Variant report

Variant	rs4326625
Chromosome Location	chr1:152223996-152223997
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 152 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:148)

rs_ID	r²[population]
rs10749669	1.00[CEU][hapmap];0.86[CHB][hapmap];0.82[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];0.86[MEX][hapmap];1.00[TSI][hapmap];0.87[EUR][1000 genomes]
rs10749670	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs10788824	1.00[CEU][hapmap];0.86[CHB][hapmap];0.95[JPT][hapmap]
rs10788828	0.85[AMR][1000 genomes];0.90[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs10788831	0.81[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs10888466	0.82[EUR][1000 genomes]
rs10888467	0.87[EUR][1000 genomes]
rs10888468	0.81[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs10888470	1.00[CEU][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.86[MEX][hapmap];1.00[TSI][hapmap];0.87[AMR][1000 genomes];0.92[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs10888471	1.00[CEU][hapmap];1.00[CHB][hapmap];0.84[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.86[MEX][hapmap];0.93[TSI][hapmap];0.86[AMR][1000 genomes];0.91[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs10888473	1.00[CEU][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.86[MEX][hapmap];1.00[TSI][hapmap];0.89[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10888475	0.88[AMR][1000 genomes];0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs10888476	0.89[ASN][1000 genomes]
rs10888477	0.81[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs10888478	0.84[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs11204933	0.87[EUR][1000 genomes]
rs11204937	0.85[AMR][1000 genomes];0.89[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs11204938	0.85[AMR][1000 genomes];0.89[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs11204939	0.86[AMR][1000 genomes];0.92[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11204944	0.94[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11204945	0.82[ASN][1000 genomes]
rs11204947	1.00[CEU][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];1.00[TSI][hapmap];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11204948	1.00[CEU][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11204949	0.91[CHB][hapmap];0.91[CHD][hapmap];0.86[GIH][hapmap];0.95[MEX][hapmap];0.87[AMR][1000 genomes];0.80[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs11204951	0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11204952	0.88[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11204976	0.81[ASN][1000 genomes]
rs11204978	0.91[CEU][hapmap];0.91[CHB][hapmap]
rs11204980	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs11204981	1.00[CEU][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];0.86[TSI][hapmap]
rs11583524	1.00[CEU][hapmap];0.86[CHB][hapmap];0.95[JPT][hapmap]
rs11584340	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs11584427	0.92[CEU][hapmap];0.91[CHB][hapmap]
rs11586114	0.93[CEU][hapmap];0.91[CHB][hapmap]
rs11587676	0.93[CEU][hapmap];0.88[CHD][hapmap];0.95[MEX][hapmap]
rs11588174	1.00[CEU][hapmap];0.86[CHB][hapmap];0.95[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];0.86[MEX][hapmap];1.00[TSI][hapmap];0.87[EUR][1000 genomes]
rs11589532	0.81[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs11589587	0.80[AMR][1000 genomes]
rs12027899	0.82[ASN][1000 genomes]
rs12045492	0.82[ASN][1000 genomes]
rs12045496	0.82[ASN][1000 genomes]
rs12063165	0.87[EUR][1000 genomes]
rs12065368	0.82[ASN][1000 genomes]
rs12117911	0.82[EUR][1000 genomes]
rs12405278	0.91[CHB][hapmap];0.95[CHD][hapmap];0.81[GIH][hapmap];0.90[MEX][hapmap]
rs12405678	0.83[AMR][1000 genomes]
rs12409762	0.81[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs12409802	0.84[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs12567463	0.86[EUR][1000 genomes]
rs12730241	0.81[ASN][1000 genomes]
rs12748016	0.87[AMR][1000 genomes];0.92[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12749966	0.81[EUR][1000 genomes]
rs1353436	0.87[EUR][1000 genomes]
rs1390485	0.86[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs1390487	0.85[AMR][1000 genomes];0.90[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs1390488	1.00[CEU][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.86[MEX][hapmap];1.00[TSI][hapmap];0.86[AMR][1000 genomes];0.92[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1390490	1.00[CEU][hapmap];0.86[CHB][hapmap];0.95[JPT][hapmap]
rs1466757	0.88[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1496045	1.00[CEU][hapmap];0.86[CHB][hapmap];0.95[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];0.86[MEX][hapmap];1.00[TSI][hapmap]
rs1496050	0.82[EUR][1000 genomes]
rs1496051	0.82[EUR][1000 genomes]
rs1552992	0.86[EUR][1000 genomes]
rs1552993	0.87[EUR][1000 genomes]
rs1552995	0.87[EUR][1000 genomes]
rs1552996	0.87[EUR][1000 genomes]
rs1845791	0.86[AMR][1000 genomes];0.90[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1858480	1.00[CEU][hapmap];1.00[CHB][hapmap];0.84[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.81[MEX][hapmap];0.83[TSI][hapmap]
rs1858482	0.93[CEU][hapmap];0.91[CHB][hapmap];0.81[GIH][hapmap]
rs1969019	0.88[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2065955	0.93[CEU][hapmap]
rs2132418	0.88[AMR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2184950	0.81[ASN][1000 genomes]
rs2184951	0.81[ASN][1000 genomes]
rs2184953	0.93[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap]
rs2291770	0.81[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs2338430	0.88[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2338431	0.87[EUR][1000 genomes]
rs2338555	0.92[CEU][hapmap];0.88[CHB][hapmap]
rs2879174	0.88[AMR][1000 genomes];0.94[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs3120659	1.00[CEU][hapmap];1.00[CHB][hapmap];0.91[CHD][hapmap];0.95[GIH][hapmap];0.95[JPT][hapmap];0.85[MEX][hapmap];0.86[TSI][hapmap]
rs3126058	0.80[ASN][1000 genomes]
rs3126060	0.80[ASN][1000 genomes]
rs3126062	0.81[ASN][1000 genomes]
rs3126066	1.00[CEU][hapmap];1.00[CHB][hapmap];0.86[JPT][hapmap]
rs3126085	0.86[CEU][hapmap];0.91[CHB][hapmap];0.82[CHD][hapmap];0.81[GIH][hapmap]
rs3126088	0.93[CEU][hapmap];0.91[CHB][hapmap];0.82[CHD][hapmap];0.83[GIH][hapmap]
rs3126091	1.00[CEU][hapmap];1.00[CHB][hapmap];0.84[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.81[MEX][hapmap];0.90[TSI][hapmap]
rs36033453	0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs41266134	0.83[AMR][1000 genomes]
rs4256811	0.83[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs4341364	0.84[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs4361987	0.93[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4415568	0.81[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs4421596	0.81[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs4456097	0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4456098	0.87[EUR][1000 genomes]
rs4466659	0.84[ASN][1000 genomes]
rs4511111	0.87[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs4511113	0.89[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4845421	0.87[EUR][1000 genomes]
rs4845423	1.00[CEU][hapmap];0.86[CHB][hapmap];0.82[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];0.86[MEX][hapmap];1.00[TSI][hapmap]
rs4845426	0.84[AMR][1000 genomes];0.92[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4845428	0.90[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4845430	0.88[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4845431	0.88[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4845733	0.82[EUR][1000 genomes]
rs4845734	0.83[EUR][1000 genomes]
rs4845736	1.00[CEU][hapmap];0.86[CHB][hapmap];0.95[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];0.90[MEX][hapmap];1.00[TSI][hapmap];0.86[EUR][1000 genomes]
rs4845737	0.91[JPT][hapmap]
rs4845740	0.81[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs4845741	0.81[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs4845742	0.81[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs4845744	0.81[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs4845745	1.00[CEU][hapmap];0.82[CHB][hapmap];0.95[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];0.90[MEX][hapmap];1.00[TSI][hapmap];0.81[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs4845750	1.00[CEU][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.86[MEX][hapmap];1.00[TSI][hapmap];0.86[AMR][1000 genomes];0.92[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4845751	0.88[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4845752	0.90[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4845753	0.83[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs55957623	0.88[AMR][1000 genomes];0.82[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs6587647	0.85[AMR][1000 genomes];0.90[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs6587651	0.85[AMR][1000 genomes];0.90[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs6587652	0.85[AMR][1000 genomes];0.89[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs6587666	1.00[CEU][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];0.86[TSI][hapmap]
rs6662450	0.85[AMR][1000 genomes];0.89[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs6666382	1.00[CEU][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];1.00[TSI][hapmap];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6670891	0.85[ASN][1000 genomes]
rs6675889	0.88[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6676012	0.82[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs6678951	0.90[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6692010	0.93[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs72696963	0.80[AMR][1000 genomes]
rs72696969	0.83[AMR][1000 genomes]
rs74127901	0.89[AMR][1000 genomes];0.92[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7520249	0.85[AMR][1000 genomes];0.90[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7531094	0.87[EUR][1000 genomes]
rs7533529	0.87[EUR][1000 genomes]
rs7534716	0.84[AMR][1000 genomes];0.92[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7535078	0.89[AMR][1000 genomes];0.99[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7535536	0.85[AMR][1000 genomes];0.89[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs7536879	0.84[ASN][1000 genomes]
rs7537637	0.89[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7540844	0.84[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7543541	0.84[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7550106	1.00[CEU][hapmap];1.00[CHB][hapmap];0.84[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.86[MEX][hapmap];0.97[TSI][hapmap];0.83[AMR][1000 genomes];0.92[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs868303	0.81[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs868304	0.81[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs877776	1.00[CEU][hapmap];0.86[CHB][hapmap];0.82[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];0.97[TSI][hapmap];0.81[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs991231	0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1007097	chr1:151832796-152227977	Strong transcription Genic enhancers Flanking Active TSS Enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Weak transcription Bivalent/Poised TSS Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	196 gene(s)	inside rSNPs	diseases
2	nsv547853	chr1:152008671-152236760	Enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Weak transcription Bivalent/Poised TSS Active TSS Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3' Strong transcription Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	83 gene(s)	inside rSNPs	diseases
3	nsv1014095	chr1:152104486-152454591	Active TSS Weak transcription Enhancers ZNF genes & repeats Flanking Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Strong transcription Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	28 gene(s)	inside rSNPs	diseases
4	nsv946325	chr1:152221751-152240196	Weak transcription ZNF genes & repeats Enhancers Strong transcription Flanking Active TSS Active TSS	lncRNA	1 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs4326625	JTB	cis	parietal	SCAN

Chromatin state (count:13 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:152218600-152224600	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
2	chr1:152219400-152230200	Weak transcription	Ovary	ovary
3	chr1:152219800-152224400	Enhancers	NHEK	skin
4	chr1:152220600-152224000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
5	chr1:152220800-152230400	Weak transcription	Brain Angular Gyrus	brain
6	chr1:152222200-152225600	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
7	chr1:152222600-152224400	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
8	chr1:152223200-152224400	Weak transcription	Breast Myoepithelial Primary Cells	Breast
9	chr1:152223200-152230400	Weak transcription	Stomach Smooth Muscle	stomach
10	chr1:152223400-152228400	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
11	chr1:152223600-152225400	Enhancers	HMEC	breast
12	chr1:152223600-152229600	Weak transcription	Duodenum Smooth Muscle	Duodenum
13	chr1:152223800-152225200	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow

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