Variant report

Variant	rs10494525
Chromosome Location	chr1:180278683-180278684
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	chr1:180275452..180277141-chr1:180277823..180280366,2	MCF-7	breast:

Extended variants
information (count: 25 )
Associated
traits (count: 0)

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

rs_ID	r²[population]
rs10913969	1.00[CEU][hapmap];0.92[EUR][1000 genomes]
rs10913970	0.81[EUR][1000 genomes]
rs10913994	1.00[CEU][hapmap]
rs10914007	1.00[CEU][hapmap];0.81[EUR][1000 genomes]
rs12039933	1.00[CEU][hapmap]
rs12091722	1.00[CEU][hapmap]
rs12402815	1.00[CEU][hapmap];0.81[EUR][1000 genomes]
rs12404209	1.00[CEU][hapmap]
rs12405902	1.00[CEU][hapmap];0.81[EUR][1000 genomes]
rs1341924	1.00[CEU][hapmap];0.92[TSI][hapmap];0.81[EUR][1000 genomes]
rs1575710	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.82[LWK][hapmap];0.88[MKK][hapmap];0.81[AFR][1000 genomes];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17372142	0.86[MEX][hapmap]
rs2278944	0.82[JPT][hapmap];0.86[MEX][hapmap]
rs2877415	1.00[CEU][hapmap]
rs3737584	1.00[CEU][hapmap];0.92[TSI][hapmap]
rs4543756	1.00[CEU][hapmap];0.87[LWK][hapmap];0.92[TSI][hapmap];0.81[EUR][1000 genomes]
rs60286873	0.81[EUR][1000 genomes]
rs6425634	1.00[CEU][hapmap];0.81[EUR][1000 genomes]
rs6687081	0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7526189	0.81[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1003739	chr1:180027760-180483292	Enhancers ZNF genes & repeats Weak transcription Flanking Bivalent TSS/Enh Strong transcription Flanking Active TSS Active TSS Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	67 gene(s)	inside rSNPs	diseases
2	nsv535217	chr1:180027760-180483292	Enhancers Active TSS Flanking Active TSS Weak transcription ZNF genes & repeats Strong transcription Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	67 gene(s)	inside rSNPs	diseases
3	nsv832004	chr1:180128502-180335540	Strong transcription Enhancers Bivalent/Poised TSS Weak transcription ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Flanking Active TSS Active TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	17 gene(s)	inside rSNPs	diseases
4	nsv1001477	chr1:180172903-180298287	Strong transcription Enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Weak transcription Bivalent/Poised TSS Active TSS Flanking Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
5	nsv535220	chr1:180172903-180298287	Bivalent Enhancer ZNF genes & repeats Weak transcription Enhancers Active TSS Flanking Active TSS Strong transcription Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:81 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:180245200-180282400	Weak transcription	Fetal Intestine Large	intestine
2	chr1:180245400-180280400	Weak transcription	Duodenum Smooth Muscle	Duodenum
3	chr1:180247800-180284200	Weak transcription	Fetal Thymus	thymus
4	chr1:180250400-180279800	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
5	chr1:180254400-180280400	Weak transcription	Fetal Stomach	stomach
6	chr1:180254800-180282400	Weak transcription	Fetal Muscle Leg	muscle
7	chr1:180257600-180289600	Weak transcription	Hela-S3	cervix
8	chr1:180257800-180279800	Weak transcription	Breast Myoepithelial Primary Cells	Breast
9	chr1:180257800-180287200	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
10	chr1:180257800-180296200	Weak transcription	Left Ventricle	heart
11	chr1:180258400-180285200	Weak transcription	Ovary	ovary
12	chr1:180261200-180284200	Weak transcription	K562	blood
13	chr1:180262800-180280000	Weak transcription	Primary B cells from cord blood	blood
14	chr1:180264000-180278800	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
15	chr1:180267000-180284400	Weak transcription	GM12878-XiMat	blood
16	chr1:180268200-180282800	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
17	chr1:180269200-180282000	Weak transcription	Pancreatic Islets	Pancreatic Islet
18	chr1:180271600-180284600	Weak transcription	Primary T helper cells fromperipheralblood	blood
19	chr1:180274600-180281600	Weak transcription	Fetal Brain Male	brain
20	chr1:180275000-180280600	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
21	chr1:180276200-180280400	Weak transcription	Liver	Liver
22	chr1:180276200-180283800	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
23	chr1:180276400-180279800	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
24	chr1:180276400-180280200	Weak transcription	Primary hematopoietic stem cells short term culture	blood
25	chr1:180276400-180280800	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
26	chr1:180276400-180281600	Weak transcription	Primary B cells from peripheral blood	blood
27	chr1:180276400-180284600	Weak transcription	Fetal Lung	lung
28	chr1:180276600-180280000	Weak transcription	Primary hematopoietic stem cells	blood
29	chr1:180276600-180280000	Weak transcription	Primary T helper cells PMA-I stimulated	--
30	chr1:180276600-180280000	Weak transcription	Dnd41	blood
31	chr1:180276600-180280200	Weak transcription	Primary T cells from cord blood	blood
32	chr1:180276600-180280600	Weak transcription	Placenta	Placenta
33	chr1:180276800-180280400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
34	chr1:180277200-180280600	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
35	chr1:180277600-180280800	Enhancers	HepG2	liver
36	chr1:180277800-180279600	Enhancers	Fetal Adrenal Gland	Adrenal Gland
37	chr1:180277800-180280200	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
38	chr1:180277800-180283800	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
39	chr1:180277800-180284200	Weak transcription	Brain Substantia Nigra	brain
40	chr1:180277800-180284800	Weak transcription	Psoas Muscle	Psoas
41	chr1:180278000-180282600	Weak transcription	HUES6 Cell Line	embryonic stem cell
42	chr1:180278000-180284200	Weak transcription	iPS-18 Cell Line	embryonic stem cell
43	chr1:180278000-180285200	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
44	chr1:180278000-180298200	Weak transcription	Esophagus	oesophagus
45	chr1:180278200-180279000	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
46	chr1:180278200-180279000	Enhancers	HSMMtube	muscle
47	chr1:180278200-180279400	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
48	chr1:180278200-180279400	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
49	chr1:180278200-180280200	Weak transcription	Aorta	Aorta
50	chr1:180278200-180281000	Flanking Active TSS	A549	lung

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