Variant report

Variant	rs2208840
Chromosome Location	chr6:11183384-11183385
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr6:11180911..11183612-chr6:11187245..11190194,2	MCF-7	breast:
2	chr6:11181022..11183446-chr6:11183581..11185850,2	MCF-7	breast:
3	chr6:11182279..11185693-chr6:11230831..11233757,3	MCF-7	breast:

Variant related genes	Relation type
ENSG00000111859	Chromatin interaction

Extended variants
information (count: 37 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:35)

rs_ID	r²[population]
rs1007741	0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10601	1.00[CEU][hapmap];0.94[YRI][hapmap];0.89[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13849	0.91[CEU][hapmap];0.89[YRI][hapmap];0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1803710	1.00[CEU][hapmap];0.86[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs2146344	0.82[AMR][1000 genomes];0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2327336	0.82[AMR][1000 genomes];0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2327338	1.00[CEU][hapmap];1.00[YRI][hapmap];0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3035	0.84[AMR][1000 genomes];0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34044517	1.00[ASN][1000 genomes]
rs4711193	1.00[CEU][hapmap];1.00[YRI][hapmap];0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4711194	1.00[CEU][hapmap];1.00[YRI][hapmap];0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4713227	0.84[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs4713228	1.00[CEU][hapmap];1.00[YRI][hapmap];0.87[AFR][1000 genomes];0.92[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs4713229	0.87[AFR][1000 genomes];0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6456946	0.84[AMR][1000 genomes];0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6456968	1.00[CEU][hapmap];0.94[YRI][hapmap];0.89[AFR][1000 genomes];0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6912556	0.88[CEU][hapmap];0.94[YRI][hapmap];0.89[AFR][1000 genomes];0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6923556	0.82[AMR][1000 genomes];0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6923725	1.00[CEU][hapmap];0.94[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6935824	0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7739880	0.86[CEU][hapmap]
rs7746976	1.00[CEU][hapmap];1.00[YRI][hapmap];0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7750787	1.00[CEU][hapmap];1.00[YRI][hapmap];0.91[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7751344	0.82[AMR][1000 genomes];0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7755052	0.91[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7755536	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7759674	0.88[AMR][1000 genomes];0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7770498	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9283888	0.87[AFR][1000 genomes];0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9295806	0.87[AFR][1000 genomes];0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9368595	0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9468537	1.00[CEU][hapmap];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9468556	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs960944	1.00[CEU][hapmap];0.94[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs960945	1.00[CEU][hapmap];0.94[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[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	nsv1021078	chr6:10819083-11558560	Enhancers Strong transcription Active TSS Flanking Active TSS Weak transcription Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	47 gene(s)	inside rSNPs	diseases
2	nsv538135	chr6:10819083-11558560	Weak transcription Enhancers Strong transcription Flanking Active TSS Bivalent Enhancer Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	47 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:115 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:11162400-11185400	Weak transcription	Esophagus	oesophagus
2	chr6:11171800-11185400	Weak transcription	Gastric	stomach
3	chr6:11172800-11195000	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
4	chr6:11173200-11183400	Weak transcription	Monocytes-CD14+_RO01746	blood
5	chr6:11173200-11183600	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
6	chr6:11173200-11183600	Weak transcription	Sigmoid Colon	Sigmoid Colon
7	chr6:11173200-11184000	Weak transcription	Primary neutrophils fromperipheralblood	blood
8	chr6:11173200-11184000	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
9	chr6:11173200-11184000	Weak transcription	Duodenum Mucosa	Duodenum
10	chr6:11173200-11184000	Weak transcription	Lung	lung
11	chr6:11173200-11184000	Weak transcription	Rectal Smooth Muscle	rectum
12	chr6:11173200-11184000	Weak transcription	Spleen	Spleen
13	chr6:11173200-11184200	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
14	chr6:11173200-11184600	Weak transcription	Colon Smooth Muscle	Colon
15	chr6:11173200-11184800	Weak transcription	Brain Cingulate Gyrus	brain
16	chr6:11173200-11184800	Weak transcription	Pancreas	Pancrea
17	chr6:11173200-11185400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
18	chr6:11173200-11185400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
19	chr6:11173200-11185400	Weak transcription	Ovary	ovary
20	chr6:11173200-11187600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
21	chr6:11173400-11183600	Weak transcription	Rectal Mucosa Donor 29	rectum
22	chr6:11173400-11183600	Weak transcription	Osteobl	bone
23	chr6:11173400-11183800	Weak transcription	GM12878-XiMat	blood
24	chr6:11173400-11184000	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
25	chr6:11173400-11184000	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
26	chr6:11173400-11184000	Weak transcription	Aorta	Aorta
27	chr6:11173400-11184200	Weak transcription	Brain Inferior Temporal Lobe	brain
28	chr6:11173400-11185400	Weak transcription	Primary T helper naive cells from peripheral blood	blood
29	chr6:11173400-11185400	Weak transcription	Brain Hippocampus Middle	brain
30	chr6:11173400-11185600	Weak transcription	H9 Cell Line	embryonic stem cell
31	chr6:11173600-11184000	Weak transcription	Fetal Kidney	kidney
32	chr6:11173800-11183600	Weak transcription	Rectal Mucosa Donor 31	rectum
33	chr6:11173800-11184000	Weak transcription	Thymus	Thymus
34	chr6:11173800-11184600	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
35	chr6:11174000-11185000	Weak transcription	Fetal Heart	heart
36	chr6:11174800-11183400	Weak transcription	Fetal Thymus	thymus
37	chr6:11174800-11184000	Weak transcription	Primary monocytes fromperipheralblood	blood
38	chr6:11174800-11185400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
39	chr6:11175000-11185400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
40	chr6:11178400-11190000	Weak transcription	Brain Anterior Caudate	brain
41	chr6:11179000-11202200	Weak transcription	Brain Substantia Nigra	brain
42	chr6:11179800-11184200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
43	chr6:11180000-11185400	Weak transcription	Brain Angular Gyrus	brain
44	chr6:11180200-11183600	Weak transcription	HSMM	muscle
45	chr6:11180200-11184000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
46	chr6:11180200-11184000	Weak transcription	Placenta	Placenta
47	chr6:11180200-11184200	Weak transcription	Fetal Intestine Large	intestine
48	chr6:11180200-11185600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
49	chr6:11180200-11190200	Weak transcription	H1 Cell Line	embryonic stem cell
50	chr6:11180200-11194600	Weak transcription	iPS-15b Cell Line	embryonic stem cell

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