Variant report

Variant	rs953856
Chromosome Location	chr1:56997139-56997140
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr1:56996284..56998415-chr1:56998780..57000786,2	MCF-7	breast:

Extended variants
information (count: 22 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:21)

rs_ID	r²[population]
rs10493211	0.84[CEU][hapmap]
rs10888977	1.00[CEU][hapmap];0.96[YRI][hapmap];0.99[AFR][1000 genomes];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs11206838	0.84[CEU][hapmap];0.88[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs12082242	0.98[AFR][1000 genomes];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs12134109	0.84[CEU][hapmap];0.88[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs1759750	0.81[AFR][1000 genomes]
rs1759752	0.93[YRI][hapmap];0.96[AFR][1000 genomes]
rs1777274	0.83[AFR][1000 genomes]
rs1777277	0.96[AFR][1000 genomes]
rs1810930	0.86[AFR][1000 genomes]
rs1930760	0.89[CEU][hapmap];0.93[YRI][hapmap];0.91[AFR][1000 genomes];0.87[EUR][1000 genomes]
rs1930762	0.96[YRI][hapmap];0.86[AFR][1000 genomes]
rs2017955	0.88[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs4532850	0.96[YRI][hapmap];0.94[AFR][1000 genomes]
rs4912377	0.86[AFR][1000 genomes]
rs55798508	0.86[AFR][1000 genomes]
rs7535757	0.96[YRI][hapmap]
rs7551402	0.85[CEU][hapmap];0.81[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs7556056	0.96[YRI][hapmap];0.81[AFR][1000 genomes]
rs953857	0.85[CEU][hapmap];0.88[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs993075	0.96[YRI][hapmap];0.94[AFR][1000 genomes]

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

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv869295	chr1:56894955-57656562	Weak transcription Strong transcription Genic enhancers Active TSS Flanking Active TSS Bivalent/Poised TSS Enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	20 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:95 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:56967000-57002000	Genic enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
2	chr1:56977800-56999200	Weak transcription	A549	lung
3	chr1:56983400-57000800	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
4	chr1:56987000-57015000	Genic enhancers	NHDF-Ad	bronchial
5	chr1:56990000-57004000	Genic enhancers	Liver	Liver
6	chr1:56990200-56998600	Enhancers	Brain Substantia Nigra	brain
7	chr1:56990600-56997800	Enhancers	Brain Anterior Caudate	brain
8	chr1:56990800-56997200	Enhancers	Brain Cingulate Gyrus	brain
9	chr1:56990800-56997400	Enhancers	Brain Hippocampus Middle	brain
10	chr1:56992000-57001200	Weak transcription	Spleen	Spleen
11	chr1:56992600-56997400	Weak transcription	Lung	lung
12	chr1:56992800-56997800	Weak transcription	HSMMtube	muscle
13	chr1:56992800-56998600	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
14	chr1:56992800-56998800	Weak transcription	Gastric	stomach
15	chr1:56992800-57011200	Weak transcription	Stomach Mucosa	stomach
16	chr1:56993000-56998800	Enhancers	Ovary	ovary
17	chr1:56993000-56999800	Weak transcription	Primary neutrophils fromperipheralblood	blood
18	chr1:56993000-57004600	Weak transcription	Hela-S3	cervix
19	chr1:56993200-57001400	Enhancers	Right Atrium	heart
20	chr1:56993600-57007800	Weak transcription	Primary B cells from cord blood	blood
21	chr1:56993800-56998000	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
22	chr1:56993800-56998200	Weak transcription	Primary B cells from peripheral blood	blood
23	chr1:56993800-57004200	Weak transcription	NH-A	brain
24	chr1:56994000-56997800	Weak transcription	Esophagus	oesophagus
25	chr1:56994000-56997800	Weak transcription	Thymus	Thymus
26	chr1:56994000-56998600	Weak transcription	Colonic Mucosa	Colon
27	chr1:56994000-56999000	Weak transcription	Aorta	Aorta
28	chr1:56994000-57000000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
29	chr1:56994000-57001200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
30	chr1:56994000-57004000	Weak transcription	HUVEC	blood vessel
31	chr1:56994000-57012400	Weak transcription	Fetal Brain Male	brain
32	chr1:56994000-57012800	Weak transcription	Fetal Brain Female	brain
33	chr1:56994200-56998000	Weak transcription	Stomach Smooth Muscle	stomach
34	chr1:56994200-56998800	Weak transcription	Rectal Mucosa Donor 31	rectum
35	chr1:56994200-56999400	Weak transcription	Rectal Mucosa Donor 29	rectum
36	chr1:56994200-57001200	Weak transcription	Dnd41	blood
37	chr1:56994200-57004400	Strong transcription	Muscle Satellite Cultured Cells	--
38	chr1:56994400-56998400	Weak transcription	Sigmoid Colon	Sigmoid Colon
39	chr1:56994400-57002600	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
40	chr1:56994600-56998400	Enhancers	Psoas Muscle	Psoas
41	chr1:56994600-56999600	Weak transcription	Duodenum Smooth Muscle	Duodenum
42	chr1:56994600-56999800	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
43	chr1:56994800-56997200	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
44	chr1:56994800-56998000	Genic enhancers	HUES48 Cell Line	embryonic stem cell
45	chr1:56994800-56999000	Genic enhancers	Cortex derived primary cultured neurospheres	brain
46	chr1:56995000-56997200	Strong transcription	Placenta	Placenta
47	chr1:56995000-56998000	Enhancers	Left Ventricle	heart
48	chr1:56995000-56998200	Weak transcription	Duodenum Mucosa	Duodenum
49	chr1:56995000-56998200	Strong transcription	Fetal Stomach	stomach
50	chr1:56995000-56998400	Enhancers	Brain Inferior Temporal Lobe	brain

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