Variant report

Variant	rs2526463
Chromosome Location	chr17:20078297-20078298
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:0)
CpG islands
(count:0)
Chromatin interactive
region (count:9)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:9 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr17:20057951..20061755-chr17:20075070..20081270,10	MCF-7	breast:
2	chr17:20076421..20078642-chr17:20093873..20095852,2	K562	blood:
3	chr17:20077595..20080145-chr17:20083243..20085538,2	MCF-7	breast:
4	chr17:20058442..20060889-chr17:20076790..20079577,2	K562	blood:
5	chr17:20076826..20080402-chr17:20081688..20085232,6	K562	blood:
6	chr17:20075874..20079142-chr17:20086103..20089019,5	MCF-7	breast:
7	chr17:19881156..19883404-chr17:20076663..20078909,2	MCF-7	breast:
8	chr17:20058442..20060889-chr17:20076790..20079577,3	K562	blood:
9	chr17:20076969..20079576-chr17:20080631..20082312,2	MCF-7	breast:

No data

Variant related genes	Relation type
ENSG00000128487	Chromatin interaction
ENSG00000108599	Chromatin interaction
ENSG00000263494	Chromatin interaction

Extended variants
information (count: 124 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:111)

rs_ID	r²[population]
rs10491107	0.91[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs11204300	0.90[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs11204423	0.85[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs11653630	0.90[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs11653869	0.89[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs11654942	0.87[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs11657161	0.93[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs11658116	0.82[EUR][1000 genomes]
rs11867585	0.81[EUR][1000 genomes]
rs11868116	0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs11869258	0.86[EUR][1000 genomes]
rs11871651	0.81[EUR][1000 genomes]
rs12603372	0.91[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs12936443	0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs12938355	0.90[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs12942568	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12942627	0.88[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs12949481	0.89[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs12950564	0.87[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs1373146	0.86[EUR][1000 genomes]
rs16960697	0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1859407	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1974745	0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1992561	0.86[EUR][1000 genomes]
rs2013443	0.89[AFR][1000 genomes];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2042046	0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2107565	0.84[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2158472	0.96[AMR][1000 genomes];0.90[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs2189709	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2526459	0.81[AFR][1000 genomes];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2526465	0.96[AMR][1000 genomes];0.90[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs2526466	0.95[AMR][1000 genomes];0.90[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs2526476	0.90[AFR][1000 genomes];0.98[AMR][1000 genomes];0.94[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2526477	0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2526478	0.89[AFR][1000 genomes];0.98[AMR][1000 genomes];0.94[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2526481	0.95[AMR][1000 genomes];0.93[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2526482	0.87[AFR][1000 genomes];0.98[AMR][1000 genomes];0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2526486	0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2703770	0.85[AMR][1000 genomes];0.92[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2703771	0.90[AFR][1000 genomes];0.98[AMR][1000 genomes];0.94[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2703776	0.90[AFR][1000 genomes];0.97[AMR][1000 genomes];0.93[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2703777	0.90[AFR][1000 genomes];0.97[AMR][1000 genomes];0.93[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2703781	0.95[AMR][1000 genomes];0.92[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2703786	0.90[AMR][1000 genomes];0.92[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs2703788	0.93[AMR][1000 genomes];0.91[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs2703795	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2703800	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2703803	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2703805	0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2703807	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2703812	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2703814	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2703819	0.95[AMR][1000 genomes];0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs28603224	0.81[EUR][1000 genomes]
rs28637614	0.81[EUR][1000 genomes]
rs28666381	0.81[EUR][1000 genomes]
rs34290687	0.81[EUR][1000 genomes]
rs34401389	0.81[EUR][1000 genomes]
rs35003563	0.81[EUR][1000 genomes]
rs36077949	0.81[EUR][1000 genomes]
rs3850779	0.96[AMR][1000 genomes];0.89[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs3850780	0.91[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs4570919	0.81[EUR][1000 genomes]
rs4924803	0.81[EUR][1000 genomes]
rs4924806	0.81[EUR][1000 genomes]
rs4925079	0.81[EUR][1000 genomes]
rs4925081	0.80[EUR][1000 genomes]
rs4925085	0.81[EUR][1000 genomes]
rs4925086	0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs4925087	0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs4925090	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4925091	0.82[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs55705283	0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs57837691	0.82[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs62066865	0.81[AFR][1000 genomes];0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs62066870	1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs62067555	0.81[EUR][1000 genomes]
rs6587060	0.81[ASN][1000 genomes]
rs6587219	0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7207625	0.81[EUR][1000 genomes]
rs7208025	0.81[EUR][1000 genomes]
rs7208365	0.81[EUR][1000 genomes]
rs7208635	0.81[EUR][1000 genomes]
rs7212500	0.89[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7212571	0.83[EUR][1000 genomes]
rs7216599	0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs7216794	0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs7219615	0.88[AFR][1000 genomes];0.98[AMR][1000 genomes];0.93[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7219908	0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7222984	0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs7222987	0.82[AFR][1000 genomes];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7223305	0.81[EUR][1000 genomes]
rs733794	0.85[AFR][1000 genomes];0.93[AMR][1000 genomes];0.91[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs757494	0.85[AFR][1000 genomes];0.93[AMR][1000 genomes];0.92[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs757495	0.87[AFR][1000 genomes];0.93[AMR][1000 genomes];0.92[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs8066143	0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs8071274	0.80[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs8078716	0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs8080649	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs888423	0.81[EUR][1000 genomes]
rs918228	0.81[EUR][1000 genomes]
rs9893832	0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs9896411	0.81[EUR][1000 genomes]
rs9897653	0.81[EUR][1000 genomes]
rs9898080	0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs9901336	0.84[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs9901796	0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs9902032	0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs9907516	0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs9907788	0.81[EUR][1000 genomes]
rs9944451	0.81[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:13 , 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	nsv907871	chr17:19927699-20088492	Active TSS ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh Enhancers Bivalent Enhancer Weak transcription Flanking Active TSS Strong transcription Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
6	nsv482438	chr17:19934376-20089005	Enhancers Weak transcription Bivalent/Poised TSS ZNF genes & repeats Flanking Active TSS Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh Genic enhancers Strong transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
7	nsv833395	chr17:19969959-20124084	Genic enhancers Weak transcription Flanking Active TSS Enhancers ZNF genes & repeats Active TSS Bivalent Enhancer Strong transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
8	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
9	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
10	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
11	nsv833396	chr17:20029183-20150808	Enhancers Strong transcription Active TSS Weak transcription Genic enhancers ZNF genes & repeats Flanking Active TSS Bivalent Enhancer 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
12	nsv2003	chr17:20046306-20090653	Bivalent Enhancer Weak transcription Flanking Active TSS Enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Active TSS Genic enhancers Strong transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
13	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

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs2526463	SPECC1	Cis_1M	lymphoblastoid	RTeQTL
rs2526463	KRT16P3	cis	Esophagus Mucosa	GTEx

Chromatin state (count:54 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr17:20060400-20079400	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
2	chr17:20060800-20092200	Weak transcription	Fetal Intestine Small	intestine
3	chr17:20061600-20080000	Weak transcription	Sigmoid Colon	Sigmoid Colon
4	chr17:20062000-20090400	Weak transcription	Aorta	Aorta
5	chr17:20073200-20079000	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
6	chr17:20073200-20079200	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
7	chr17:20073200-20079400	Enhancers	Brain Substantia Nigra	brain
8	chr17:20073200-20080600	Enhancers	Brain Hippocampus Middle	brain
9	chr17:20073400-20079400	Enhancers	Brain Cingulate Gyrus	brain
10	chr17:20073400-20080400	Enhancers	HUES6 Cell Line	embryonic stem cell
11	chr17:20073800-20078600	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
12	chr17:20074800-20078400	Enhancers	HMEC	breast
13	chr17:20074800-20080400	Enhancers	H1 Cell Line	embryonic stem cell
14	chr17:20075000-20078600	Enhancers	Ovary	ovary
15	chr17:20075000-20080400	Enhancers	HUES48 Cell Line	embryonic stem cell
16	chr17:20075200-20078400	Enhancers	HSMMtube	muscle
17	chr17:20075200-20078600	Enhancers	NH-A	brain
18	chr17:20075200-20079200	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
19	chr17:20075200-20080200	Enhancers	HUES64 Cell Line	embryonic stem cell
20	chr17:20075200-20080400	Enhancers	iPS-15b Cell Line	embryonic stem cell
21	chr17:20075200-20080400	Enhancers	iPS-18 Cell Line	embryonic stem cell
22	chr17:20075200-20080800	Enhancers	iPS-20b Cell Line	embryonic stem cell
23	chr17:20075400-20078400	Enhancers	A549	lung
24	chr17:20075800-20090800	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
25	chr17:20076000-20080000	Weak transcription	Brain Germinal Matrix	brain
26	chr17:20076000-20087400	Weak transcription	Primary monocytes fromperipheralblood	blood
27	chr17:20076200-20078600	Enhancers	Muscle Satellite Cultured Cells	--
28	chr17:20076200-20079000	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
29	chr17:20076200-20079800	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
30	chr17:20076400-20078600	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
31	chr17:20076400-20078600	Enhancers	HSMM	muscle
32	chr17:20076600-20078600	Enhancers	HUVEC	blood vessel
33	chr17:20076800-20078600	Enhancers	Brain Dorsolateral Prefrontal Cortex	brain
34	chr17:20076800-20079200	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
35	chr17:20077000-20087600	Weak transcription	Monocytes-CD14+_RO01746	blood
36	chr17:20077600-20078400	Flanking Active TSS	Osteobl	bone
37	chr17:20077600-20078600	Flanking Active TSS	Hela-S3	cervix
38	chr17:20077600-20079200	Enhancers	Fetal Adrenal Gland	Adrenal Gland
39	chr17:20077800-20078600	Enhancers	iPS DF 6.9 Cell Line	embryonic stem cell
40	chr17:20077800-20078600	Enhancers	Brain Anterior Caudate	brain
41	chr17:20077800-20079200	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
42	chr17:20077800-20079200	Enhancers	K562	blood
43	chr17:20077800-20080400	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
44	chr17:20078000-20078400	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
45	chr17:20078000-20078600	Enhancers	Brain Inferior Temporal Lobe	brain
46	chr17:20078000-20078800	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
47	chr17:20078000-20079600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
48	chr17:20078000-20079600	Enhancers	Brain Angular Gyrus	brain
49	chr17:20078000-20079800	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
50	chr17:20078000-20080000	Weak transcription	H9 Cell Line	embryonic stem cell

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