Variant report

Variant	rs6439622
Chromosome Location	chr3:135784877-135784878
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 81 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:79)

rs_ID	r²[population]
rs10048942	0.82[YRI][hapmap]
rs12630389	0.90[ASN][1000 genomes]
rs12632791	0.82[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs12633805	0.86[CHB][hapmap];1.00[JPT][hapmap];0.98[ASN][1000 genomes]
rs12637541	0.92[ASN][1000 genomes]
rs13059064	0.90[ASN][1000 genomes]
rs13065499	0.94[CHB][hapmap];0.95[JPT][hapmap];0.98[ASN][1000 genomes]
rs13069408	0.94[CHB][hapmap];1.00[JPT][hapmap];0.85[AMR][1000 genomes];0.98[ASN][1000 genomes]
rs13072433	0.94[CHB][hapmap];1.00[JPT][hapmap];0.98[ASN][1000 genomes]
rs13072690	1.00[CHB][hapmap];0.90[JPT][hapmap];0.90[ASN][1000 genomes]
rs13072782	1.00[CHB][hapmap];0.90[JPT][hapmap];0.90[ASN][1000 genomes]
rs13075579	0.96[ASN][1000 genomes]
rs13078865	0.94[CHB][hapmap];0.90[JPT][hapmap];0.88[ASN][1000 genomes]
rs13084404	0.94[CHB][hapmap];0.90[JPT][hapmap];0.85[ASN][1000 genomes]
rs13092707	0.94[CHB][hapmap];1.00[JPT][hapmap];0.86[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs13097172	1.00[CHB][hapmap];0.90[JPT][hapmap];0.85[ASN][1000 genomes]
rs13097176	0.85[ASN][1000 genomes]
rs13097267	0.98[ASN][1000 genomes]
rs13100235	0.85[ASN][1000 genomes]
rs1523593	0.94[CHB][hapmap];1.00[JPT][hapmap];0.80[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs1523598	0.85[ASN][1000 genomes]
rs1523599	0.94[CHB][hapmap];1.00[JPT][hapmap];0.92[ASN][1000 genomes]
rs1523600	0.94[CHB][hapmap];1.00[JPT][hapmap];0.98[ASN][1000 genomes]
rs16843560	0.91[ASN][1000 genomes]
rs16843611	0.94[CHB][hapmap];1.00[JPT][hapmap];0.97[ASN][1000 genomes]
rs2140450	1.00[CHB][hapmap];0.90[JPT][hapmap];0.90[ASN][1000 genomes]
rs2177407	0.94[CHB][hapmap];1.00[JPT][hapmap];0.98[ASN][1000 genomes]
rs2400649	0.90[ASN][1000 genomes]
rs34447526	0.84[AMR][1000 genomes];0.98[ASN][1000 genomes]
rs35097316	0.92[ASN][1000 genomes]
rs35209948	0.89[ASN][1000 genomes]
rs35532770	0.97[ASN][1000 genomes]
rs35946332	0.90[ASN][1000 genomes]
rs35961065	0.90[AFR][1000 genomes];0.98[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs3946444	1.00[CHB][hapmap];0.90[JPT][hapmap];0.90[ASN][1000 genomes]
rs4075999	0.94[CHB][hapmap];1.00[JPT][hapmap];0.98[ASN][1000 genomes]
rs4331626	0.89[ASN][1000 genomes]
rs4678224	0.95[ASN][1000 genomes]
rs4678288	0.84[AMR][1000 genomes];0.98[ASN][1000 genomes]
rs4678432	0.94[CHB][hapmap];1.00[JPT][hapmap];0.96[ASN][1000 genomes]
rs4678434	0.94[CHB][hapmap];1.00[JPT][hapmap];0.97[ASN][1000 genomes]
rs4678435	0.94[CHB][hapmap];1.00[JPT][hapmap];0.97[ASN][1000 genomes]
rs55873361	0.98[ASN][1000 genomes]
rs56152207	0.85[AMR][1000 genomes];0.98[ASN][1000 genomes]
rs57594457	0.98[ASN][1000 genomes]
rs60070757	0.98[ASN][1000 genomes]
rs61791712	0.81[AMR][1000 genomes];0.98[ASN][1000 genomes]
rs61791714	0.84[AMR][1000 genomes];0.98[ASN][1000 genomes]
rs6439603	0.91[ASN][1000 genomes]
rs6439605	1.00[CHB][hapmap];0.90[JPT][hapmap];0.88[ASN][1000 genomes]
rs6439609	0.92[ASN][1000 genomes]
rs6439610	1.00[CHB][hapmap];0.90[JPT][hapmap];0.89[ASN][1000 genomes]
rs6439614	0.89[ASN][1000 genomes]
rs6439615	0.90[ASN][1000 genomes]
rs6439618	0.90[ASN][1000 genomes]
rs6439623	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6439624	0.94[CHB][hapmap];1.00[JPT][hapmap];0.98[ASN][1000 genomes]
rs6770366	0.86[ASN][1000 genomes]
rs6771950	0.85[AMR][1000 genomes];0.98[ASN][1000 genomes]
rs6775261	0.90[ASN][1000 genomes]
rs6779903	0.94[CHB][hapmap];1.00[JPT][hapmap];0.97[ASN][1000 genomes]
rs6793273	0.90[ASN][1000 genomes]
rs6803786	0.94[CHB][hapmap];1.00[JPT][hapmap];0.85[AMR][1000 genomes];0.98[ASN][1000 genomes]
rs7433592	0.98[ASN][1000 genomes]
rs7610302	0.90[ASN][1000 genomes]
rs7625177	1.00[CHB][hapmap];0.90[JPT][hapmap];0.90[ASN][1000 genomes]
rs7625607	0.92[ASN][1000 genomes]
rs7635621	0.90[ASN][1000 genomes]
rs7650079	0.88[CHB][hapmap];1.00[JPT][hapmap];0.94[ASN][1000 genomes]
rs9289501	0.84[ASN][1000 genomes]
rs940229	1.00[CHB][hapmap];0.90[JPT][hapmap];0.90[ASN][1000 genomes]
rs9682712	1.00[CHB][hapmap];0.90[JPT][hapmap];0.90[ASN][1000 genomes]
rs9758578	0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9846554	1.00[CHB][hapmap];0.89[JPT][hapmap];0.88[ASN][1000 genomes]
rs9852009	1.00[CHB][hapmap];0.90[JPT][hapmap];0.90[ASN][1000 genomes]
rs9852169	1.00[CHB][hapmap];0.90[JPT][hapmap];0.90[ASN][1000 genomes]
rs9856799	1.00[CHB][hapmap];0.89[JPT][hapmap];0.90[ASN][1000 genomes]
rs9866235	1.00[CHB][hapmap];0.90[JPT][hapmap]
rs9868239	1.00[CHB][hapmap];0.90[JPT][hapmap];0.90[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:60 , 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	chr3:135763000-135785600	Weak transcription	Brain Anterior Caudate	brain
5	chr3:135764400-135790400	Weak transcription	Brain Cingulate Gyrus	brain
6	chr3:135764800-135790400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
7	chr3:135765000-135786000	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
8	chr3:135765000-135801800	Weak transcription	Esophagus	oesophagus
9	chr3:135765600-135785400	Weak transcription	Pancreas	Pancrea
10	chr3:135768800-135800800	Weak transcription	HUES64 Cell Line	embryonic stem cell
11	chr3:135769800-135789400	Weak transcription	Colon Smooth Muscle	Colon
12	chr3:135769800-135789800	Weak transcription	Psoas Muscle	Psoas
13	chr3:135769800-135790000	Weak transcription	Aorta	Aorta
14	chr3:135769800-135790400	Weak transcription	Primary hematopoietic stem cells	blood
15	chr3:135770000-135787200	Weak transcription	Osteobl	bone
16	chr3:135770000-135789800	Weak transcription	Duodenum Smooth Muscle	Duodenum
17	chr3:135770000-135800800	Weak transcription	Fetal Intestine Large	intestine
18	chr3:135770400-135789800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
19	chr3:135771200-135802000	Weak transcription	Brain Germinal Matrix	brain
20	chr3:135771200-135809600	Weak transcription	Gastric	stomach
21	chr3:135771400-135789000	Weak transcription	HSMMtube	muscle
22	chr3:135772600-135789600	Weak transcription	Rectal Mucosa Donor 29	rectum
23	chr3:135772600-135789800	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
24	chr3:135772600-135789800	Weak transcription	Ovary	ovary
25	chr3:135773000-135787400	Weak transcription	Muscle Satellite Cultured Cells	--
26	chr3:135774400-135802000	Weak transcription	Sigmoid Colon	Sigmoid Colon
27	chr3:135774600-135788800	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
28	chr3:135774800-135789000	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
29	chr3:135774800-135789800	Weak transcription	Left Ventricle	heart
30	chr3:135775000-135785000	Weak transcription	HSMM	muscle
31	chr3:135775000-135785200	Weak transcription	NHDF-Ad	bronchial
32	chr3:135775000-135785400	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
33	chr3:135775000-135787600	Weak transcription	Rectal Smooth Muscle	rectum
34	chr3:135775000-135788800	Weak transcription	NHEK	skin
35	chr3:135775000-135789200	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
36	chr3:135775000-135789200	Weak transcription	Fetal Muscle Trunk	muscle
37	chr3:135775000-135789400	Weak transcription	Stomach Smooth Muscle	stomach
38	chr3:135775000-135789800	Weak transcription	Adipose Nuclei	Adipose
39	chr3:135775000-135809600	Weak transcription	Fetal Brain Male	brain
40	chr3:135775000-135809600	Weak transcription	Rectal Mucosa Donor 31	rectum
41	chr3:135775200-135785200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
42	chr3:135775200-135788800	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
43	chr3:135775600-135787400	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
44	chr3:135775600-135788800	Weak transcription	Fetal Heart	heart
45	chr3:135778800-135785200	Weak transcription	Fetal Lung	lung
46	chr3:135779400-135785200	Weak transcription	Skeletal Muscle Male	skeletal muscle
47	chr3:135780600-135789800	Weak transcription	Fetal Stomach	stomach
48	chr3:135781400-135785400	Weak transcription	Fetal Muscle Leg	muscle
49	chr3:135781400-135786400	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
50	chr3:135781400-135786600	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin

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