Variant report

Variant	rs4642852
Chromosome Location	chr1:180356025-180356026
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr1:180353732..180356120-chr1:180367249..180368760,2	MCF-7	breast:
2	chr1:180354979..180356991-chr1:180360915..180363474,2	MCF-7	breast:

Extended variants
information (count: 145 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:137)

rs_ID	r²[population]
rs10158367	0.81[ASN][1000 genomes]
rs10494527	0.85[CHB][hapmap];0.82[CHD][hapmap];0.83[ASN][1000 genomes]
rs10737342	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs10753209	0.89[CHB][hapmap];0.83[ASN][1000 genomes]
rs10753211	0.90[CHB][hapmap];0.82[ASN][1000 genomes]
rs10753212	0.82[ASN][1000 genomes]
rs10753217	0.83[CEU][hapmap]
rs10798745	0.95[CEU][hapmap];0.95[CHB][hapmap];0.94[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs10798746	0.90[CHB][hapmap]
rs10798752	1.00[ASN][1000 genomes]
rs10798753	1.00[ASN][1000 genomes]
rs10798754	0.96[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10798756	0.83[ASN][1000 genomes]
rs10798757	0.83[ASN][1000 genomes]
rs10798759	0.90[CHB][hapmap];0.82[CHD][hapmap];0.83[ASN][1000 genomes]
rs10798760	0.82[ASN][1000 genomes]
rs10798761	0.95[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs10798762	0.90[CHB][hapmap];0.82[CHD][hapmap];0.81[ASN][1000 genomes]
rs10798766	0.82[ASN][1000 genomes]
rs10798767	1.00[CHB][hapmap];1.00[JPT][hapmap];0.99[ASN][1000 genomes]
rs10798769	0.82[CHB][hapmap]
rs10913969	0.90[CHB][hapmap];0.95[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];0.81[CHD][hapmap];0.83[ASN][1000 genomes]
rs10913981	0.90[CHB][hapmap];0.83[ASN][1000 genomes]
rs10913982	0.83[ASN][1000 genomes]
rs10913983	0.83[ASN][1000 genomes]
rs10913984	0.90[CHB][hapmap];0.83[ASN][1000 genomes]
rs10913985	0.90[CHB][hapmap];0.82[CHD][hapmap];0.81[ASN][1000 genomes]
rs10913986	0.83[ASN][1000 genomes]
rs10913987	0.83[ASN][1000 genomes]
rs10913994	0.90[CHB][hapmap];0.95[JPT][hapmap];0.91[ASN][1000 genomes]
rs10913998	0.81[ASN][1000 genomes]
rs10914001	0.82[ASN][1000 genomes]
rs10914002	1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[JPT][hapmap];0.99[ASN][1000 genomes]
rs10914005	0.82[CHB][hapmap]
rs10914007	0.94[JPT][hapmap];0.89[ASN][1000 genomes]
rs10914014	0.80[ASN][1000 genomes]
rs10914017	0.89[CHB][hapmap]
rs10914018	0.86[CHB][hapmap]
rs10914023	0.80[CHD][hapmap];0.81[JPT][hapmap]
rs11580793	0.90[CHB][hapmap]
rs12024156	0.83[ASN][1000 genomes]
rs12034217	0.90[CHB][hapmap];0.83[ASN][1000 genomes]
rs12034669	0.91[ASN][1000 genomes]
rs12039331	0.85[JPT][hapmap]
rs12039933	0.90[CHB][hapmap];0.95[JPT][hapmap];0.91[ASN][1000 genomes]
rs12045123	0.91[ASN][1000 genomes]
rs12045636	0.94[AFR][1000 genomes];0.98[AMR][1000 genomes];0.93[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12085808	0.91[ASN][1000 genomes]
rs12091722	0.90[CHB][hapmap];0.86[JPT][hapmap];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]
rs12142124	0.99[ASN][1000 genomes]
rs12402815	0.93[ASN][1000 genomes]
rs12403665	0.93[ASN][1000 genomes]
rs12404209	0.90[CHB][hapmap];0.95[JPT][hapmap];0.89[ASN][1000 genomes]
rs12405902	0.90[CHB][hapmap];0.95[JPT][hapmap];0.93[ASN][1000 genomes]
rs12407122	0.91[ASN][1000 genomes]
rs12565492	0.86[CHB][hapmap]
rs12691484	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs12730889	0.90[CHB][hapmap];0.82[ASN][1000 genomes]
rs1341924	0.90[CHB][hapmap];0.92[CHD][hapmap];0.95[JPT][hapmap];0.93[ASN][1000 genomes]
rs1418102	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs1538620	0.90[CHB][hapmap]
rs1890731	0.82[ASN][1000 genomes]
rs1925339	0.96[CEU][hapmap];0.90[CHB][hapmap];0.91[EUR][1000 genomes]
rs2296378	0.90[CHB][hapmap]
rs2764463	0.91[EUR][1000 genomes]
rs2794962	0.85[CHB][hapmap]
rs28506072	0.89[ASN][1000 genomes]
rs2877399	1.00[ASN][1000 genomes]
rs2877415	0.90[CHB][hapmap];0.95[JPT][hapmap];0.91[ASN][1000 genomes]
rs3737584	0.90[CHB][hapmap];0.90[CHD][hapmap];0.90[JPT][hapmap];0.86[ASN][1000 genomes]
rs3806300	0.85[CHB][hapmap];0.82[CHD][hapmap];0.85[JPT][hapmap];0.84[ASN][1000 genomes]
rs3923222	0.82[ASN][1000 genomes]
rs4058058	0.90[CHB][hapmap]
rs4076403	0.90[CHB][hapmap];0.82[CHD][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	0.90[CHB][hapmap];0.83[ASN][1000 genomes]
rs4424469	0.87[CHB][hapmap];0.90[JPT][hapmap];1.00[ASN][1000 genomes]
rs4436345	1.00[ASN][1000 genomes]
rs4442335	0.85[CHB][hapmap];0.80[CHD][hapmap];0.81[ASN][1000 genomes]
rs4483365	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs4543756	0.90[CHB][hapmap];0.92[CHD][hapmap];0.95[JPT][hapmap];0.93[ASN][1000 genomes]
rs4562579	0.99[ASN][1000 genomes]
rs4578179	0.81[CEU][hapmap];0.90[CHB][hapmap];0.82[CHD][hapmap];0.83[ASN][1000 genomes]
rs4593778	0.99[ASN][1000 genomes]
rs4607831	0.82[ASN][1000 genomes]
rs4634864	0.83[ASN][1000 genomes]
rs4651064	0.90[CHB][hapmap];0.82[ASN][1000 genomes]
rs4652493	0.85[CHB][hapmap]
rs4652495	0.99[ASN][1000 genomes]
rs4652496	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs4652498	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs4652499	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs4652505	0.90[CHB][hapmap];0.81[ASN][1000 genomes]
rs55874160	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs60286873	0.91[ASN][1000 genomes]
rs6425625	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs6425634	0.90[CHB][hapmap];0.95[JPT][hapmap];0.93[ASN][1000 genomes]
rs6657492	0.99[ASN][1000 genomes]
rs6659513	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6661208	1.00[ASW][hapmap];1.00[CEU][hapmap];0.95[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.95[LWK][hapmap];0.95[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6665719	0.90[CHB][hapmap]
rs6670544	0.90[CHB][hapmap];0.82[ASN][1000 genomes]
rs6674244	0.82[ASN][1000 genomes]
rs6678216	1.00[ASN][1000 genomes]
rs6680368	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.99[ASN][1000 genomes]
rs6697924	0.82[CHB][hapmap]
rs6699076	0.83[JPT][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	0.93[ASN][1000 genomes]
rs7528650	0.90[CHB][hapmap];0.82[ASN][1000 genomes]
rs7532806	0.88[CHB][hapmap];0.81[JPT][hapmap];0.83[ASN][1000 genomes]
rs7538219	1.00[ASN][1000 genomes]
rs7538303	1.00[ASN][1000 genomes]
rs7539910	1.00[CHB][hapmap];0.95[JPT][hapmap];0.96[ASN][1000 genomes]
rs7544585	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs822706	1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[ASN][1000 genomes]
rs9701037	0.84[ASN][1000 genomes]
rs9729819	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:8 , 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
8	nsv1009742	chr1:180342203-180385459	Weak transcription Enhancers Strong transcription ZNF genes & repeats Genic enhancers Flanking Active TSS Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs4642852	TOR1AIP1	cis	cerebellum	SCAN
rs4642852	ACBD6	cis	parietal	SCAN

Chromatin state (count:33 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:180333000-180356200	Weak transcription	Ovary	ovary
2	chr1:180341200-180401400	Weak transcription	Osteobl	bone
3	chr1:180343600-180356400	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
4	chr1:180348200-180382600	Weak transcription	Pancreas	Pancrea
5	chr1:180349400-180356600	Weak transcription	Aorta	Aorta
6	chr1:180349400-180364200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
7	chr1:180349400-180407000	Weak transcription	Esophagus	oesophagus
8	chr1:180351600-180378400	Weak transcription	HSMM	muscle
9	chr1:180352400-180381400	Weak transcription	Hela-S3	cervix
10	chr1:180352800-180356400	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
11	chr1:180352800-180399400	Weak transcription	Fetal Thymus	thymus
12	chr1:180353800-180357000	ZNF genes & repeats	Primary hematopoietic stem cells G-CSF-mobilized Male	--
13	chr1:180354200-180364200	Weak transcription	NH-A	brain
14	chr1:180354600-180374000	Weak transcription	HUES48 Cell Line	embryonic stem cell
15	chr1:180354800-180356400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
16	chr1:180354800-180358600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
17	chr1:180354800-180386600	Weak transcription	Primary T helper naive cells from peripheral blood	blood
18	chr1:180355000-180356200	Weak transcription	Primary B cells from cord blood	blood
19	chr1:180355000-180356200	Weak transcription	A549	lung
20	chr1:180355000-180360600	Weak transcription	Monocytes-CD14+_RO01746	blood
21	chr1:180355200-180356200	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
22	chr1:180355200-180356400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
23	chr1:180355200-180356400	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
24	chr1:180355200-180357000	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
25	chr1:180355200-180364800	Weak transcription	K562	blood
26	chr1:180355200-180402600	Weak transcription	HMEC	breast
27	chr1:180355400-180356200	Weak transcription	Fetal Intestine Large	intestine
28	chr1:180355400-180361200	Weak transcription	Small Intestine	intestine
29	chr1:180355400-180378800	Weak transcription	Sigmoid Colon	Sigmoid Colon
30	chr1:180355600-180356800	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
31	chr1:180355600-180378400	Weak transcription	Placenta	Placenta
32	chr1:180355600-180390800	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
33	chr1:180356000-180357000	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin

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