Variant report

Variant	rs2703784
Chromosome Location	chr17:20151320-20151321
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	chr17:20144551..20147091-chr17:20150035..20152753,2	MCF-7	breast:

Extended variants
information (count: 131 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:113)

rs_ID	r²[population]
rs1009082	0.93[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10438824	0.88[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11870147	1.00[ASN][1000 genomes]
rs11871827	1.00[ASN][1000 genomes]
rs11871945	1.00[ASN][1000 genomes]
rs12937827	1.00[ASN][1000 genomes]
rs12941200	0.87[AMR][1000 genomes];0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12947950	0.88[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12948178	0.87[AMR][1000 genomes];0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12949485	0.89[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12952398	1.00[ASN][1000 genomes]
rs1373147	1.00[ASN][1000 genomes]
rs1544421	1.00[ASN][1000 genomes]
rs1561974	1.00[ASN][1000 genomes]
rs17686622	0.87[AMR][1000 genomes];0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17686839	1.00[ASN][1000 genomes]
rs17759923	1.00[ASN][1000 genomes]
rs1812934	1.00[ASN][1000 genomes]
rs1985810	1.00[ASN][1000 genomes]
rs1992562	1.00[ASN][1000 genomes]
rs2013441	1.00[ASN][1000 genomes]
rs2013576	0.83[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs2034109	1.00[ASN][1000 genomes]
rs2080673	1.00[ASN][1000 genomes]
rs2107566	1.00[ASN][1000 genomes]
rs2120282	1.00[ASN][1000 genomes]
rs2158473	1.00[ASN][1000 genomes]
rs2165897	1.00[ASN][1000 genomes]
rs2189710	1.00[ASN][1000 genomes]
rs2243732	1.00[ASN][1000 genomes]
rs2263175	1.00[ASN][1000 genomes]
rs2386429	1.00[ASN][1000 genomes]
rs2386485	1.00[ASN][1000 genomes]
rs2526458	1.00[ASN][1000 genomes]
rs2526460	1.00[ASN][1000 genomes]
rs2526464	1.00[ASN][1000 genomes]
rs2526467	0.83[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs2526468	1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2526469	0.84[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2526470	0.84[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2526471	0.84[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2526472	1.00[ASN][1000 genomes]
rs2526473	0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2526474	1.00[ASN][1000 genomes]
rs2526475	1.00[ASN][1000 genomes]
rs2526480	1.00[ASN][1000 genomes]
rs2526483	1.00[ASN][1000 genomes]
rs2526484	1.00[ASN][1000 genomes]
rs2526488	1.00[ASN][1000 genomes]
rs2526490	1.00[ASN][1000 genomes]
rs2526491	0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2526492	0.93[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2703772	1.00[ASN][1000 genomes]
rs2703773	0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2703774	1.00[ASN][1000 genomes]
rs2703778	1.00[ASN][1000 genomes]
rs2703779	0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2703780	1.00[ASN][1000 genomes]
rs2703782	1.00[ASN][1000 genomes]
rs2703785	0.83[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs2703787	0.83[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs2703789	0.83[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs2703790	0.83[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs2703791	0.83[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs2703792	0.82[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs2703794	1.00[ASN][1000 genomes]
rs2703797	0.93[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2703799	1.00[ASN][1000 genomes]
rs2703801	1.00[ASN][1000 genomes]
rs2703802	1.00[ASN][1000 genomes]
rs2703804	1.00[ASN][1000 genomes]
rs2703806	1.00[ASN][1000 genomes]
rs2703808	1.00[ASN][1000 genomes]
rs2703810	1.00[ASN][1000 genomes]
rs2703811	0.90[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs2703813	0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2703815	1.00[ASN][1000 genomes]
rs2703816	1.00[ASN][1000 genomes]
rs2703817	1.00[ASN][1000 genomes]
rs2703818	1.00[ASN][1000 genomes]
rs2703820	1.00[ASN][1000 genomes]
rs2703821	1.00[ASN][1000 genomes]
rs34089239	1.00[ASN][1000 genomes]
rs34644796	1.00[ASN][1000 genomes]
rs34712254	1.00[ASN][1000 genomes]
rs35103332	0.95[AMR][1000 genomes];0.92[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs3850783	1.00[ASN][1000 genomes]
rs3850784	1.00[ASN][1000 genomes]
rs3850785	1.00[ASN][1000 genomes]
rs4588033	1.00[ASN][1000 genomes]
rs4924809	1.00[ASN][1000 genomes]
rs4924810	1.00[ASN][1000 genomes]
rs4925089	1.00[ASN][1000 genomes]
rs62066869	0.88[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62067558	0.89[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6587063	0.83[ASN][1000 genomes]
rs6587064	0.84[AFR][1000 genomes];0.83[AMR][1000 genomes];0.94[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs7207611	1.00[ASN][1000 genomes]
rs7207817	0.84[AFR][1000 genomes];0.81[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs7223488	0.83[ASN][1000 genomes]
rs8070401	0.84[AFR][1000 genomes];0.81[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs8071665	1.00[ASN][1000 genomes]
rs8074047	0.82[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs8079701	1.00[ASN][1000 genomes]
rs9325894	1.00[ASN][1000 genomes]
rs9892630	0.81[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs9896221	0.81[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs9896709	0.81[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs9897328	0.83[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs9900166	1.00[ASN][1000 genomes]
rs9904928	0.81[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs9905493	1.00[ASN][1000 genomes]
rs9915059	0.82[AMR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:18 , 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	nsv1065363	chr17:20118499-20162888	Enhancers Strong transcription Weak transcription Genic enhancers ZNF genes & repeats Flanking Active TSS Transcr. at gene 5' and 3'	Chromatin interactive region	2 gene(s)	inside rSNPs	diseases
14	nsv1059774	chr17:20118499-20163560	Weak transcription Enhancers Genic enhancers Strong transcription ZNF genes & repeats Flanking Active TSS Transcr. at gene 5' and 3'	Chromatin interactive region	2 gene(s)	inside rSNPs	diseases
15	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
16	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
17	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
18	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

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs2703784	SPECC1	Cis_1M	lymphoblastoid	RTeQTL

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr17:20111600-20166000	Weak transcription	Right Ventricle	heart
2	chr17:20128800-20157000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
3	chr17:20129200-20161600	Weak transcription	Fetal Brain Female	brain
4	chr17:20129600-20161600	Weak transcription	Placenta Amnion	Placenta Amnion
5	chr17:20130600-20161200	Weak transcription	Skeletal Muscle Male	skeletal muscle
6	chr17:20130600-20170000	Weak transcription	K562	blood
7	chr17:20130600-20170200	Weak transcription	Skeletal Muscle Female	skeletal muscle
8	chr17:20131800-20164400	Strong transcription	Monocytes-CD14+_RO01746	blood
9	chr17:20136000-20151400	Weak transcription	Brain Germinal Matrix	brain
10	chr17:20136000-20151400	Weak transcription	Esophagus	oesophagus
11	chr17:20136200-20157200	Weak transcription	Fetal Muscle Trunk	muscle
12	chr17:20136200-20161600	Weak transcription	Lung	lung
13	chr17:20136400-20151400	Weak transcription	Left Ventricle	heart
14	chr17:20136400-20160800	Weak transcription	Fetal Stomach	stomach
15	chr17:20136400-20161200	Weak transcription	Fetal Lung	lung
16	chr17:20136400-20209800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
17	chr17:20138200-20157400	Weak transcription	Gastric	stomach
18	chr17:20138400-20151400	Weak transcription	NHEK	skin
19	chr17:20138400-20165200	Weak transcription	Primary B cells from cord blood	blood
20	chr17:20139600-20151400	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
21	chr17:20139600-20152400	Weak transcription	Fetal Muscle Leg	muscle
22	chr17:20140400-20160800	Weak transcription	Rectal Smooth Muscle	rectum
23	chr17:20148200-20151400	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
24	chr17:20148200-20157400	Strong transcription	iPS-20b Cell Line	embryonic stem cell
25	chr17:20148200-20165000	Strong transcription	HUES64 Cell Line	embryonic stem cell
26	chr17:20148200-20165600	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
27	chr17:20148400-20151400	Enhancers	Primary T helper cells PMA-I stimulated	--
28	chr17:20148400-20151800	Strong transcription	H9 Cell Line	embryonic stem cell
29	chr17:20148400-20152000	Strong transcription	iPS-15b Cell Line	embryonic stem cell
30	chr17:20148400-20152200	Strong transcription	Rectal Mucosa Donor 31	rectum
31	chr17:20148400-20152400	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
32	chr17:20148400-20161200	Weak transcription	Muscle Satellite Cultured Cells	--
33	chr17:20148400-20161600	Strong transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
34	chr17:20148400-20161600	Strong transcription	HUES6 Cell Line	embryonic stem cell
35	chr17:20148600-20151600	Enhancers	Primary T helper cells fromperipheralblood	blood
36	chr17:20148600-20152000	Strong transcription	Duodenum Mucosa	Duodenum
37	chr17:20148600-20152400	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
38	chr17:20148600-20152600	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
39	chr17:20148600-20154400	Strong transcription	H1 Cell Line	embryonic stem cell
40	chr17:20148600-20155200	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
41	chr17:20148600-20157800	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
42	chr17:20148600-20160400	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
43	chr17:20148600-20161400	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
44	chr17:20148800-20153600	Strong transcription	Brain Hippocampus Middle	brain
45	chr17:20148800-20153800	Strong transcription	Sigmoid Colon	Sigmoid Colon
46	chr17:20148800-20154200	Strong transcription	iPS-18 Cell Line	embryonic stem cell
47	chr17:20148800-20157600	Strong transcription	Hela-S3	cervix
48	chr17:20149000-20152000	Strong transcription	Brain Cingulate Gyrus	brain
49	chr17:20149000-20152600	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
50	chr17:20149000-20154800	Strong transcription	Osteobl	bone

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