Variant report

Variant	rs6907027
Chromosome Location	chr6:53689508-53689509
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr6:53657877..53659758-chr6:53688042..53690060,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000228614	Chromatin interaction
ENSG00000137269	Chromatin interaction

Extended variants
information (count: 56 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:54)

rs_ID	r²[population]
rs10948783	0.92[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10948784	0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs12193567	0.93[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12194768	0.89[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs12209621	0.89[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs3935664	0.93[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs4128619	0.94[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4236114	0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs4260754	0.87[AFR][1000 genomes];0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs4265034	0.86[AMR][1000 genomes];0.85[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs4273680	1.00[CEU][hapmap];0.85[CHB][hapmap];0.85[JPT][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs4331986	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4392712	0.94[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4583974	0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs4612163	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4624872	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.91[AFR][1000 genomes];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs4645423	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6458967	0.93[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6458968	0.91[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6904545	0.85[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6906921	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6910777	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6913431	0.92[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6935621	0.93[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6935838	0.93[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7453639	0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7745548	0.93[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7749635	0.93[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7749749	0.93[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7751036	1.00[CEU][hapmap];0.90[CHB][hapmap];1.00[JPT][hapmap];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7755924	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7761285	0.94[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs9296722	0.86[AMR][1000 genomes];0.85[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs9296723	0.82[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs9349682	0.94[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9349683	0.93[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9349684	0.93[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs9367543	0.94[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs9370234	0.91[AFR][1000 genomes];0.91[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs9370237	0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs9370238	0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs9370240	0.84[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs9382240	0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9382242	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9382243	0.86[CHB][hapmap]
rs9382245	0.94[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs9382247	0.93[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9382254	0.85[CHB][hapmap]
rs9395879	0.91[AFR][1000 genomes];0.90[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs9395880	0.93[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9395882	0.89[AFR][1000 genomes];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs9395883	0.91[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs9395884	0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs9395887	0.86[AMR][1000 genomes];0.85[EUR][1000 genomes];0.82[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	nsv1034955	chr6:53447607-53931055	Enhancers Bivalent Enhancer Weak transcription Flanking Active TSS Flanking Bivalent TSS/Enh Active TSS Strong transcription Bivalent/Poised TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	35 gene(s)	inside rSNPs	diseases
2	nsv1021506	chr6:53600338-53770482	Flanking Active TSS Weak transcription Enhancers Active TSS Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Strong transcription Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:53 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:53670800-53693200	Weak transcription	H9 Cell Line	embryonic stem cell
2	chr6:53676200-53697800	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
3	chr6:53678600-53692200	Weak transcription	Esophagus	oesophagus
4	chr6:53680400-53690000	Weak transcription	Fetal Intestine Small	intestine
5	chr6:53680400-53690200	Weak transcription	Fetal Thymus	thymus
6	chr6:53680400-53691800	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
7	chr6:53680400-53692400	Weak transcription	Pancreas	Pancrea
8	chr6:53680400-53721600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
9	chr6:53680600-53694400	Weak transcription	iPS-20b Cell Line	embryonic stem cell
10	chr6:53680800-53689600	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
11	chr6:53681200-53689800	Weak transcription	Osteobl	bone
12	chr6:53683600-53689800	Weak transcription	Dnd41	blood
13	chr6:53684000-53691400	Weak transcription	Hela-S3	cervix
14	chr6:53684000-53692400	Weak transcription	Left Ventricle	heart
15	chr6:53684000-53694000	Weak transcription	iPS-15b Cell Line	embryonic stem cell
16	chr6:53684000-53710200	Weak transcription	Primary T cells from cord blood	blood
17	chr6:53684600-53690600	Weak transcription	Muscle Satellite Cultured Cells	--
18	chr6:53684600-53697000	Enhancers	Brain Substantia Nigra	brain
19	chr6:53684800-53689800	Weak transcription	HMEC	breast
20	chr6:53685000-53689600	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
21	chr6:53685000-53689800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
22	chr6:53685000-53690200	Weak transcription	NHEK	skin
23	chr6:53686000-53690400	Weak transcription	Gastric	stomach
24	chr6:53687200-53692400	Weak transcription	Thymus	Thymus
25	chr6:53687400-53690400	Weak transcription	Duodenum Smooth Muscle	Duodenum
26	chr6:53687400-53691600	Weak transcription	Right Atrium	heart
27	chr6:53687600-53692400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
28	chr6:53687600-53693000	Weak transcription	Stomach Smooth Muscle	stomach
29	chr6:53687600-53702000	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
30	chr6:53687800-53689600	Weak transcription	HepG2	liver
31	chr6:53687800-53689800	Weak transcription	Rectal Smooth Muscle	rectum
32	chr6:53687800-53690800	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
33	chr6:53687800-53691200	Weak transcription	H1 Cell Line	embryonic stem cell
34	chr6:53687800-53692200	Weak transcription	HSMM	muscle
35	chr6:53687800-53692800	Weak transcription	HSMMtube	muscle
36	chr6:53688000-53689600	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
37	chr6:53688000-53690200	Weak transcription	Brain Inferior Temporal Lobe	brain
38	chr6:53688000-53690400	Weak transcription	Aorta	Aorta
39	chr6:53688000-53692000	Weak transcription	Brain Angular Gyrus	brain
40	chr6:53688000-53692400	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
41	chr6:53688000-53694600	Weak transcription	Fetal Muscle Leg	muscle
42	chr6:53688200-53689600	Weak transcription	Brain Hippocampus Middle	brain
43	chr6:53688200-53690000	Weak transcription	Brain Cingulate Gyrus	brain
44	chr6:53689200-53689800	Enhancers	Brain Anterior Caudate	brain
45	chr6:53689200-53690200	Enhancers	Rectal Mucosa Donor 29	rectum
46	chr6:53689400-53689800	Weak transcription	Colon Smooth Muscle	Colon
47	chr6:53689400-53689800	Enhancers	Pancreatic Islets	Pancreatic Islet
48	chr6:53689400-53690200	Enhancers	Rectal Mucosa Donor 31	rectum
49	chr6:53689400-53691400	Enhancers	Breast Myoepithelial Primary Cells	Breast
50	chr6:53689400-53692000	Enhancers	Colonic Mucosa	Colon

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