Variant report

Variant	rs1494555
Chromosome Location	chr5:35871190-35871191
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 57 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:53)

rs_ID	r²[population]
rs10044838	1.00[CEU][hapmap];0.83[GIH][hapmap];0.96[MEX][hapmap];1.00[TSI][hapmap];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs10044883	0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs10058453	0.99[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs10063445	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10074095	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10074127	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10461959	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs10941267	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.96[MEX][hapmap];0.88[MKK][hapmap];0.97[TSI][hapmap];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11567686	0.84[AFR][1000 genomes];0.96[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs11567737	1.00[CEU][hapmap];0.83[GIH][hapmap];0.96[MEX][hapmap];1.00[TSI][hapmap];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs11567762	0.91[CHB][hapmap];1.00[CHD][hapmap];0.86[JPT][hapmap];1.00[ASN][1000 genomes]
rs12055232	0.84[ASN][1000 genomes]
rs12516343	0.81[ASN][1000 genomes]
rs12516866	0.87[CHB][hapmap];0.95[JPT][hapmap];0.84[ASN][1000 genomes]
rs1353250	1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs1353251	1.00[CHB][hapmap];0.98[CHD][hapmap];1.00[JPT][hapmap];0.99[ASN][1000 genomes]
rs1353252	1.00[CEU][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs1389830	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1389831	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1389832	1.00[CEU][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs1423657	0.95[ASN][1000 genomes]
rs1423658	0.95[ASN][1000 genomes]
rs1494556	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1494557	0.98[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1494558	1.00[CEU][hapmap];0.83[GIH][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.92[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs1494560	1.00[ASW][hapmap];1.00[CEU][hapmap];0.83[GIH][hapmap];0.94[LWK][hapmap];1.00[MEX][hapmap];0.84[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs1494561	1.00[CEU][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs1494562	0.82[AFR][1000 genomes];0.94[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs1494567	0.91[JPT][hapmap]
rs1862634	0.84[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2201408	0.87[ASN][1000 genomes]
rs2361396	0.91[ASN][1000 genomes]
rs3777090	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4141646	0.95[ASN][1000 genomes]
rs6451226	1.00[CEU][hapmap];0.83[GIH][hapmap];0.96[MEX][hapmap];1.00[TSI][hapmap];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs6451227	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6451228	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6451230	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6451231	1.00[ASW][hapmap];1.00[CEU][hapmap];0.96[GIH][hapmap];1.00[MEX][hapmap];0.89[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.84[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs6862142	0.82[CHB][hapmap];0.95[JPT][hapmap]
rs6870944	0.84[ASN][1000 genomes]
rs6893142	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7701111	0.97[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs7711202	1.00[CEU][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7711208	1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs7711268	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7716064	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.89[MKK][hapmap];0.97[TSI][hapmap];1.00[YRI][hapmap];0.84[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7720993	0.97[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs852249	0.86[JPT][hapmap]
rs852250	0.86[JPT][hapmap]
rs9292616	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9292617	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.89[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.84[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs969129	1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[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	nsv1022761	chr5:35775802-35902546	Enhancers Weak transcription Genic enhancers Flanking Active TSS Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Strong transcription Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
2	nsv471011	chr5:35861068-36003217	Weak transcription Bivalent Enhancer Enhancers Bivalent/Poised TSS Active TSS Genic enhancers Flanking Active TSS Strong transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
3	nsv830261	chr5:35863084-36018048	Weak transcription ZNF genes & repeats Active TSS Genic enhancers Flanking Active TSS Transcr. at gene 5' and 3' Enhancers Bivalent Enhancer Bivalent/Poised TSS Strong transcription Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
4	nsv597815	chr5:35864590-35871684	Weak transcription Transcr. at gene 5' and 3' Genic enhancers Enhancers ZNF genes & repeats Flanking Active TSS Strong transcription Active TSS	TF binding region	1 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs1494555	NIPBL	cis	parietal	SCAN
rs1494555	WDR70	cis	parietal	SCAN

Chromatin state (count:34 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:35860000-35876600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
2	chr5:35860400-35872800	Weak transcription	Spleen	Spleen
3	chr5:35860400-35883800	Weak transcription	Small Intestine	intestine
4	chr5:35862600-35876200	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
5	chr5:35863800-35876200	Weak transcription	NHDF-Ad	bronchial
6	chr5:35864600-35876600	Weak transcription	Muscle Satellite Cultured Cells	--
7	chr5:35866000-35873400	Genic enhancers	Primary T helper memory cells from peripheral blood 2	blood
8	chr5:35866200-35878400	Genic enhancers	Primary T killer naive cells fromperipheralblood	blood
9	chr5:35866400-35872400	Genic enhancers	Primary T helper cells fromperipheralblood	blood
10	chr5:35866600-35872200	Genic enhancers	Primary T helper memory cells from peripheral blood 1	blood
11	chr5:35866600-35878800	Genic enhancers	Primary T helper naive cells from peripheral blood	blood
12	chr5:35866600-35882000	Genic enhancers	Dnd41	blood
13	chr5:35867200-35872200	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
14	chr5:35867600-35878000	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
15	chr5:35867800-35876400	Strong transcription	NHLF	lung
16	chr5:35867800-35879800	Genic enhancers	Primary T helper naive cells fromperipheralblood	blood
17	chr5:35868200-35876000	Genic enhancers	Primary T killer memory cells from peripheral blood	blood
18	chr5:35869200-35872200	Genic enhancers	Primary T helper cells PMA-I stimulated	--
19	chr5:35869200-35872400	Genic enhancers	Primary T cells from cord blood	blood
20	chr5:35869200-35873400	Strong transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
21	chr5:35869200-35876600	Weak transcription	HMEC	breast
22	chr5:35869400-35876600	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
23	chr5:35869800-35875400	Weak transcription	Osteobl	bone
24	chr5:35870000-35876200	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
25	chr5:35870200-35873200	Strong transcription	Primary T helper 17 cells PMA-I stimulated	--
26	chr5:35870400-35875800	Weak transcription	Primary hematopoietic stem cells short term culture	blood
27	chr5:35870400-35876200	Weak transcription	Primary hematopoietic stem cells	blood
28	chr5:35870600-35878200	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
29	chr5:35870800-35871800	Genic enhancers	Thymus	Thymus
30	chr5:35871000-35873600	Strong transcription	Primary T cells fromperipheralblood	blood
31	chr5:35871000-35875400	Strong transcription	Fetal Thymus	thymus
32	chr5:35871000-35875400	Weak transcription	HSMM	muscle
33	chr5:35871000-35875800	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
34	chr5:35871000-35875800	Weak transcription	Lung	lung

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