Variant report

Variant	rs58698408
Chromosome Location	chr6:37950995-37950996
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 85 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:76)

rs_ID	r²[population]
rs10046397	0.84[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs10080245	1.00[EUR][1000 genomes]
rs11759344	1.00[EUR][1000 genomes]
rs11961284	1.00[EUR][1000 genomes]
rs12178911	0.83[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs12663406	1.00[EUR][1000 genomes]
rs12663450	1.00[EUR][1000 genomes]
rs12665229	1.00[EUR][1000 genomes]
rs13437101	1.00[EUR][1000 genomes]
rs55933649	1.00[EUR][1000 genomes]
rs56739079	1.00[EUR][1000 genomes]
rs56957219	1.00[EUR][1000 genomes]
rs56958593	0.87[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs57527781	0.87[AFR][1000 genomes]
rs57953063	1.00[EUR][1000 genomes]
rs58305294	0.83[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs58860274	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs59074919	1.00[EUR][1000 genomes]
rs59170481	1.00[EUR][1000 genomes]
rs59430914	1.00[EUR][1000 genomes]
rs60075988	1.00[EUR][1000 genomes]
rs60774419	1.00[EUR][1000 genomes]
rs60997161	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs6904932	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs6906120	0.87[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs6912045	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs6917912	1.00[EUR][1000 genomes]
rs6918445	1.00[EUR][1000 genomes]
rs6924117	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs6926669	0.87[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs73730818	0.83[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs73730823	0.87[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs73730827	0.87[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs73730832	0.87[AFR][1000 genomes];0.80[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73730849	0.94[AFR][1000 genomes];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73730859	1.00[EUR][1000 genomes]
rs73730877	1.00[EUR][1000 genomes]
rs73730883	1.00[EUR][1000 genomes]
rs73730892	1.00[EUR][1000 genomes]
rs73730893	1.00[EUR][1000 genomes]
rs73730896	1.00[EUR][1000 genomes]
rs73730897	1.00[EUR][1000 genomes]
rs73734319	1.00[EUR][1000 genomes]
rs73734320	1.00[EUR][1000 genomes]
rs73734323	1.00[EUR][1000 genomes]
rs7745340	1.00[EUR][1000 genomes]
rs7747924	1.00[EUR][1000 genomes]
rs7748913	1.00[EUR][1000 genomes]
rs7756841	0.87[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs7765448	1.00[EUR][1000 genomes]
rs7769848	0.87[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs7770297	1.00[EUR][1000 genomes]
rs9462362	1.00[EUR][1000 genomes]
rs9462367	0.82[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs9462370	1.00[EUR][1000 genomes]
rs9462371	1.00[EUR][1000 genomes]
rs9462375	1.00[EUR][1000 genomes]
rs9462390	1.00[EUR][1000 genomes]
rs9462397	1.00[EUR][1000 genomes]
rs9470711	0.81[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs9470715	0.83[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs9470716	0.83[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs9470717	0.82[AFR][1000 genomes]
rs9470719	0.83[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs9470722	0.87[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs9470729	0.87[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs9470731	0.87[AFR][1000 genomes];0.80[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs9470733	1.00[EUR][1000 genomes]
rs9470736	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs9470744	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs9470745	0.92[AFR][1000 genomes];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs9470757	0.80[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs9470766	1.00[EUR][1000 genomes]
rs9470770	1.00[EUR][1000 genomes]
rs9470771	1.00[EUR][1000 genomes]
rs9470781	1.00[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:9 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1028825	chr6:37495154-38278320	Enhancers Active TSS Weak transcription Bivalent/Poised TSS Flanking Active TSS Bivalent Enhancer Strong transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	19 gene(s)	inside rSNPs	diseases
2	nsv1024016	chr6:37567651-37981590	Weak transcription Enhancers Active TSS Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Genic enhancers Flanking Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases
3	nsv1017051	chr6:37789341-38084719	Weak transcription Enhancers Flanking Active TSS ZNF genes & repeats Strong transcription Genic enhancers Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
4	nsv538203	chr6:37789341-38084719	Enhancers Weak transcription Strong transcription Flanking Active TSS ZNF genes & repeats Genic enhancers Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
5	nsv1018711	chr6:37813397-37981590	Enhancers Weak transcription Flanking Active TSS Active TSS Strong transcription ZNF genes & repeats Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
6	nsv1020625	chr6:37833591-38155622	Weak transcription Enhancers Strong transcription Flanking Active TSS ZNF genes & repeats Genic enhancers Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	4 gene(s)	inside rSNPs	diseases
7	nsv1021991	chr6:37893949-38738720	Weak transcription Enhancers Strong transcription Flanking Active TSS Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Active TSS Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	20 gene(s)	inside rSNPs	diseases
8	nsv602956	chr6:37909084-37986489	Weak transcription Enhancers ZNF genes & repeats Strong transcription Flanking Active TSS Genic enhancers Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
9	esv2761037	chr6:37930659-37966762	Weak transcription Enhancers ZNF genes & repeats Genic enhancers Strong transcription Flanking Active TSS Active TSS	Chromatin interactive region	1 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:79 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:37922800-37957600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
2	chr6:37922800-37958600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
3	chr6:37926800-37955000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
4	chr6:37929400-37953200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
5	chr6:37942400-37953200	Weak transcription	Esophagus	oesophagus
6	chr6:37942800-37953600	Weak transcription	HepG2	liver
7	chr6:37942800-37956800	Weak transcription	Aorta	Aorta
8	chr6:37943000-37951600	Weak transcription	NHDF-Ad	bronchial
9	chr6:37943000-37953000	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
10	chr6:37943000-37955800	Weak transcription	Fetal Heart	heart
11	chr6:37943200-37951600	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
12	chr6:37943600-37951800	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
13	chr6:37943600-37952400	Weak transcription	Gastric	stomach
14	chr6:37944800-37952000	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
15	chr6:37946200-37953200	Weak transcription	GM12878-XiMat	blood
16	chr6:37946800-37955800	Weak transcription	Primary B cells from cord blood	blood
17	chr6:37947200-37951600	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
18	chr6:37947400-37951800	Weak transcription	Primary T helper naive cells from peripheral blood	blood
19	chr6:37948000-37952000	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
20	chr6:37948000-37954400	Weak transcription	A549	lung
21	chr6:37948000-37955400	Weak transcription	Left Ventricle	heart
22	chr6:37948000-37955400	Weak transcription	Rectal Smooth Muscle	rectum
23	chr6:37948000-37956800	Weak transcription	Pancreas	Pancrea
24	chr6:37948200-37951400	Weak transcription	NHEK	skin
25	chr6:37948200-37955200	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
26	chr6:37948200-37955600	Weak transcription	Primary hematopoietic stem cells	blood
27	chr6:37948400-37951200	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
28	chr6:37948400-37951400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
29	chr6:37948400-37951600	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
30	chr6:37948400-37951600	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
31	chr6:37948400-37954800	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
32	chr6:37948400-37955400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
33	chr6:37948400-37957600	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
34	chr6:37948400-37958600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
35	chr6:37948600-37951600	Weak transcription	Primary T cells from cord blood	blood
36	chr6:37948600-37957800	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
37	chr6:37948800-37952200	Weak transcription	Liver	Liver
38	chr6:37949000-37951400	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
39	chr6:37949000-37952000	Weak transcription	Primary T killer memory cells from peripheral blood	blood
40	chr6:37949000-37952000	Weak transcription	Colon Smooth Muscle	Colon
41	chr6:37949000-37952000	Weak transcription	Fetal Stomach	stomach
42	chr6:37949000-37953800	Weak transcription	Stomach Mucosa	stomach
43	chr6:37949200-37951600	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
44	chr6:37949200-37952000	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
45	chr6:37949200-37955400	Weak transcription	Fetal Kidney	kidney
46	chr6:37949200-37955400	Weak transcription	Right Ventricle	heart
47	chr6:37949400-37954000	Weak transcription	Fetal Lung	lung
48	chr6:37949400-37954400	Weak transcription	Muscle Satellite Cultured Cells	--
49	chr6:37949600-37955400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
50	chr6:37949800-37951600	Weak transcription	Fetal Adrenal Gland	Adrenal Gland

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