Variant report

Variant	rs6533239
Chromosome Location	chr4:78661686-78661687
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr4:78660857..78662460-chr4:78663917..78665509,2	K562	blood:

Extended variants
information (count: 137 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:134)

rs_ID	r²[population]
rs10005741	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.98[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10007837	1.00[CHB][hapmap];1.00[JPT][hapmap];0.98[ASN][1000 genomes]
rs1010728	0.92[CHB][hapmap];0.88[CHD][hapmap]
rs10222901	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.93[ASN][1000 genomes]
rs1039403	1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[ASN][1000 genomes]
rs1039467	0.87[CEU][hapmap];0.92[CHB][hapmap];0.88[CHD][hapmap];1.00[MEX][hapmap];0.90[TSI][hapmap];0.88[AMR][1000 genomes]
rs10428319	0.92[CHB][hapmap]
rs10856982	0.93[ASN][1000 genomes]
rs11097935	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[YRI][hapmap];0.91[AFR][1000 genomes];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs11097965	0.85[CHB][hapmap];0.88[CHD][hapmap]
rs1156059	0.88[ASN][1000 genomes]
rs11721383	0.87[CEU][hapmap];0.92[CHB][hapmap];0.85[AMR][1000 genomes]
rs11723029	0.90[AFR][1000 genomes];0.86[AMR][1000 genomes]
rs11723221	0.87[CEU][hapmap];1.00[CHB][hapmap];0.83[YRI][hapmap];0.88[AMR][1000 genomes]
rs11727993	0.93[AFR][1000 genomes];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs11729703	0.85[AMR][1000 genomes]
rs11730329	0.91[AMR][1000 genomes]
rs11730403	0.81[AFR][1000 genomes];0.91[AMR][1000 genomes]
rs11731374	1.00[CHB][hapmap]
rs11732039	0.87[CEU][hapmap];0.92[CHB][hapmap];0.88[AMR][1000 genomes]
rs11733759	1.00[ASW][hapmap];0.87[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.93[GIH][hapmap];0.82[LWK][hapmap];1.00[MEX][hapmap];0.88[MKK][hapmap];1.00[TSI][hapmap];0.89[YRI][hapmap];0.81[AFR][1000 genomes];0.91[AMR][1000 genomes]
rs11734428	0.88[AMR][1000 genomes]
rs11737353	1.00[CHB][hapmap];0.96[CHD][hapmap]
rs11737861	1.00[CHB][hapmap];1.00[CHD][hapmap]
rs12108312	0.92[CHB][hapmap];0.88[CHD][hapmap]
rs12510593	1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[ASN][1000 genomes]
rs12643960	0.95[ASN][1000 genomes]
rs13105201	0.92[ASN][1000 genomes]
rs13111592	1.00[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs13118459	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.98[ASN][1000 genomes]
rs13128914	0.92[ASN][1000 genomes]
rs13131896	0.84[AFR][1000 genomes];0.97[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs13137909	0.93[ASN][1000 genomes]
rs13138341	0.98[AFR][1000 genomes];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs13144225	0.89[AFR][1000 genomes];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs13144226	0.93[ASN][1000 genomes]
rs1402626	0.85[AFR][1000 genomes];0.91[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs1501373	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1521419	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.82[LWK][hapmap];1.00[MEX][hapmap];0.92[MKK][hapmap];1.00[TSI][hapmap];0.94[YRI][hapmap];0.84[AFR][1000 genomes];0.97[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs1553386	0.88[AMR][1000 genomes]
rs1554457	1.00[CEU][hapmap];1.00[CHB][hapmap];0.89[YRI][hapmap];0.84[AFR][1000 genomes];0.97[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs17002823	0.97[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs17002825	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];0.92[MKK][hapmap];1.00[TSI][hapmap];0.89[YRI][hapmap];0.83[AFR][1000 genomes];0.97[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs17002829	1.00[CEU][hapmap];1.00[CHB][hapmap];0.89[YRI][hapmap];0.83[AFR][1000 genomes];0.91[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs17002831	0.83[AFR][1000 genomes];0.91[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs1813725	0.87[AFR][1000 genomes];0.86[AMR][1000 genomes];0.96[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1814033	1.00[ASW][hapmap];1.00[CEU][hapmap];0.85[CHB][hapmap];1.00[GIH][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.98[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.88[AFR][1000 genomes];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs1847216	0.87[CEU][hapmap];0.92[CHB][hapmap];0.88[CHD][hapmap];1.00[MEX][hapmap];0.90[TSI][hapmap];0.88[AMR][1000 genomes]
rs1980266	0.84[AFR][1000 genomes];0.97[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs2008222	0.81[ASN][1000 genomes]
rs2030463	0.95[ASN][1000 genomes]
rs2062637	0.92[JPT][hapmap];0.85[ASN][1000 genomes]
rs2102116	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.98[ASN][1000 genomes]
rs2134048	0.92[CHB][hapmap];0.96[CHD][hapmap];0.93[JPT][hapmap];0.93[ASN][1000 genomes]
rs2134459	0.88[AMR][1000 genomes]
rs2173869	1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[ASN][1000 genomes]
rs2174080	0.92[CHB][hapmap]
rs2866444	0.92[AFR][1000 genomes];0.83[AMR][1000 genomes];0.90[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2866688	1.00[CHB][hapmap];1.00[CHD][hapmap]
rs2866689	1.00[CEU][hapmap];1.00[CHB][hapmap];0.93[JPT][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2866690	1.00[CHB][hapmap];0.96[CHD][hapmap];0.93[JPT][hapmap];0.92[ASN][1000 genomes]
rs28796999	0.88[AMR][1000 genomes]
rs28891692	0.88[AMR][1000 genomes]
rs2903291	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.98[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs3205281	0.92[CHB][hapmap];0.95[CHD][hapmap];1.00[JPT][hapmap];0.93[ASN][1000 genomes]
rs4078523	0.81[AFR][1000 genomes];0.91[AMR][1000 genomes]
rs4304001	1.00[CHB][hapmap];1.00[CHD][hapmap]
rs4331798	0.82[AMR][1000 genomes]
rs4365752	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];0.82[MKK][hapmap];1.00[TSI][hapmap];0.97[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs4388114	1.00[CHB][hapmap];0.96[CHD][hapmap]
rs4410552	1.00[CHB][hapmap];1.00[CHD][hapmap]
rs4417999	0.85[AMR][1000 genomes]
rs4472161	0.89[ASN][1000 genomes]
rs4473672	0.82[AMR][1000 genomes]
rs4541532	0.93[ASN][1000 genomes]
rs4561950	0.92[CHB][hapmap];0.87[CHD][hapmap]
rs4859506	0.99[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4859871	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.96[CHD][hapmap];1.00[GIH][hapmap];0.92[JPT][hapmap];0.97[LWK][hapmap];0.88[MEX][hapmap];0.86[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.99[AFR][1000 genomes];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4859872	1.00[ASN][1000 genomes]
rs4859876	0.98[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4859878	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.98[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.90[AFR][1000 genomes];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs55694923	0.91[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs55886549	0.83[AFR][1000 genomes];0.97[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs57221952	0.88[AMR][1000 genomes]
rs57246363	0.97[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs57868780	0.85[AMR][1000 genomes]
rs58054752	0.88[AMR][1000 genomes]
rs58218398	0.88[AMR][1000 genomes]
rs6533217	0.90[ASN][1000 genomes]
rs6533226	0.95[ASN][1000 genomes]
rs6533269	0.93[ASN][1000 genomes]
rs6533270	0.91[AFR][1000 genomes];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6533271	0.93[ASN][1000 genomes]
rs6533272	0.89[AFR][1000 genomes];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6533274	0.89[ASN][1000 genomes]
rs6533290	0.83[AFR][1000 genomes];0.91[AMR][1000 genomes]
rs6533358	0.84[AMR][1000 genomes]
rs6533359	0.88[AMR][1000 genomes]
rs6814830	0.82[AFR][1000 genomes];0.84[ASN][1000 genomes]
rs6817305	1.00[CHB][hapmap];1.00[CHD][hapmap]
rs6817823	0.93[ASN][1000 genomes]
rs6821826	0.92[CHB][hapmap]
rs6822317	0.82[CEU][hapmap];0.91[CHB][hapmap];0.82[JPT][hapmap];0.84[YRI][hapmap];0.84[AFR][1000 genomes];0.97[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs6823465	0.98[ASN][1000 genomes]
rs6827822	1.00[CHB][hapmap];1.00[CHD][hapmap]
rs6828302	0.88[ASN][1000 genomes]
rs6830993	0.82[AMR][1000 genomes]
rs6833179	1.00[ASN][1000 genomes]
rs6839504	1.00[CHB][hapmap];1.00[JPT][hapmap];0.99[ASN][1000 genomes]
rs6849922	0.89[ASN][1000 genomes]
rs6850049	0.92[AFR][1000 genomes];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6850111	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.98[ASN][1000 genomes]
rs6850590	0.88[AMR][1000 genomes]
rs6855336	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6857067	0.89[AFR][1000 genomes];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs73827443	0.81[AMR][1000 genomes]
rs73827456	0.82[AMR][1000 genomes]
rs73827459	0.88[AMR][1000 genomes]
rs73827460	0.88[AMR][1000 genomes]
rs7439347	0.85[CHB][hapmap];0.88[CHD][hapmap]
rs7655949	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.98[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7657658	1.00[ASW][hapmap];0.85[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.88[GIH][hapmap];0.82[LWK][hapmap];0.89[MEX][hapmap];1.00[TSI][hapmap];0.94[YRI][hapmap];0.83[AFR][1000 genomes];0.91[AMR][1000 genomes]
rs7659122	0.92[CHB][hapmap];0.88[CHD][hapmap]
rs7661064	1.00[CHB][hapmap];0.96[CHD][hapmap]
rs7663359	0.92[CHB][hapmap]
rs7669988	0.98[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7671941	0.92[CHB][hapmap];0.88[CHD][hapmap]
rs7674744	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.95[ASN][1000 genomes]
rs7687170	0.92[CHB][hapmap];0.88[CHD][hapmap]
rs7687812	1.00[CHB][hapmap];0.96[CHD][hapmap]
rs7693256	0.92[AFR][1000 genomes];0.88[AMR][1000 genomes];0.89[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs885376	0.96[AFR][1000 genomes];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs9991424	0.88[AMR][1000 genomes]
rs9993942	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.98[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv829976	chr4:78576657-78757798	Enhancers Weak transcription Strong transcription Genic enhancers ZNF genes & repeats Flanking Active TSS Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region miRNA target site	11 gene(s)	inside rSNPs	diseases
2	nsv518757	chr4:78637265-78695138	Flanking Active TSS Weak transcription Strong transcription ZNF genes & repeats Enhancers Genic enhancers Active TSS	TF binding region CpG island Chromatin interactive region miRNA target site	1 gene(s)	inside rSNPs	diseases
3	nsv879501	chr4:78647634-78866007	Active TSS Flanking Active TSS Strong transcription Weak transcription Enhancers ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	12 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:105 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:78629200-78676600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
2	chr4:78632600-78697800	Weak transcription	Colonic Mucosa	Colon
3	chr4:78637400-78673200	Weak transcription	Cortex derived primary cultured neurospheres	brain
4	chr4:78639400-78671200	Weak transcription	Brain Germinal Matrix	brain
5	chr4:78640800-78697800	Weak transcription	Stomach Mucosa	stomach
6	chr4:78641000-78665000	Weak transcription	Fetal Brain Male	brain
7	chr4:78643800-78714000	Weak transcription	Lung	lung
8	chr4:78644800-78666600	Weak transcription	Pancreatic Islets	Pancreatic Islet
9	chr4:78645000-78664000	Weak transcription	A549	lung
10	chr4:78645000-78676600	Weak transcription	Hela-S3	cervix
11	chr4:78645400-78696200	Weak transcription	Placenta Amnion	Placenta Amnion
12	chr4:78645600-78663200	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
13	chr4:78646000-78664000	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
14	chr4:78646200-78663800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
15	chr4:78646800-78677200	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
16	chr4:78650000-78663200	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
17	chr4:78650000-78682400	Weak transcription	Brain Substantia Nigra	brain
18	chr4:78650000-78683800	Weak transcription	NHDF-Ad	bronchial
19	chr4:78650200-78661800	Weak transcription	Brain Cingulate Gyrus	brain
20	chr4:78650200-78662600	Weak transcription	Right Ventricle	heart
21	chr4:78650200-78663800	Weak transcription	Fetal Brain Female	brain
22	chr4:78650200-78673000	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
23	chr4:78650200-78673000	Weak transcription	Fetal Muscle Trunk	muscle
24	chr4:78650200-78697800	Weak transcription	Gastric	stomach
25	chr4:78650200-78697800	Weak transcription	Rectal Smooth Muscle	rectum
26	chr4:78650200-78702800	Weak transcription	Stomach Smooth Muscle	stomach
27	chr4:78650200-78720000	Weak transcription	Spleen	Spleen
28	chr4:78650600-78665800	Weak transcription	Fetal Muscle Leg	muscle
29	chr4:78650800-78697800	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
30	chr4:78653200-78673200	Weak transcription	Fetal Heart	heart
31	chr4:78654200-78697600	Weak transcription	HSMMtube	muscle
32	chr4:78656600-78667800	Strong transcription	Fetal Thymus	thymus
33	chr4:78657000-78695600	Weak transcription	Small Intestine	intestine
34	chr4:78657400-78673000	Weak transcription	Fetal Intestine Small	intestine
35	chr4:78657800-78663400	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
36	chr4:78657800-78664800	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
37	chr4:78658600-78669400	Strong transcription	Primary B cells from peripheral blood	blood
38	chr4:78658800-78664400	Strong transcription	Primary monocytes fromperipheralblood	blood
39	chr4:78659000-78662600	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
40	chr4:78659000-78662600	Strong transcription	Breast Myoepithelial Primary Cells	Breast
41	chr4:78659000-78662600	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
42	chr4:78659000-78663000	Strong transcription	Primary hematopoietic stem cells short term culture	blood
43	chr4:78659000-78663200	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
44	chr4:78659000-78663200	Strong transcription	Liver	Liver
45	chr4:78659000-78663800	Strong transcription	Primary hematopoietic stem cells	blood
46	chr4:78659000-78663800	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
47	chr4:78659000-78663800	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
48	chr4:78659000-78663800	Strong transcription	Monocytes-CD14+_RO01746	blood
49	chr4:78659000-78664000	Strong transcription	Duodenum Mucosa	Duodenum
50	chr4:78659000-78676600	Weak transcription	Fetal Stomach	stomach

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