Variant report

Variant	rs10044838
Chromosome Location	chr5:35864590-35864591
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 47 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:39)

rs_ID	r²[population]
rs10044883	0.93[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs10058453	1.00[CHB][hapmap];1.00[JPT][hapmap];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10063445	1.00[CEU][hapmap];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs10074095	1.00[CEU][hapmap];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs10074127	1.00[CEU][hapmap];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs10941267	1.00[ASW][hapmap];1.00[CEU][hapmap];0.83[GIH][hapmap];0.96[LWK][hapmap];1.00[MEX][hapmap];0.85[MKK][hapmap];0.97[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs11567686	0.94[AMR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11567715	0.88[YRI][hapmap]
rs11567737	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[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][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]
rs1353250	0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1353252	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1389830	1.00[CEU][hapmap];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs1389831	0.97[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs1389832	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1494555	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]
rs1494556	1.00[CEU][hapmap];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs1494557	0.95[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs1494558	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.96[MEX][hapmap];1.00[TSI][hapmap];0.91[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1494560	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.96[MEX][hapmap];0.89[MKK][hapmap];1.00[TSI][hapmap];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1494561	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1494562	0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1862634	0.96[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs3777090	1.00[CEU][hapmap];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs6451226	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[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][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]
rs6451227	0.97[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs6451228	0.97[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs6451230	0.97[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs6451231	1.00[CEU][hapmap];0.96[MEX][hapmap];1.00[TSI][hapmap];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs6893142	1.00[CEU][hapmap];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs7701111	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7711202	1.00[CEU][hapmap];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs7711208	0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7711268	0.97[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs7716064	1.00[CEU][hapmap];0.83[GIH][hapmap];0.96[MEX][hapmap];0.97[TSI][hapmap];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs7720993	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9282751	0.88[YRI][hapmap]
rs9292616	1.00[CEU][hapmap];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs9292617	1.00[CEU][hapmap];0.83[GIH][hapmap];0.96[MEX][hapmap];1.00[TSI][hapmap];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs969129	0.96[AMR][1000 genomes];0.99[EUR][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	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	nsv880610	chr5:35850693-35866265	ZNF genes & repeats Weak transcription Flanking Active TSS Strong transcription Enhancers Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
3	nsv880517	chr5:35850693-35870814	Flanking Active TSS Enhancers Active TSS Transcr. at gene 5' and 3' Weak transcription Genic enhancers Strong transcription ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
4	nsv597813	chr5:35855264-35864590	Flanking Active TSS Active TSS Transcr. at gene 5' and 3' Weak transcription Enhancers Genic enhancers ZNF genes & repeats Strong transcription	TF binding region CpG island Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
5	nsv880591	chr5:35859863-35870588	Weak transcription Transcr. at gene 5' and 3' Active TSS Enhancers Genic enhancers Strong transcription ZNF genes & repeats Flanking Active TSS	TF binding region CpG island Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
6	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
7	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
8	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
rs10044838	WDR70	cis	parietal	SCAN
rs10044838	NIPBL	cis	parietal	SCAN

Chromatin state (count:38 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:35857400-35869200	Transcr. at gene 5' and 3'	Primary T helper cells PMA-I stimulated	--
2	chr5:35857800-35866600	Transcr. at gene 5' and 3'	Dnd41	blood
3	chr5:35858200-35864800	Transcr. at gene 5' and 3'	Primary T helper 17 cells PMA-I stimulated	--
4	chr5:35858800-35864800	Transcr. at gene 5' and 3'	Primary T helper memory cells from peripheral blood 2	blood
5	chr5:35858800-35865000	Transcr. at gene 5' and 3'	Primary T cells effector/memory enriched fromperipheralblood	blood
6	chr5:35858800-35865400	Transcr. at gene 5' and 3'	Primary T helper memory cells from peripheral blood 1	blood
7	chr5:35858800-35866600	Transcr. at gene 5' and 3'	Primary T cells fromperipheralblood	blood
8	chr5:35859000-35864800	Transcr. at gene 5' and 3'	Primary T cells from cord blood	blood
9	chr5:35859000-35864800	Transcr. at gene 5' and 3'	Primary T helper naive cells from peripheral blood	blood
10	chr5:35859000-35865000	Transcr. at gene 5' and 3'	Primary T helper cells fromperipheralblood	blood
11	chr5:35860000-35869000	Weak transcription	HMEC	breast
12	chr5:35860000-35876600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
13	chr5:35860400-35872800	Weak transcription	Spleen	Spleen
14	chr5:35860400-35883800	Weak transcription	Small Intestine	intestine
15	chr5:35860600-35864800	Transcr. at gene 5' and 3'	Primary T killer naive cells fromperipheralblood	blood
16	chr5:35860800-35864800	Transcr. at gene 5' and 3'	Primary T killer memory cells from peripheral blood	blood
17	chr5:35860800-35865000	Transcr. at gene 5' and 3'	Primary T helper naive cells fromperipheralblood	blood
18	chr5:35861200-35870400	Weak transcription	Rectal Mucosa Donor 29	rectum
19	chr5:35862400-35865200	Weak transcription	NH-A	brain
20	chr5:35862400-35870400	Weak transcription	Duodenum Mucosa	Duodenum
21	chr5:35862600-35864600	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
22	chr5:35862600-35868200	Strong transcription	Fetal Thymus	thymus
23	chr5:35862600-35868600	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
24	chr5:35862600-35876200	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
25	chr5:35863200-35864800	Transcr. at gene 5' and 3'	Primary T regulatory cells fromperipheralblood	blood
26	chr5:35863600-35864800	Strong transcription	Osteobl	bone
27	chr5:35863600-35868800	Weak transcription	Lung	lung
28	chr5:35863800-35864800	Active TSS	Primary mononuclear cells fromperipheralblood	Blood
29	chr5:35863800-35864800	Active TSS	Thymus	Thymus
30	chr5:35863800-35868400	Weak transcription	HSMM	muscle
31	chr5:35863800-35868800	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
32	chr5:35863800-35869000	Weak transcription	GM12878-XiMat	blood
33	chr5:35863800-35876200	Weak transcription	NHDF-Ad	bronchial
34	chr5:35864000-35864600	Active TSS	Primary Natural Killer cells fromperipheralblood	blood
35	chr5:35864200-35867800	Weak transcription	NHLF	lung
36	chr5:35864200-35869600	Weak transcription	Primary B cells from cord blood	blood
37	chr5:35864400-35864600	ZNF genes & repeats	Muscle Satellite Cultured Cells	--
38	chr5:35864400-35864800	ZNF genes & repeats	IMR90 fetal lung fibroblasts Cell Line	lung

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