rs16869886	0.96[AFR][1000 genomes];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs16869889	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17622371	1.00[CHB][hapmap]
rs1985322	0.94[ASW][hapmap];0.90[CEU][hapmap];0.86[CHD][hapmap];1.00[JPT][hapmap];0.98[LWK][hapmap];1.00[MKK][hapmap];0.98[TSI][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2052775	1.00[CEU][hapmap];1.00[CHB][hapmap];0.88[JPT][hapmap];0.96[YRI][hapmap];0.99[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2114472	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2114473	0.98[AFR][1000 genomes];0.89[AMR][1000 genomes];0.93[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2288308	0.94[ASW][hapmap];0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.98[LWK][hapmap];0.88[MEX][hapmap];1.00[MKK][hapmap];0.98[TSI][hapmap];1.00[YRI][hapmap];0.99[AFR][1000 genomes];0.92[AMR][1000 genomes];0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2322688	1.00[ASW][hapmap];0.91[CEU][hapmap];0.86[CHD][hapmap];0.80[GIH][hapmap];0.88[JPT][hapmap];0.98[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];0.93[TSI][hapmap];0.96[YRI][hapmap];0.90[AFR][1000 genomes];0.83[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs28524474	1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28637181	0.90[AFR][1000 genomes];0.83[AMR][1000 genomes];0.91[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs28714128	0.85[AFR][1000 genomes];0.81[AMR][1000 genomes];0.82[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs28788006	0.97[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3764964	1.00[ASW][hapmap];1.00[CEU][hapmap];0.81[CHB][hapmap];0.95[CHD][hapmap];0.80[GIH][hapmap];0.88[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];0.96[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs3764965	0.81[CHB][hapmap];0.86[JPT][hapmap];0.85[YRI][hapmap];0.87[ASN][1000 genomes]
rs3764966	1.00[CEU][hapmap];0.81[CHB][hapmap];0.88[JPT][hapmap];0.96[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs3764967	0.90[CHB][hapmap];0.91[CHD][hapmap];0.88[JPT][hapmap];1.00[ASN][1000 genomes]
rs3796639	1.00[ASN][1000 genomes]
rs3815872	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4414951	0.84[AFR][1000 genomes];0.86[EUR][1000 genomes]
rs4431223	0.89[AFR][1000 genomes];0.84[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs4510461	0.99[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4640668	0.90[AFR][1000 genomes]
rs55794413	0.89[ASN][1000 genomes]
rs55874299	0.89[ASN][1000 genomes]
rs56152829	0.89[ASN][1000 genomes]
rs57740160	0.84[AFR][1000 genomes];0.81[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs59335491	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62410092	0.80[ASN][1000 genomes]
rs62410099	0.89[ASN][1000 genomes]
rs62410126	1.00[ASN][1000 genomes]
rs62410129	0.95[ASN][1000 genomes]
rs62410159	0.94[AFR][1000 genomes];0.84[AMR][1000 genomes];0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs62411662	0.92[ASN][1000 genomes]
rs6447974	0.99[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6447975	0.95[CEU][hapmap];0.96[YRI][hapmap];0.94[AFR][1000 genomes];0.83[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs6447976	0.95[CEU][hapmap];0.81[CHB][hapmap];0.86[JPT][hapmap];0.96[YRI][hapmap];0.95[AFR][1000 genomes];0.87[AMR][1000 genomes];0.93[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs6447978	0.94[ASW][hapmap];0.95[CEU][hapmap];1.00[GIH][hapmap];0.98[LWK][hapmap];0.94[MEX][hapmap];1.00[MKK][hapmap];0.95[TSI][hapmap];0.96[YRI][hapmap];0.84[AFR][1000 genomes];0.80[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs6447982	0.84[CEU][hapmap];0.86[YRI][hapmap];0.84[AFR][1000 genomes];0.82[EUR][1000 genomes]
rs6811030	0.94[ASW][hapmap];0.95[CEU][hapmap];0.81[CHB][hapmap];0.95[CHD][hapmap];0.80[GIH][hapmap];0.88[JPT][hapmap];0.98[LWK][hapmap];0.94[MEX][hapmap];1.00[MKK][hapmap];0.95[TSI][hapmap];0.96[YRI][hapmap];0.99[AFR][1000 genomes];0.92[AMR][1000 genomes];0.93[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs6811505	0.95[CEU][hapmap];0.90[CHB][hapmap];0.86[JPT][hapmap];0.87[YRI][hapmap];0.94[AFR][1000 genomes];0.86[AMR][1000 genomes];0.93[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs6815738	0.87[ASN][1000 genomes]
rs6817475	0.83[CEU][hapmap];0.83[AFR][1000 genomes];0.82[ASN][1000 genomes]
rs6831295	0.82[CEU][hapmap];0.86[AFR][1000 genomes];0.83[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs6831516	0.95[CEU][hapmap];0.85[CHB][hapmap];0.95[LWK][hapmap];0.88[MEX][hapmap];0.96[YRI][hapmap];0.94[AFR][1000 genomes];0.83[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs73240292	1.00[ASN][1000 genomes]
rs7438098	0.91[AFR][1000 genomes];0.99[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs755155	0.80[ASN][1000 genomes]
rs7655154	0.94[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.88[JPT][hapmap];0.95[LWK][hapmap];1.00[MEX][hapmap];0.98[MKK][hapmap];0.98[TSI][hapmap];0.89[YRI][hapmap];0.99[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7660006	0.90[AFR][1000 genomes];0.80[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs7666288	0.84[YRI][hapmap];1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7673805	0.99[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs7674453	1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7681691	1.00[CEU][hapmap];1.00[CHB][hapmap];0.86[JPT][hapmap];0.96[YRI][hapmap];1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs7685481	0.90[AFR][1000 genomes];0.80[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs7696618	0.99[AFR][1000 genomes];0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs990206	0.84[CEU][hapmap];0.81[CHB][hapmap];0.88[JPT][hapmap];0.86[YRI][hapmap];0.84[AFR][1000 genomes];0.82[AMR][1000 genomes];0.82[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs9995438	0.85[AFR][1000 genomes]
rs9995697	1.00[CEU][hapmap];1.00[CHB][hapmap];0.88[JPT][hapmap];0.96[YRI][hapmap]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1013077	chr4:20599841-20732558	Weak transcription ZNF genes & repeats Flanking Active TSS Active TSS Strong transcription Enhancers Bivalent/Poised TSS Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
2	nsv1010145	chr4:20601908-21057992	ZNF genes & repeats Enhancers Weak transcription Active TSS Strong transcription Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	6 gene(s)	inside rSNPs	diseases
3	nsv537052	chr4:20601908-21057992	Enhancers Weak transcription Active TSS Flanking Active TSS Strong transcription ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	6 gene(s)	inside rSNPs	diseases
4	nsv1014941	chr4:20611726-21345226	Weak transcription Enhancers ZNF genes & repeats Flanking Active TSS Active TSS Bivalent/Poised TSS Genic enhancers Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	7 gene(s)	inside rSNPs	diseases
5	nsv537053	chr4:20611726-21345226	ZNF genes & repeats Weak transcription Enhancers Flanking Active TSS Active TSS Strong transcription Bivalent/Poised TSS Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	7 gene(s)	inside rSNPs	diseases
6	nsv829876	chr4:20638736-20835621	Weak transcription Enhancers Strong transcription ZNF genes & repeats Active TSS Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	3 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:123 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:20702400-20722600	Weak transcription	Spleen	Spleen
2	chr4:20702600-20717200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
3	chr4:20703000-20717200	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
4	chr4:20703000-20717400	Weak transcription	Fetal Heart	heart
5	chr4:20703000-20721800	Weak transcription	Rectal Smooth Muscle	rectum
6	chr4:20703000-20722800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
7	chr4:20703000-20741400	Weak transcription	Stomach Mucosa	stomach
8	chr4:20703200-20714400	Weak transcription	Placenta Amnion	Placenta Amnion
9	chr4:20703200-20715000	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
10	chr4:20703200-20722800	Weak transcription	Pancreatic Islets	Pancreatic Islet
11	chr4:20703200-20741000	Weak transcription	Primary T killer memory cells from peripheral blood	blood
12	chr4:20703400-20722800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
13	chr4:20703400-20722800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
14	chr4:20703400-20723600	Weak transcription	Pancreas	Pancrea
15	chr4:20703400-20724000	Weak transcription	A549	lung
16	chr4:20703600-20715000	Weak transcription	Ovary	ovary
17	chr4:20703600-20716200	Weak transcription	Hela-S3	cervix
18	chr4:20703600-20717200	Weak transcription	Brain Germinal Matrix	brain
19	chr4:20703800-20714800	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
20	chr4:20705000-20718200	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
21	chr4:20705400-20718200	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
22	chr4:20705600-20715400	Strong transcription	HUES64 Cell Line	embryonic stem cell
23	chr4:20706000-20711200	Strong transcription	Primary T cells from cord blood	blood
24	chr4:20706000-20711200	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
25	chr4:20706000-20711200	Strong transcription	Skeletal Muscle Female	skeletal muscle
26	chr4:20706000-20712000	Strong transcription	HUES48 Cell Line	embryonic stem cell
27	chr4:20706000-20712200	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
28	chr4:20706000-20715200	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
29	chr4:20706000-20715400	Strong transcription	iPS-20b Cell Line	embryonic stem cell
30	chr4:20706000-20717400	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
31	chr4:20706200-20711200	Strong transcription	Stomach Smooth Muscle	stomach
32	chr4:20706200-20711400	Strong transcription	Adipose Nuclei	Adipose
33	chr4:20706200-20711600	Strong transcription	Primary T helper cells fromperipheralblood	blood
34	chr4:20706200-20711600	Strong transcription	Liver	Liver
35	chr4:20706200-20711600	Strong transcription	Duodenum Mucosa	Duodenum
36	chr4:20706200-20711800	Strong transcription	Placenta	Placenta
37	chr4:20706200-20712000	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
38	chr4:20706200-20712000	Strong transcription	Duodenum Smooth Muscle	Duodenum
39	chr4:20706200-20712400	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
40	chr4:20706200-20712800	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
41	chr4:20706200-20713400	Strong transcription	Fetal Lung	lung
42	chr4:20706200-20714000	Strong transcription	Breast Myoepithelial Primary Cells	Breast
43	chr4:20706200-20715200	Strong transcription	Primary T helper cells PMA-I stimulated	--
44	chr4:20706200-20715400	Strong transcription	Monocytes-CD14+_RO01746	blood
45	chr4:20706200-20715600	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
46	chr4:20706200-20715600	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
47	chr4:20706400-20712000	Strong transcription	Primary monocytes fromperipheralblood	blood
48	chr4:20706400-20713400	Strong transcription	HUES6 Cell Line	embryonic stem cell
49	chr4:20706600-20722600	Weak transcription	Gastric	stomach
50	chr4:20706800-20738600	Weak transcription	Psoas Muscle	Psoas

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