Variant report

Variant	rs253961
Chromosome Location	chr5:115687715-115687716
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr5:115685651..115688638-chr5:115690874..115693480,2	K562	blood:

Extended variants
information (count: 70 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:64)

rs_ID	r²[population]
rs10037895	0.84[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs10051072	0.82[CEU][hapmap];0.83[YRI][hapmap]
rs10051302	0.82[CEU][hapmap]
rs10054441	0.86[AFR][1000 genomes];0.93[AMR][1000 genomes];0.93[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs10056823	0.87[CEU][hapmap];0.84[JPT][hapmap];0.85[TSI][hapmap]
rs10063312	0.82[CEU][hapmap];0.86[CHD][hapmap];0.88[TSI][hapmap]
rs10066081	0.82[CEU][hapmap];0.82[CHB][hapmap];0.83[YRI][hapmap]
rs10077013	0.82[CEU][hapmap]
rs1090078	0.82[AFR][1000 genomes];0.87[ASN][1000 genomes]
rs11241374	0.82[CEU][hapmap];0.86[CHD][hapmap];0.88[TSI][hapmap]
rs11241375	0.82[CEU][hapmap]
rs12109104	0.87[CEU][hapmap];0.86[CHD][hapmap];0.90[JPT][hapmap];0.85[TSI][hapmap]
rs12516272	0.84[AMR][1000 genomes];0.88[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs12657249	0.82[CEU][hapmap];0.86[CHD][hapmap];0.85[TSI][hapmap]
rs13159102	0.82[CEU][hapmap]
rs13161987	0.81[CEU][hapmap];0.84[JPT][hapmap]
rs1421846	0.85[AMR][1000 genomes];0.86[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs1421847	0.84[AMR][1000 genomes];0.88[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs149131	0.81[ASN][1000 genomes]
rs1508875	0.82[CEU][hapmap];0.86[CHD][hapmap];0.80[LWK][hapmap];0.83[TSI][hapmap];0.83[YRI][hapmap]
rs153580	0.81[ASN][1000 genomes]
rs153593	0.81[ASN][1000 genomes]
rs153594	0.81[ASN][1000 genomes]
rs1644268	0.80[ASN][1000 genomes]
rs1669135	0.86[CEU][hapmap];0.88[JPT][hapmap];0.83[YRI][hapmap]
rs1669136	0.87[CEU][hapmap];0.89[JPT][hapmap]
rs1677405	0.87[CEU][hapmap]
rs1677406	0.86[CEU][hapmap];0.90[JPT][hapmap]
rs1677415	0.97[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs173813	0.85[ASN][1000 genomes]
rs185263	0.83[CHB][hapmap];1.00[JPT][hapmap];0.84[ASN][1000 genomes]
rs187592	0.83[AMR][1000 genomes]
rs253950	0.87[CEU][hapmap];0.86[CHD][hapmap];0.90[JPT][hapmap];0.83[TSI][hapmap]
rs253959	0.87[CEU][hapmap];0.86[CHD][hapmap];0.83[TSI][hapmap]
rs254150	0.81[JPT][hapmap]
rs254151	0.89[CHD][hapmap];1.00[JPT][hapmap];0.84[ASN][1000 genomes]
rs254152	0.82[CHD][hapmap];0.81[JPT][hapmap]
rs254171	0.87[CEU][hapmap];0.89[JPT][hapmap]
rs254172	0.87[CEU][hapmap];0.89[JPT][hapmap]
rs254173	0.87[CEU][hapmap];0.90[JPT][hapmap]
rs254174	0.87[CEU][hapmap];0.89[CHD][hapmap];0.90[JPT][hapmap];0.85[TSI][hapmap]
rs27125	0.81[ASN][1000 genomes]
rs27368	0.94[AFR][1000 genomes];0.93[AMR][1000 genomes];0.93[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs28031	0.94[AFR][1000 genomes];0.90[AMR][1000 genomes];0.90[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6594952	0.90[YRI][hapmap]
rs6594967	0.81[AFR][1000 genomes];0.89[AMR][1000 genomes];0.92[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs6897517	0.86[AMR][1000 genomes];0.89[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs712561	0.82[CEU][hapmap]
rs712591	0.84[ASN][1000 genomes]
rs712601	0.85[ASN][1000 genomes]
rs7701723	0.80[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs7705679	0.88[AMR][1000 genomes];0.87[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs7708765	0.90[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs7722563	0.80[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs7723358	0.81[CEU][hapmap]
rs784479	0.87[CEU][hapmap];0.89[JPT][hapmap]
rs785367	0.84[CHD][hapmap];0.81[JPT][hapmap]
rs785373	0.84[ASN][1000 genomes]
rs785375	0.83[ASN][1000 genomes]
rs785377	0.85[ASN][1000 genomes]
rs803967	0.87[CEU][hapmap];0.90[JPT][hapmap]
rs809210	0.89[CEU][hapmap]
rs929752	0.95[AFR][1000 genomes];0.89[AMR][1000 genomes];0.88[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs9327000	0.90[AMR][1000 genomes];0.87[EUR][1000 genomes];0.82[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv34146	chr5:115315944-115729919	Flanking Active TSS Enhancers ZNF genes & repeats Weak transcription Strong transcription Active TSS 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	29 gene(s)	inside rSNPs	diseases
2	esv2755349	chr5:115384101-115733101	Active TSS Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Strong transcription 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	24 gene(s)	inside rSNPs	diseases
3	nsv882746	chr5:115566026-115704566	Weak transcription Strong transcription ZNF genes & repeats Flanking Bivalent TSS/Enh Enhancers Active TSS Flanking Active TSS Bivalent/Poised TSS Genic enhancers Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
4	nsv1017983	chr5:115578765-115713688	Weak transcription ZNF genes & repeats Active TSS Enhancers Strong transcription Flanking Active TSS Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
5	nsv869754	chr5:115634234-115696094	Weak transcription Enhancers Strong transcription ZNF genes & repeats Active TSS Flanking Active TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
6	nsv4968	chr5:115635771-115714856	Flanking Active TSS Strong transcription ZNF genes & repeats Weak transcription Bivalent/Poised TSS Enhancers Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs253961	COMMD10	cis	parietal	SCAN
rs253961	COMMD10	cis	lymphoblastoid	seeQTL
rs253961	COMMD10	cis	multi-tissue	Pritchard

Chromatin state (count:30 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:115649000-115692800	Weak transcription	Fetal Heart	heart
2	chr5:115680000-115693200	Weak transcription	Skeletal Muscle Male	skeletal muscle
3	chr5:115680600-115695800	Weak transcription	Ovary	ovary
4	chr5:115683200-115689000	Weak transcription	Primary T helper cells PMA-I stimulated	--
5	chr5:115684400-115694400	Weak transcription	Skeletal Muscle Female	skeletal muscle
6	chr5:115684400-115705800	Weak transcription	Primary T helper cells fromperipheralblood	blood
7	chr5:115684600-115690200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
8	chr5:115684800-115688600	Weak transcription	Primary B cells from peripheral blood	blood
9	chr5:115684800-115697800	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
10	chr5:115685000-115721400	Weak transcription	Primary T cells fromperipheralblood	blood
11	chr5:115685200-115689000	Weak transcription	Monocytes-CD14+_RO01746	blood
12	chr5:115685200-115690000	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
13	chr5:115685200-115696800	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
14	chr5:115686400-115692000	ZNF genes & repeats	Primary hematopoietic stem cells G-CSF-mobilized Male	--
15	chr5:115686400-115697000	Weak transcription	Fetal Lung	lung
16	chr5:115686600-115693800	Weak transcription	Fetal Muscle Trunk	muscle
17	chr5:115686600-115697400	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
18	chr5:115686800-115689200	Strong transcription	Left Ventricle	heart
19	chr5:115686800-115690000	Strong transcription	Primary T cells from cord blood	blood
20	chr5:115687000-115688000	ZNF genes & repeats	Primary hematopoietic stem cells	blood
21	chr5:115687000-115688800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
22	chr5:115687200-115688000	ZNF genes & repeats	Ganglion Eminence derived primary cultured neurospheres	brain
23	chr5:115687200-115693400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
24	chr5:115687200-115706400	Weak transcription	Liver	Liver
25	chr5:115687400-115687800	ZNF genes & repeats	Primary neutrophils fromperipheralblood	blood
26	chr5:115687600-115687800	ZNF genes & repeats	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
27	chr5:115687600-115687800	ZNF genes & repeats	Fetal Muscle Leg	muscle
28	chr5:115687600-115687800	ZNF genes & repeats	Pancreas	Pancrea
29	chr5:115687600-115688000	ZNF genes & repeats	Primary B cells from cord blood	blood
30	chr5:115687600-115688000	ZNF genes & repeats	Foreskin Melanocyte Primary Cells skin03	Skin

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