Variant report

Variant	rs2005722
Chromosome Location	chr17:20167867-20167868
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	chr17:20159792..20163252-chr17:20165134..20168652,3	MCF-7	breast:

Extended variants
information (count: 119 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:102)

rs_ID	r²[population]
rs11654025	0.84[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs11870147	0.82[AFR][1000 genomes];0.95[EUR][1000 genomes]
rs11871827	0.82[AFR][1000 genomes];0.95[EUR][1000 genomes]
rs11871945	0.82[AFR][1000 genomes];0.95[EUR][1000 genomes]
rs12451216	0.82[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs12937827	0.87[EUR][1000 genomes]
rs12952398	0.81[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs1373147	0.82[AFR][1000 genomes];0.95[EUR][1000 genomes]
rs1544421	0.82[AFR][1000 genomes];0.86[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs1561974	0.94[AFR][1000 genomes];0.89[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs17686798	0.82[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs17686839	0.87[EUR][1000 genomes]
rs17759923	0.83[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs17759959	0.87[EUR][1000 genomes]
rs1811453	0.82[EUR][1000 genomes]
rs1812934	0.82[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs1985810	0.82[AFR][1000 genomes];0.82[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs1992562	0.95[EUR][1000 genomes]
rs2013441	0.83[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs2013576	0.94[AFR][1000 genomes];0.93[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs2034109	0.94[AFR][1000 genomes];0.89[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs2058971	0.92[EUR][1000 genomes]
rs2080673	0.82[AFR][1000 genomes];0.86[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs2107566	0.86[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs2120282	0.82[AFR][1000 genomes];0.95[EUR][1000 genomes]
rs2158473	0.82[AFR][1000 genomes];0.89[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs2165897	0.82[AFR][1000 genomes];0.95[EUR][1000 genomes]
rs2189710	0.82[AFR][1000 genomes];0.86[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs2243732	0.82[AFR][1000 genomes];0.86[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs2263175	0.82[AFR][1000 genomes];0.89[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs2386429	0.82[AFR][1000 genomes];0.95[EUR][1000 genomes]
rs2386485	0.82[AFR][1000 genomes];0.86[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs2526458	0.82[AFR][1000 genomes];0.86[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs2526460	0.82[AFR][1000 genomes];0.86[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs2526462	0.82[AFR][1000 genomes];0.86[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs2526464	0.82[AFR][1000 genomes];0.86[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs2526467	0.94[AFR][1000 genomes];0.93[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs2526472	0.82[AFR][1000 genomes];0.89[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs2526474	0.82[AFR][1000 genomes];0.89[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs2526475	0.82[AFR][1000 genomes];0.89[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs2526480	0.82[AFR][1000 genomes];0.89[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs2526483	0.82[AFR][1000 genomes];0.86[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs2526484	0.86[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs2526488	0.86[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs2526490	0.82[AFR][1000 genomes];0.86[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs2703772	0.82[AFR][1000 genomes];0.89[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs2703774	0.82[AFR][1000 genomes];0.88[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs2703778	0.82[AFR][1000 genomes];0.89[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs2703780	0.82[AFR][1000 genomes];0.89[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs2703782	0.89[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs2703785	0.94[AFR][1000 genomes];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs2703787	0.94[AFR][1000 genomes];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs2703789	0.94[AFR][1000 genomes];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs2703790	0.94[AFR][1000 genomes];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs2703791	0.94[AFR][1000 genomes];0.93[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs2703792	0.92[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs2703794	0.82[AFR][1000 genomes];0.86[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs2703799	0.82[AFR][1000 genomes];0.86[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs2703801	0.82[AFR][1000 genomes];0.86[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs2703802	0.82[AFR][1000 genomes];0.86[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs2703804	0.86[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs2703806	0.82[AFR][1000 genomes];0.86[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs2703808	0.82[AFR][1000 genomes];0.86[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs2703810	0.82[AFR][1000 genomes];0.86[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs2703815	0.82[AFR][1000 genomes];0.89[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs2703816	0.82[AFR][1000 genomes];0.89[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs2703817	0.82[AFR][1000 genomes];0.89[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs2703818	0.82[AFR][1000 genomes];0.89[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs2703820	0.82[AFR][1000 genomes];0.89[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs2703821	0.82[AFR][1000 genomes];0.89[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs34089239	0.82[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs34644796	0.82[AFR][1000 genomes];0.85[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs34712254	0.82[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs35041742	0.86[EUR][1000 genomes]
rs35429894	0.92[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs36051592	0.81[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs3850782	0.91[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs3850783	0.94[AFR][1000 genomes];0.89[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs3850784	0.94[AFR][1000 genomes];0.89[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs3850785	0.94[AFR][1000 genomes];0.89[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs4588033	0.82[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs4924808	0.87[EUR][1000 genomes]
rs4924809	0.82[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs4924810	0.82[AFR][1000 genomes];0.86[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs4925089	0.82[AFR][1000 genomes];0.86[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs6587063	0.94[AFR][1000 genomes];0.89[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs7207611	0.82[AFR][1000 genomes];0.95[EUR][1000 genomes]
rs8071665	0.82[AFR][1000 genomes];0.95[EUR][1000 genomes]
rs8074047	0.92[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs8079701	0.82[AFR][1000 genomes];0.95[EUR][1000 genomes]
rs9325894	0.94[AFR][1000 genomes];0.89[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs972966	0.81[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs9892630	0.94[AFR][1000 genomes];0.91[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs9896221	0.94[AFR][1000 genomes];0.91[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs9896709	0.94[AFR][1000 genomes];0.91[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs9897328	0.94[AFR][1000 genomes];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs9900166	0.94[AFR][1000 genomes];0.89[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs9904928	0.88[AFR][1000 genomes];0.91[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs9905493	0.94[AFR][1000 genomes];0.89[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs9913818	0.88[EUR][1000 genomes]
rs9915059	0.92[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs9915628	0.81[AMR][1000 genomes];0.93[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:17 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1062853	chr17:19547912-20206601	Enhancers Weak transcription Flanking Active TSS Flanking Bivalent TSS/Enh Genic enhancers Strong transcription ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	63 gene(s)	inside rSNPs	diseases
2	nsv907868	chr17:19768924-20217122	Enhancers Flanking Active TSS ZNF genes & repeats Strong transcription Weak transcription Active TSS Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	25 gene(s)	inside rSNPs	diseases
3	nsv1060337	chr17:19828636-20204872	Active TSS Weak transcription Flanking Active TSS Bivalent Enhancer Enhancers Flanking Bivalent TSS/Enh Genic enhancers Strong transcription ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	21 gene(s)	inside rSNPs	diseases
4	nsv543257	chr17:19828636-20204872	Enhancers Weak transcription Flanking Bivalent TSS/Enh Flanking Active TSS Transcr. at gene 5' and 3' Genic enhancers Strong transcription Active TSS ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	21 gene(s)	inside rSNPs	diseases
5	nsv1067100	chr17:20007480-20464520	Flanking Active TSS Weak transcription Strong transcription Enhancers Genic enhancers ZNF genes & repeats Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	37 gene(s)	inside rSNPs	diseases
6	nsv543260	chr17:20007480-20464520	Strong transcription Weak transcription Enhancers Active TSS Flanking Active TSS ZNF genes & repeats Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	37 gene(s)	inside rSNPs	diseases
7	nsv482830	chr17:20012748-20169153	Weak transcription Strong transcription Enhancers Genic enhancers Active TSS Flanking Active TSS 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	10 gene(s)	inside rSNPs	diseases
8	nsv428669	chr17:20071969-20245033	Weak transcription Enhancers Flanking Active TSS Strong transcription Genic enhancers ZNF genes & repeats Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
9	nsv1064854	chr17:20086562-20225751	Enhancers Weak transcription Genic enhancers Strong transcription Flanking Active TSS ZNF genes & repeats Active TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
10	esv2761953	chr17:20086562-20225763	Enhancers ZNF genes & repeats Weak transcription Strong transcription Flanking Active TSS Genic enhancers Active TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
11	nsv1063833	chr17:20088333-20206601	Enhancers Weak transcription Strong transcription Genic enhancers ZNF genes & repeats Flanking Active TSS Active TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
12	nsv574581	chr17:20088492-20699545	Strong transcription Weak transcription Enhancers Flanking Active TSS ZNF genes & repeats Genic enhancers Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	53 gene(s)	inside rSNPs	diseases
13	nsv1062124	chr17:20139384-20206601	Weak transcription Genic enhancers Enhancers Strong transcription ZNF genes & repeats Flanking Active TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region	2 gene(s)	inside rSNPs	diseases
14	nsv543261	chr17:20139384-20206601	Weak transcription Enhancers Bivalent Enhancer Flanking Active TSS Strong transcription Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region	2 gene(s)	inside rSNPs	diseases
15	nsv1065758	chr17:20141912-20464366	Enhancers Strong transcription Active TSS Weak transcription Genic enhancers Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	29 gene(s)	inside rSNPs	diseases
16	nsv543262	chr17:20141912-20464366	Enhancers Weak transcription Active TSS Strong transcription Flanking Active TSS Genic enhancers ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	29 gene(s)	inside rSNPs	diseases
17	nsv1057389	chr17:20158343-20256498	Weak transcription Strong transcription Enhancers ZNF genes & repeats Genic enhancers Flanking Active TSS Active TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs2005722	SPECC1	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:99 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr17:20130600-20170000	Weak transcription	K562	blood
2	chr17:20130600-20170200	Weak transcription	Skeletal Muscle Female	skeletal muscle
3	chr17:20136400-20209800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
4	chr17:20150400-20170200	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
5	chr17:20151600-20170800	Weak transcription	GM12878-XiMat	blood
6	chr17:20151600-20190000	Weak transcription	Colonic Mucosa	Colon
7	chr17:20152800-20169800	Strong transcription	Cortex derived primary cultured neurospheres	brain
8	chr17:20152800-20176200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
9	chr17:20159800-20168200	Weak transcription	Fetal Heart	heart
10	chr17:20161800-20180200	Weak transcription	Placenta Amnion	Placenta Amnion
11	chr17:20162000-20172600	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
12	chr17:20162000-20172800	Weak transcription	Skeletal Muscle Male	skeletal muscle
13	chr17:20162000-20174600	Weak transcription	Thymus	Thymus
14	chr17:20162000-20176600	Weak transcription	Fetal Brain Male	brain
15	chr17:20162000-20187600	Weak transcription	Pancreas	Pancrea
16	chr17:20162200-20170200	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
17	chr17:20162200-20170200	Weak transcription	Muscle Satellite Cultured Cells	--
18	chr17:20162200-20170400	Weak transcription	Fetal Lung	lung
19	chr17:20163800-20170400	Weak transcription	Lung	lung
20	chr17:20164000-20170200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
21	chr17:20164000-20172800	Weak transcription	Left Ventricle	heart
22	chr17:20164000-20200200	Weak transcription	Fetal Intestine Large	intestine
23	chr17:20164000-20205600	Weak transcription	Esophagus	oesophagus
24	chr17:20164200-20170200	Weak transcription	Fetal Intestine Small	intestine
25	chr17:20164200-20170200	Weak transcription	Osteobl	bone
26	chr17:20164200-20170400	Weak transcription	Fetal Stomach	stomach
27	chr17:20164200-20172600	Weak transcription	Adipose Nuclei	Adipose
28	chr17:20164200-20176200	Weak transcription	Fetal Brain Female	brain
29	chr17:20164200-20200200	Weak transcription	H1 Cell Line	embryonic stem cell
30	chr17:20164400-20170600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
31	chr17:20164400-20202200	Weak transcription	Duodenum Mucosa	Duodenum
32	chr17:20164600-20170000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
33	chr17:20164600-20170200	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
34	chr17:20164600-20170400	Weak transcription	Ovary	ovary
35	chr17:20164600-20203800	Weak transcription	Sigmoid Colon	Sigmoid Colon
36	chr17:20164600-20204000	Weak transcription	Gastric	stomach
37	chr17:20164800-20170000	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
38	chr17:20165000-20168000	Enhancers	Primary T helper cells fromperipheralblood	blood
39	chr17:20165000-20173600	Strong transcription	Primary monocytes fromperipheralblood	blood
40	chr17:20165000-20182000	Enhancers	Primary T killer naive cells fromperipheralblood	blood
41	chr17:20165600-20177200	Strong transcription	Monocytes-CD14+_RO01746	blood
42	chr17:20165800-20168200	Weak transcription	Brain Angular Gyrus	brain
43	chr17:20165800-20171000	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
44	chr17:20165800-20180400	Weak transcription	Rectal Mucosa Donor 31	rectum
45	chr17:20166000-20170000	Weak transcription	Hela-S3	cervix
46	chr17:20166000-20170200	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
47	chr17:20166000-20185000	Weak transcription	Rectal Mucosa Donor 29	rectum
48	chr17:20166200-20168200	Weak transcription	Rectal Smooth Muscle	rectum
49	chr17:20166200-20168400	Weak transcription	Primary T killer memory cells from peripheral blood	blood
50	chr17:20166200-20170000	Weak transcription	HUES6 Cell Line	embryonic stem cell

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