Variant report

Variant	rs4652499
Chromosome Location	chr1:180339190-180339191
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr1:180329129..180331822-chr1:180337969..180339999,2	K562	blood:
2	chr1:180338679..180340699-chr1:180366769..180368773,2	K562	blood:
3	chr1:180334858..180337165-chr1:180338509..180341951,3	K562	blood:
4	chr1:180334858..180336416-chr1:180338509..180341789,3	K562	blood:
5	chr1:180338174..180341966-chr1:180380791..180382462,3	MCF-7	breast:

Extended variants
information (count: 148 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:141)

rs_ID	r²[population]
rs10158367	0.81[ASN][1000 genomes]
rs10494527	0.85[CHB][hapmap];0.83[ASN][1000 genomes]
rs10737342	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[YRI][hapmap];0.87[AFR][1000 genomes];0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10753209	0.89[CHB][hapmap];0.83[ASN][1000 genomes]
rs10753211	0.91[CHB][hapmap];0.82[ASN][1000 genomes]
rs10753212	0.82[ASN][1000 genomes]
rs10798745	0.95[CHB][hapmap];0.84[ASN][1000 genomes]
rs10798746	0.91[CHB][hapmap]
rs10798752	0.82[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10798753	0.93[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10798754	1.00[ASN][1000 genomes]
rs10798756	0.83[ASN][1000 genomes]
rs10798757	0.83[ASN][1000 genomes]
rs10798759	0.90[CHB][hapmap];0.83[ASN][1000 genomes]
rs10798760	0.82[ASN][1000 genomes]
rs10798761	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.87[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10798762	0.90[CHB][hapmap];0.81[ASN][1000 genomes]
rs10798766	0.82[ASN][1000 genomes]
rs10798767	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.80[YRI][hapmap];0.81[AFR][1000 genomes];0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10798769	0.81[CHB][hapmap]
rs10913969	0.90[CHB][hapmap];0.87[JPT][hapmap];0.89[ASN][1000 genomes]
rs10913970	0.89[ASN][1000 genomes]
rs10913974	0.83[ASN][1000 genomes]
rs10913976	0.83[ASN][1000 genomes]
rs10913978	0.83[ASN][1000 genomes]
rs10913980	0.90[CHB][hapmap];0.83[ASN][1000 genomes]
rs10913981	0.91[CHB][hapmap];0.83[ASN][1000 genomes]
rs10913982	0.83[ASN][1000 genomes]
rs10913983	0.83[ASN][1000 genomes]
rs10913984	0.91[CHB][hapmap];0.83[ASN][1000 genomes]
rs10913985	0.90[CHB][hapmap];0.81[ASN][1000 genomes]
rs10913986	0.83[ASN][1000 genomes]
rs10913987	0.83[ASN][1000 genomes]
rs10913994	0.90[CHB][hapmap];0.87[JPT][hapmap];0.90[YRI][hapmap];0.85[AFR][1000 genomes];0.91[ASN][1000 genomes]
rs10913998	0.81[ASN][1000 genomes]
rs10914001	0.82[ASN][1000 genomes]
rs10914002	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[YRI][hapmap];0.87[AFR][1000 genomes];0.89[AMR][1000 genomes];0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10914005	0.81[CHB][hapmap]
rs10914007	0.83[JPT][hapmap];0.81[YRI][hapmap];0.89[ASN][1000 genomes]
rs10914014	0.80[ASN][1000 genomes]
rs10914017	0.89[CHB][hapmap]
rs10914018	0.85[CHB][hapmap]
rs10914023	0.81[JPT][hapmap]
rs11580793	0.91[CHB][hapmap]
rs11799870	0.81[CHB][hapmap]
rs12024156	0.83[ASN][1000 genomes]
rs12034217	0.91[CHB][hapmap];0.83[ASN][1000 genomes]
rs12034669	0.91[ASN][1000 genomes]
rs12039933	0.90[CHB][hapmap];0.87[JPT][hapmap];0.91[ASN][1000 genomes]
rs12045123	0.91[ASN][1000 genomes]
rs12045636	0.95[ASN][1000 genomes]
rs12085808	0.85[AFR][1000 genomes];0.91[ASN][1000 genomes]
rs12091722	0.90[CHB][hapmap];1.00[YRI][hapmap];0.92[AFR][1000 genomes];0.80[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs12122338	0.82[ASN][1000 genomes]
rs12127886	0.82[ASN][1000 genomes]
rs12128560	0.82[ASN][1000 genomes]
rs12129511	0.82[ASN][1000 genomes]
rs12129784	0.83[ASN][1000 genomes]
rs12131071	0.82[ASN][1000 genomes]
rs12132837	0.80[ASN][1000 genomes]
rs12135463	0.82[ASN][1000 genomes]
rs12141848	0.81[CHB][hapmap]
rs12142124	0.83[AFR][1000 genomes];0.89[AMR][1000 genomes];0.93[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12402815	0.85[AFR][1000 genomes];0.93[ASN][1000 genomes]
rs12403665	0.93[ASN][1000 genomes]
rs12404209	0.90[CHB][hapmap];0.87[JPT][hapmap];0.89[ASN][1000 genomes]
rs12405902	0.90[CHB][hapmap];0.87[JPT][hapmap];1.00[YRI][hapmap];0.93[AFR][1000 genomes];0.80[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs12407122	0.85[AFR][1000 genomes];0.91[ASN][1000 genomes]
rs12565492	0.85[CHB][hapmap]
rs12691484	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[YRI][hapmap];0.91[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12730889	0.91[CHB][hapmap];0.82[ASN][1000 genomes]
rs1341924	0.90[CHB][hapmap];0.90[JPT][hapmap];0.88[YRI][hapmap];0.89[AFR][1000 genomes];0.93[ASN][1000 genomes]
rs1416821	0.80[CHB][hapmap]
rs1418102	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[YRI][hapmap];0.89[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1538620	0.90[CHB][hapmap]
rs1890731	0.82[ASN][1000 genomes]
rs1925339	0.90[CHB][hapmap]
rs2296378	0.90[CHB][hapmap]
rs2794962	0.81[CHB][hapmap]
rs2794978	0.90[EUR][1000 genomes]
rs28506072	0.89[ASN][1000 genomes]
rs2877399	0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2877415	0.90[CHB][hapmap];0.87[JPT][hapmap];0.90[YRI][hapmap];0.82[AFR][1000 genomes];0.91[ASN][1000 genomes]
rs3737584	0.90[CHB][hapmap];0.85[JPT][hapmap];0.86[ASN][1000 genomes]
rs3806300	0.84[CHB][hapmap];0.81[JPT][hapmap];0.84[ASN][1000 genomes]
rs3923222	0.82[ASN][1000 genomes]
rs4058058	0.90[CHB][hapmap]
rs4076403	0.90[CHB][hapmap];0.83[ASN][1000 genomes]
rs4142992	0.82[ASN][1000 genomes]
rs4418555	0.80[ASN][1000 genomes]
rs4420052	0.83[ASN][1000 genomes]
rs4421553	0.91[CHB][hapmap];0.83[ASN][1000 genomes]
rs4424469	0.89[CEU][hapmap];0.88[CHB][hapmap];0.91[JPT][hapmap];0.89[YRI][hapmap];0.89[AFR][1000 genomes];0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4436345	0.88[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4442335	0.84[CHB][hapmap];0.81[ASN][1000 genomes]
rs4483365	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4543756	0.90[CHB][hapmap];0.90[JPT][hapmap];0.93[ASN][1000 genomes]
rs4562579	0.81[AFR][1000 genomes];0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4578179	0.90[CHB][hapmap];0.83[ASN][1000 genomes]
rs4593778	0.87[AFR][1000 genomes];0.89[AMR][1000 genomes];0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4607831	0.82[ASN][1000 genomes]
rs4634864	0.83[ASN][1000 genomes]
rs4642852	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs4651064	0.91[CHB][hapmap];0.82[ASN][1000 genomes]
rs4652493	0.86[CHB][hapmap]
rs4652495	0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4652496	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[YRI][hapmap];0.92[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4652498	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4652505	0.90[CHB][hapmap];0.81[ASN][1000 genomes]
rs55874160	1.00[ASN][1000 genomes]
rs60286873	0.91[ASN][1000 genomes]
rs6425625	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6425634	0.90[CHB][hapmap];0.87[JPT][hapmap];0.93[ASN][1000 genomes]
rs6657492	0.88[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6658310	1.00[CEU][hapmap];0.95[EUR][1000 genomes]
rs6659513	1.00[ASN][1000 genomes]
rs6661208	0.95[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs6665719	0.91[CHB][hapmap]
rs6670544	0.91[CHB][hapmap];0.82[ASN][1000 genomes]
rs6674244	0.82[ASN][1000 genomes]
rs6678216	0.82[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6680368	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[AFR][1000 genomes];0.91[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6697924	0.82[CHB][hapmap]
rs6700986	0.82[ASN][1000 genomes]
rs72720915	0.83[ASN][1000 genomes]
rs72720917	0.83[ASN][1000 genomes]
rs7523003	0.81[ASN][1000 genomes]
rs7523857	0.82[ASN][1000 genomes]
rs7526189	0.89[AFR][1000 genomes];0.80[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs7528650	0.90[CHB][hapmap];0.82[ASN][1000 genomes]
rs7532806	0.88[CHB][hapmap];0.82[JPT][hapmap];0.83[ASN][1000 genomes]
rs7538219	0.81[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7538303	0.82[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7539910	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.90[YRI][hapmap];0.89[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7544585	1.00[ASN][1000 genomes]
rs822706	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9425497	0.93[EUR][1000 genomes]
rs9425878	0.89[EUR][1000 genomes]
rs9425880	0.93[EUR][1000 genomes]
rs9701037	0.84[ASN][1000 genomes]
rs9729819	0.96[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:7 , 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	nsv527918	chr1:180279710-180443808	Weak transcription Enhancers Genic enhancers Strong transcription ZNF genes & repeats Flanking Active TSS Bivalent Enhancer Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	6 gene(s)	inside rSNPs	diseases
4	nsv1013716	chr1:180287338-180477072	Active TSS Enhancers Weak transcription Strong transcription ZNF genes & repeats Bivalent Enhancer Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA	39 gene(s)	inside rSNPs	diseases
5	nsv535221	chr1:180287338-180477072	Weak transcription Enhancers Active TSS Flanking Active TSS Strong transcription ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA	39 gene(s)	inside rSNPs	diseases
6	esv2762200	chr1:180300936-180493841	ZNF genes & repeats Strong transcription Flanking Active TSS Enhancers Weak transcription Active TSS Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA	40 gene(s)	inside rSNPs	diseases
7	nsv1003359	chr1:180300936-180727561	Enhancers Strong transcription Active TSS Weak transcription Flanking Active TSS ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA	48 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:27 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:180309600-180345400	Weak transcription	Primary T cells from cord blood	blood
2	chr1:180310000-180348200	Weak transcription	Primary B cells from cord blood	blood
3	chr1:180314000-180345800	Weak transcription	Primary hematopoietic stem cells short term culture	blood
4	chr1:180324000-180341600	Weak transcription	Fetal Intestine Small	intestine
5	chr1:180330200-180345400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
6	chr1:180330600-180349000	Weak transcription	HMEC	breast
7	chr1:180333000-180356200	Weak transcription	Ovary	ovary
8	chr1:180333600-180343400	Weak transcription	iPS-15b Cell Line	embryonic stem cell
9	chr1:180334200-180348000	Weak transcription	Primary T helper cells fromperipheralblood	blood
10	chr1:180335800-180343200	Weak transcription	Fetal Lung	lung
11	chr1:180335800-180349000	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
12	chr1:180336200-180340400	Weak transcription	HSMM	muscle
13	chr1:180336200-180340600	Weak transcription	Osteobl	bone
14	chr1:180336200-180344400	Weak transcription	Psoas Muscle	Psoas
15	chr1:180336200-180347600	Weak transcription	NHDF-Ad	bronchial
16	chr1:180337000-180349000	Weak transcription	Esophagus	oesophagus
17	chr1:180337800-180348000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
18	chr1:180338000-180342200	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
19	chr1:180338400-180345000	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
20	chr1:180338400-180348400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
21	chr1:180338600-180347800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
22	chr1:180338600-180347800	Weak transcription	Aorta	Aorta
23	chr1:180338600-180348000	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
24	chr1:180338600-180349000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
25	chr1:180338600-180349000	Weak transcription	Left Ventricle	heart
26	chr1:180339000-180339600	Enhancers	Pancreatic Islets	Pancreatic Islet
27	chr1:180339000-180342600	Weak transcription	HUES64 Cell Line	embryonic stem cell

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