Variant report

Variant	rs2793794
Chromosome Location	chr1:179108960-179108961
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	chr1:179108694..179110499-chr1:179120494..179123045,2	MCF-7	breast:

Extended variants
information (count: 81 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:78)

rs_ID	r²[population]
rs10913690	0.86[ASN][1000 genomes]
rs10913692	0.90[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs10913693	0.88[AMR][1000 genomes];0.94[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs10913695	0.89[ASN][1000 genomes]
rs10913697	0.92[ASN][1000 genomes]
rs1325195	0.88[ASN][1000 genomes]
rs1763022	0.81[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs1826183	0.81[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs1856968	0.92[ASN][1000 genomes]
rs1858551	0.92[ASN][1000 genomes]
rs2087559	0.88[ASN][1000 genomes]
rs2171958	0.85[AMR][1000 genomes];0.90[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs2171959	0.91[ASN][1000 genomes]
rs2258217	0.85[ASN][1000 genomes]
rs2258221	0.92[ASN][1000 genomes]
rs2306941	0.84[EUR][1000 genomes]
rs2486995	0.92[ASN][1000 genomes]
rs2486997	0.91[ASN][1000 genomes]
rs2486998	0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2487563	0.82[AFR][1000 genomes];0.85[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs2493123	0.95[AMR][1000 genomes];0.90[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2493124	0.91[ASN][1000 genomes]
rs2636274	0.94[ASN][1000 genomes]
rs2636275	0.90[AMR][1000 genomes];0.90[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2636276	0.94[ASN][1000 genomes]
rs2636277	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2636291	0.81[AFR][1000 genomes];0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2791936	0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2791940	0.92[ASN][1000 genomes]
rs2791941	0.94[ASN][1000 genomes]
rs2791942	0.90[ASN][1000 genomes]
rs2791943	0.94[ASN][1000 genomes]
rs2791944	0.85[AMR][1000 genomes];0.82[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2791945	0.96[AMR][1000 genomes];0.93[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2793790	0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2793793	0.88[ASN][1000 genomes]
rs2793795	0.88[ASN][1000 genomes]
rs2793796	0.92[ASN][1000 genomes]
rs2793797	0.92[ASN][1000 genomes]
rs2793798	0.92[ASN][1000 genomes]
rs2793800	0.80[EUR][1000 genomes]
rs2793801	0.82[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs2793802	0.85[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs2793810	0.81[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2793813	0.82[AMR][1000 genomes];0.92[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2816166	0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2816168	0.82[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs2816183	0.92[ASN][1000 genomes]
rs2816184	0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2816185	0.92[ASN][1000 genomes]
rs2816186	0.83[ASN][1000 genomes]
rs2816187	0.92[ASN][1000 genomes]
rs2816189	0.87[ASN][1000 genomes]
rs2816191	0.80[AFR][1000 genomes];0.94[AMR][1000 genomes];0.90[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2816196	0.89[ASN][1000 genomes]
rs2816200	0.81[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs2816201	0.85[AMR][1000 genomes];0.92[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2816207	0.85[AMR][1000 genomes];0.89[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs2816212	0.86[EUR][1000 genomes]
rs2816218	0.86[AMR][1000 genomes];0.90[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs3121198	0.85[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs36122838	0.88[ASN][1000 genomes]
rs3813642	0.88[ASN][1000 genomes]
rs3813643	0.88[ASN][1000 genomes]
rs3829794	0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs413613	0.87[EUR][1000 genomes]
rs4651012	0.88[ASN][1000 genomes]
rs4651013	0.88[ASN][1000 genomes]
rs7556011	0.81[ASN][1000 genomes]
rs9286921	0.89[AFR][1000 genomes];0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9425839	0.85[AMR][1000 genomes];0.90[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs965401	0.88[ASN][1000 genomes]
rs9662858	0.89[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs9726961	0.92[ASN][1000 genomes]
rs9727252	0.92[ASN][1000 genomes]
rs9728480	0.92[ASN][1000 genomes]
rs9729129	0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9729199	0.88[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1012667	chr1:179094571-179120280	Weak transcription Enhancers ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Strong transcription Flanking Active TSS Active TSS	TF binding region CpG island Chromatin interactive region	3 gene(s)	inside rSNPs	diseases
2	nsv1002253	chr1:179094571-179120938	Strong transcription Genic enhancers Enhancers Weak transcription Flanking Active TSS Transcr. at gene 5' and 3' Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region	3 gene(s)	inside rSNPs	diseases
3	nsv1001191	chr1:179097246-179120938	Weak transcription Flanking Active TSS Enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Strong transcription Genic enhancers Active TSS	TF binding region CpG island Chromatin interactive region	3 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:87 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:179063200-179112000	Weak transcription	Fetal Kidney	kidney
2	chr1:179079600-179109800	Weak transcription	Small Intestine	intestine
3	chr1:179087800-179113000	Weak transcription	Placenta Amnion	Placenta Amnion
4	chr1:179091000-179109000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
5	chr1:179091000-179109200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
6	chr1:179093400-179117200	Weak transcription	Fetal Stomach	stomach
7	chr1:179096600-179110200	Weak transcription	Cortex derived primary cultured neurospheres	brain
8	chr1:179098200-179112000	Weak transcription	Lung	lung
9	chr1:179099200-179110200	Weak transcription	Primary hematopoietic stem cells	blood
10	chr1:179099200-179110400	Weak transcription	Brain Angular Gyrus	brain
11	chr1:179099200-179110400	Weak transcription	Brain Anterior Caudate	brain
12	chr1:179099200-179114800	Weak transcription	Brain Cingulate Gyrus	brain
13	chr1:179099400-179110000	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
14	chr1:179099400-179110400	Weak transcription	Duodenum Smooth Muscle	Duodenum
15	chr1:179099400-179112000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
16	chr1:179099400-179112000	Weak transcription	Left Ventricle	heart
17	chr1:179099600-179109200	Weak transcription	Primary T cells from cord blood	blood
18	chr1:179099600-179109800	Weak transcription	Primary monocytes fromperipheralblood	blood
19	chr1:179099600-179109800	Weak transcription	Primary T cells fromperipheralblood	blood
20	chr1:179099600-179110000	Weak transcription	Monocytes-CD14+_RO01746	blood
21	chr1:179099600-179110200	Weak transcription	Primary B cells from peripheral blood	blood
22	chr1:179099600-179110600	Weak transcription	Rectal Smooth Muscle	rectum
23	chr1:179099600-179110800	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
24	chr1:179099600-179116800	Weak transcription	Thymus	Thymus
25	chr1:179099600-179119400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
26	chr1:179099600-179122600	Weak transcription	Stomach Smooth Muscle	stomach
27	chr1:179099800-179109400	Weak transcription	Primary B cells from cord blood	blood
28	chr1:179099800-179111800	Weak transcription	HepG2	liver
29	chr1:179100000-179121000	Weak transcription	Rectal Mucosa Donor 31	rectum
30	chr1:179100200-179110000	Weak transcription	Primary hematopoietic stem cells short term culture	blood
31	chr1:179100600-179110800	Weak transcription	Brain Inferior Temporal Lobe	brain
32	chr1:179100600-179112000	Weak transcription	Sigmoid Colon	Sigmoid Colon
33	chr1:179100600-179117200	Weak transcription	Fetal Intestine Small	intestine
34	chr1:179100800-179110400	Weak transcription	HUES48 Cell Line	embryonic stem cell
35	chr1:179100800-179110400	Weak transcription	K562	blood
36	chr1:179101000-179109200	Weak transcription	iPS-20b Cell Line	embryonic stem cell
37	chr1:179101000-179110000	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
38	chr1:179106800-179109000	Genic enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
39	chr1:179106800-179110200	Transcr. at gene 5' and 3'	Foreskin Melanocyte Primary Cells skin03	Skin
40	chr1:179106800-179110400	Transcr. at gene 5' and 3'	Foreskin Fibroblast Primary Cells skin01	Skin
41	chr1:179107000-179109000	Enhancers	HMEC	breast
42	chr1:179107000-179110000	Transcr. at gene 5' and 3'	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
43	chr1:179107200-179109000	Weak transcription	Right Atrium	heart
44	chr1:179107200-179110200	Weak transcription	Primary neutrophils fromperipheralblood	blood
45	chr1:179107200-179110200	Weak transcription	Primary T killer memory cells from peripheral blood	blood
46	chr1:179107200-179110800	Weak transcription	Skeletal Muscle Female	skeletal muscle
47	chr1:179107200-179112000	Weak transcription	Brain Substantia Nigra	brain
48	chr1:179107400-179110200	Weak transcription	Adipose Nuclei	Adipose
49	chr1:179107400-179111000	Weak transcription	Skeletal Muscle Male	skeletal muscle
50	chr1:179107600-179110400	Weak transcription	Pancreatic Islets	Pancreatic Islet

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