Variant report

Variant	rs3934775
Chromosome Location	chr1:159753979-159753980
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr1:159750371..159754204-chr1:159835784..159840214,4	MCF-7	breast:

Variant related genes	Relation type
ENSG00000272668	Chromatin interaction

Extended variants
information (count: 21 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:20)

rs_ID	r²[population]
rs11591079	1.00[CHB][hapmap]
rs12067754	0.96[EUR][1000 genomes]
rs1320570	1.00[CHB][hapmap]
rs17427209	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[YRI][hapmap];0.91[AFR][1000 genomes];0.86[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs17467492	1.00[CEU][hapmap];1.00[CHB][hapmap];0.86[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs2789415	1.00[CHB][hapmap]
rs2789416	1.00[CHB][hapmap]
rs2789417	1.00[CHB][hapmap]
rs2789418	1.00[CHB][hapmap]
rs2820579	1.00[CHB][hapmap]
rs2820584	1.00[CHB][hapmap]
rs2840583	1.00[CHB][hapmap]
rs2840588	1.00[CHB][hapmap]
rs3001288	1.00[CHB][hapmap]
rs3934772	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs3934773	1.00[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs6662675	1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[EUR][1000 genomes]
rs6662918	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[YRI][hapmap];0.91[AFR][1000 genomes];0.86[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs6686214	0.86[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs876538	1.00[CHB][hapmap]

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	nsv1005195	chr1:159452759-159910337	Active TSS Enhancers Weak transcription Genic enhancers Flanking Active TSS Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	90 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:49 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:159751400-159754000	Enhancers	Spleen	Spleen
2	chr1:159751400-159756800	Weak transcription	Aorta	Aorta
3	chr1:159751400-159760000	Weak transcription	Placenta	Placenta
4	chr1:159751600-159754200	Weak transcription	Primary B cells from cord blood	blood
5	chr1:159751600-159754400	Weak transcription	Fetal Lung	lung
6	chr1:159751600-159756800	Weak transcription	Ovary	ovary
7	chr1:159751800-159756400	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
8	chr1:159752000-159754400	Weak transcription	Monocytes-CD14+_RO01746	blood
9	chr1:159752000-159754600	Enhancers	Breast Myoepithelial Primary Cells	Breast
10	chr1:159752000-159755400	Weak transcription	Sigmoid Colon	Sigmoid Colon
11	chr1:159752000-159756400	Weak transcription	NHEK	skin
12	chr1:159752000-159756600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
13	chr1:159752000-159756600	Weak transcription	Fetal Muscle Leg	muscle
14	chr1:159752000-159756600	Weak transcription	Rectal Smooth Muscle	rectum
15	chr1:159752000-159757000	Weak transcription	HMEC	breast
16	chr1:159752000-159760000	Weak transcription	Fetal Intestine Large	intestine
17	chr1:159752000-159760200	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
18	chr1:159752200-159754000	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
19	chr1:159752200-159755400	Weak transcription	Colonic Mucosa	Colon
20	chr1:159752200-159756400	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
21	chr1:159752400-159755200	Weak transcription	Stomach Smooth Muscle	stomach
22	chr1:159752400-159756600	Weak transcription	Esophagus	oesophagus
23	chr1:159752600-159754200	Enhancers	H1 Cell Line	embryonic stem cell
24	chr1:159752600-159760400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
25	chr1:159752800-159754400	Weak transcription	Brain Cingulate Gyrus	brain
26	chr1:159752800-159755600	Weak transcription	Lung	lung
27	chr1:159752800-159756000	Weak transcription	Pancreas	Pancrea
28	chr1:159752800-159760000	Weak transcription	Fetal Intestine Small	intestine
29	chr1:159753000-159754600	Enhancers	iPS-18 Cell Line	embryonic stem cell
30	chr1:159753000-159755600	Weak transcription	Primary hematopoietic stem cells short term culture	blood
31	chr1:159753000-159756000	Weak transcription	HUVEC	blood vessel
32	chr1:159753000-159756400	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
33	chr1:159753200-159754200	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
34	chr1:159753400-159754000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
35	chr1:159753400-159754000	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
36	chr1:159753400-159754000	Enhancers	A549	lung
37	chr1:159753400-159754200	Enhancers	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
38	chr1:159753400-159754200	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
39	chr1:159753400-159754600	Enhancers	HUES48 Cell Line	embryonic stem cell
40	chr1:159753400-159754800	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
41	chr1:159753600-159754200	Enhancers	Foreskin Melanocyte Primary Cells skin01	Skin
42	chr1:159753600-159754600	Weak transcription	Brain Hippocampus Middle	brain
43	chr1:159753600-159754800	Enhancers	ES-I3 Cell Line	embryonic stem cell
44	chr1:159753600-159755000	Enhancers	HUES6 Cell Line	embryonic stem cell
45	chr1:159753600-159756200	Weak transcription	Muscle Satellite Cultured Cells	--
46	chr1:159753800-159754000	Enhancers	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
47	chr1:159753800-159754200	Weak transcription	H9 Cell Line	embryonic stem cell
48	chr1:159753800-159754200	Enhancers	iPS DF 6.9 Cell Line	embryonic stem cell
49	chr1:159753800-159756000	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin

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