Variant report

Variant	rs6539
Chromosome Location	chr6:30037990-30037991
allele	A/C/G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr6:30037349..30040198-chr6:30056751..30058986,2	MCF-7	breast:
2	chr6:30037077..30039641-chr6:30068261..30070312,3	MCF-7	breast:

Extended variants
information (count: 41 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:37)

rs_ID	r²[population]
rs1061536	0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1632873	0.84[ASN][1000 genomes]
rs3016019	0.84[ASN][1000 genomes]
rs3094145	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3121593	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3121595	0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3121596	1.00[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3121597	0.83[ASN][1000 genomes]
rs3132128	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3132130	0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3132683	1.00[AFR][1000 genomes];0.89[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3134881	0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3893259	0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3893465	0.83[EUR][1000 genomes]
rs4472395	0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4959036	0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs5025708	0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6928431	0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7763159	0.94[EUR][1000 genomes]
rs9260676	0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9260685	0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9260702	0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9260706	0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9260761	0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9260786	0.81[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9260808	0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9260857	0.85[AFR][1000 genomes];0.84[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9260973	0.81[AFR][1000 genomes];0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9260997	0.89[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9261061	0.95[AFR][1000 genomes];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9261136	0.95[AFR][1000 genomes];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9261142	0.85[AFR][1000 genomes];0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs9261143	0.89[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9261211	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9261212	0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9261269	0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9261402	0.83[AMR][1000 genomes];0.95[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1031115	chr6:29934199-30058223	Flanking Bivalent TSS/Enh Enhancers Active TSS Flanking Active TSS Weak transcription Strong transcription Bivalent Enhancer Bivalent/Poised TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	57 gene(s)	inside rSNPs	diseases
2	nsv538172	chr6:29934199-30058223	Active TSS Enhancers Weak transcription Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent Enhancer Genic enhancers Bivalent/Poised TSS Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	57 gene(s)	inside rSNPs	diseases
3	nsv432866	chr6:30026321-30080921	Active TSS Genic enhancers ZNF genes & repeats Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Weak transcription Strong transcription Enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	53 gene(s)	inside rSNPs	diseases
4	nsv884049	chr6:30037353-30047403	Strong transcription Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Weak transcription Active TSS Genic enhancers Flanking Active TSS Enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region	7 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:107 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:30035600-30041000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
2	chr6:30035800-30038000	Weak transcription	HUES6 Cell Line	embryonic stem cell
3	chr6:30035800-30038800	Weak transcription	Right Atrium	heart
4	chr6:30036000-30038000	Weak transcription	Brain Substantia Nigra	brain
5	chr6:30036000-30038200	Weak transcription	HUVEC	blood vessel
6	chr6:30036000-30038600	Weak transcription	iPS-18 Cell Line	embryonic stem cell
7	chr6:30036000-30038600	Weak transcription	Primary hematopoietic stem cells	blood
8	chr6:30036000-30038600	Weak transcription	NH-A	brain
9	chr6:30036200-30038000	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
10	chr6:30036200-30038200	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
11	chr6:30036200-30038200	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
12	chr6:30036200-30038200	Strong transcription	Fetal Muscle Leg	muscle
13	chr6:30036200-30038400	Strong transcription	Fetal Intestine Large	intestine
14	chr6:30036200-30038600	Strong transcription	Thymus	Thymus
15	chr6:30036200-30038800	Weak transcription	Muscle Satellite Cultured Cells	--
16	chr6:30036200-30038800	Strong transcription	Placenta	Placenta
17	chr6:30036200-30039400	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
18	chr6:30036400-30038000	Strong transcription	Primary monocytes fromperipheralblood	blood
19	chr6:30036400-30038000	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
20	chr6:30036400-30038000	Strong transcription	Aorta	Aorta
21	chr6:30036400-30038000	Strong transcription	Left Ventricle	heart
22	chr6:30036400-30038000	Strong transcription	Pancreas	Pancrea
23	chr6:30036400-30038000	Strong transcription	Rectal Smooth Muscle	rectum
24	chr6:30036400-30038000	Strong transcription	Sigmoid Colon	Sigmoid Colon
25	chr6:30036400-30038200	Strong transcription	Primary neutrophils fromperipheralblood	blood
26	chr6:30036400-30038200	Strong transcription	Primary B cells from cord blood	blood
27	chr6:30036400-30038200	Strong transcription	Primary T cells from cord blood	blood
28	chr6:30036400-30038200	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
29	chr6:30036400-30038200	Strong transcription	Adipose Nuclei	Adipose
30	chr6:30036400-30038200	Strong transcription	Liver	Liver
31	chr6:30036400-30038200	Strong transcription	Colonic Mucosa	Colon
32	chr6:30036400-30038200	Strong transcription	Fetal Intestine Small	intestine
33	chr6:30036400-30038200	Strong transcription	Fetal Muscle Trunk	muscle
34	chr6:30036400-30038200	Strong transcription	Fetal Stomach	stomach
35	chr6:30036400-30038200	Strong transcription	Psoas Muscle	Psoas
36	chr6:30036400-30038200	Strong transcription	Rectal Mucosa Donor 29	rectum
37	chr6:30036400-30038200	Strong transcription	Stomach Smooth Muscle	stomach
38	chr6:30036400-30038400	Strong transcription	Primary B cells from peripheral blood	blood
39	chr6:30036400-30038400	Strong transcription	Primary hematopoietic stem cells short term culture	blood
40	chr6:30036400-30038400	Strong transcription	Brain Cingulate Gyrus	brain
41	chr6:30036400-30038600	Strong transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
42	chr6:30036400-30038800	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
43	chr6:30036400-30040000	Weak transcription	Stomach Mucosa	stomach
44	chr6:30036600-30038000	Strong transcription	Primary T killer memory cells from peripheral blood	blood
45	chr6:30036600-30038200	Strong transcription	Primary T cells fromperipheralblood	blood
46	chr6:30036600-30038200	Strong transcription	Primary T helper 17 cells PMA-I stimulated	--
47	chr6:30036600-30038200	Strong transcription	Foreskin Melanocyte Primary Cells skin01	Skin
48	chr6:30036600-30038200	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
49	chr6:30036600-30038200	Strong transcription	Skeletal Muscle Female	skeletal muscle
50	chr6:30036600-30038400	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived

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