Variant report

Variant	rs6439624
Chromosome Location	chr3:135787586-135787587
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

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

rSNPs within LD-proxies of this variant (count:81)

rs_ID	r²[population]
rs12630389	0.92[ASN][1000 genomes]
rs12632791	0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12633805	1.00[CEU][hapmap];0.92[CHB][hapmap];1.00[JPT][hapmap];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12637541	0.88[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs13059064	0.88[ASN][1000 genomes]
rs13065499	1.00[CHB][hapmap];0.94[JPT][hapmap];0.87[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13069408	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13072433	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13072690	0.94[CHB][hapmap];0.88[JPT][hapmap];0.88[ASN][1000 genomes]
rs13072782	0.94[CHB][hapmap];0.88[JPT][hapmap];0.88[ASN][1000 genomes]
rs13075579	0.98[ASN][1000 genomes]
rs13078865	0.88[CHB][hapmap];0.88[JPT][hapmap];0.87[ASN][1000 genomes]
rs13084404	1.00[CHB][hapmap];0.88[JPT][hapmap];0.83[ASN][1000 genomes]
rs13092707	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs13097172	0.94[CHB][hapmap];0.87[JPT][hapmap];0.83[ASN][1000 genomes]
rs13097176	0.83[ASN][1000 genomes]
rs13097267	0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13100235	0.84[ASN][1000 genomes]
rs1523593	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1523598	0.83[ASN][1000 genomes]
rs1523599	0.94[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1523600	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[YRI][hapmap];0.95[AFR][1000 genomes];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs16843560	0.87[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs16843611	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[YRI][hapmap];0.85[AFR][1000 genomes];0.85[AMR][1000 genomes];0.93[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2140450	0.94[CHB][hapmap];0.87[JPT][hapmap];0.88[ASN][1000 genomes]
rs2177407	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2400649	0.88[ASN][1000 genomes]
rs34447526	0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34683314	0.87[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs34706807	0.89[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs35097316	0.88[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs35209948	0.93[AMR][1000 genomes];0.92[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs35264626	0.88[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs35532770	0.94[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs35946332	0.88[ASN][1000 genomes]
rs35961065	0.92[ASN][1000 genomes]
rs3946444	0.94[CHB][hapmap];0.88[JPT][hapmap];0.88[ASN][1000 genomes]
rs4075999	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4331626	0.88[ASN][1000 genomes]
rs4678224	0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4678288	0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4678432	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[YRI][hapmap];0.87[AMR][1000 genomes];0.93[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4678434	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[YRI][hapmap];0.81[AFR][1000 genomes];0.87[AMR][1000 genomes];0.94[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4678435	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[AMR][1000 genomes];0.94[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs55873361	0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs56152207	0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs57594457	0.81[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs60070757	0.81[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61791712	0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61791714	0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6439603	0.87[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6439605	0.93[CHB][hapmap];0.87[JPT][hapmap];0.87[ASN][1000 genomes]
rs6439609	0.82[AMR][1000 genomes];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6439610	0.94[CHB][hapmap];0.88[JPT][hapmap];0.88[ASN][1000 genomes]
rs6439614	0.87[ASN][1000 genomes]
rs6439615	0.88[ASN][1000 genomes]
rs6439618	0.88[ASN][1000 genomes]
rs6439622	0.94[CHB][hapmap];1.00[JPT][hapmap];0.98[ASN][1000 genomes]
rs6439623	0.94[CHB][hapmap];1.00[JPT][hapmap];0.98[ASN][1000 genomes]
rs6770366	0.85[ASN][1000 genomes]
rs6771950	0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6775261	0.88[ASN][1000 genomes]
rs6779903	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[AMR][1000 genomes];0.93[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6793273	0.88[ASN][1000 genomes]
rs6803786	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7433592	0.84[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7610302	0.88[ASN][1000 genomes]
rs7625177	0.94[CHB][hapmap];0.87[JPT][hapmap];0.88[ASN][1000 genomes]
rs7625607	0.90[ASN][1000 genomes]
rs7635621	0.88[ASN][1000 genomes]
rs7650079	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.95[AFR][1000 genomes];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9289501	0.85[ASN][1000 genomes]
rs940229	0.93[CHB][hapmap];0.88[JPT][hapmap];0.88[ASN][1000 genomes]
rs9682712	0.93[CHB][hapmap];0.88[JPT][hapmap];0.88[ASN][1000 genomes]
rs9758578	0.97[ASN][1000 genomes]
rs9846554	0.93[CHB][hapmap];0.87[JPT][hapmap];0.87[ASN][1000 genomes]
rs9852009	0.94[CHB][hapmap];0.87[JPT][hapmap];0.88[ASN][1000 genomes]
rs9852169	0.94[CHB][hapmap];0.87[JPT][hapmap];0.88[ASN][1000 genomes]
rs9856799	0.94[CHB][hapmap];0.86[JPT][hapmap];0.88[ASN][1000 genomes]
rs9866235	0.94[CHB][hapmap];0.87[JPT][hapmap]
rs9868239	0.94[CHB][hapmap];0.87[JPT][hapmap];0.88[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv869409	chr3:135649101-136164174	Strong transcription Genic enhancers Enhancers Active TSS Weak transcription ZNF genes & repeats Flanking Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	50 gene(s)	inside rSNPs	diseases
2	nsv4023	chr3:135772198-135816635	ZNF genes & repeats Weak transcription Strong transcription Enhancers Genic enhancers Flanking Active TSS Transcr. at gene 5' and 3' Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:64 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:135746200-135790000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
2	chr3:135755200-135801400	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
3	chr3:135761000-135802400	Weak transcription	iPS-18 Cell Line	embryonic stem cell
4	chr3:135764400-135790400	Weak transcription	Brain Cingulate Gyrus	brain
5	chr3:135764800-135790400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
6	chr3:135765000-135801800	Weak transcription	Esophagus	oesophagus
7	chr3:135768800-135800800	Weak transcription	HUES64 Cell Line	embryonic stem cell
8	chr3:135769800-135789400	Weak transcription	Colon Smooth Muscle	Colon
9	chr3:135769800-135789800	Weak transcription	Psoas Muscle	Psoas
10	chr3:135769800-135790000	Weak transcription	Aorta	Aorta
11	chr3:135769800-135790400	Weak transcription	Primary hematopoietic stem cells	blood
12	chr3:135770000-135789800	Weak transcription	Duodenum Smooth Muscle	Duodenum
13	chr3:135770000-135800800	Weak transcription	Fetal Intestine Large	intestine
14	chr3:135770400-135789800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
15	chr3:135771200-135802000	Weak transcription	Brain Germinal Matrix	brain
16	chr3:135771200-135809600	Weak transcription	Gastric	stomach
17	chr3:135771400-135789000	Weak transcription	HSMMtube	muscle
18	chr3:135772600-135789600	Weak transcription	Rectal Mucosa Donor 29	rectum
19	chr3:135772600-135789800	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
20	chr3:135772600-135789800	Weak transcription	Ovary	ovary
21	chr3:135774400-135802000	Weak transcription	Sigmoid Colon	Sigmoid Colon
22	chr3:135774600-135788800	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
23	chr3:135774800-135789000	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
24	chr3:135774800-135789800	Weak transcription	Left Ventricle	heart
25	chr3:135775000-135787600	Weak transcription	Rectal Smooth Muscle	rectum
26	chr3:135775000-135788800	Weak transcription	NHEK	skin
27	chr3:135775000-135789200	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
28	chr3:135775000-135789200	Weak transcription	Fetal Muscle Trunk	muscle
29	chr3:135775000-135789400	Weak transcription	Stomach Smooth Muscle	stomach
30	chr3:135775000-135789800	Weak transcription	Adipose Nuclei	Adipose
31	chr3:135775000-135809600	Weak transcription	Fetal Brain Male	brain
32	chr3:135775000-135809600	Weak transcription	Rectal Mucosa Donor 31	rectum
33	chr3:135775200-135788800	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
34	chr3:135775600-135788800	Weak transcription	Fetal Heart	heart
35	chr3:135780600-135789800	Weak transcription	Fetal Stomach	stomach
36	chr3:135781400-135788800	Weak transcription	Skeletal Muscle Female	skeletal muscle
37	chr3:135781400-135789800	Weak transcription	HUES6 Cell Line	embryonic stem cell
38	chr3:135781400-135790400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
39	chr3:135781400-135801600	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
40	chr3:135781400-135802000	Weak transcription	Fetal Intestine Small	intestine
41	chr3:135781400-135803000	Weak transcription	Right Ventricle	heart
42	chr3:135781800-135789200	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
43	chr3:135784200-135805600	Weak transcription	Stomach Mucosa	stomach
44	chr3:135785000-135798400	Weak transcription	HUES48 Cell Line	embryonic stem cell
45	chr3:135785200-135789800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
46	chr3:135785600-135787600	Weak transcription	Skeletal Muscle Male	skeletal muscle
47	chr3:135785600-135792200	Weak transcription	Fetal Lung	lung
48	chr3:135785600-135799000	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
49	chr3:135785600-135801800	Weak transcription	Pancreas	Pancrea
50	chr3:135785800-135789200	Weak transcription	Fetal Muscle Leg	muscle

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