Variant report

Variant	rs17139253
Chromosome Location	chr5:115576139-115576140
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 153 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:127)

rs_ID	r²[population]
rs1001014	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.85[AFR][1000 genomes];0.82[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs10051047	0.85[CHB][hapmap]
rs10059969	0.85[CHB][hapmap]
rs10059989	0.84[CHB][hapmap]
rs10068730	0.85[CHB][hapmap]
rs10069565	0.85[CHB][hapmap]
rs10071359	0.85[CHB][hapmap]
rs10073199	0.85[CHB][hapmap];0.90[CHD][hapmap]
rs10074746	0.85[CHB][hapmap]
rs10076543	0.85[CHB][hapmap]
rs10076661	0.84[CHB][hapmap]
rs10077113	0.91[CHB][hapmap]
rs10477550	0.85[CHB][hapmap]
rs10478286	0.85[CHB][hapmap];0.90[CHD][hapmap]
rs10478287	0.85[CHB][hapmap];0.90[CHD][hapmap]
rs10519443	0.85[CEU][hapmap];0.87[LWK][hapmap];0.89[MKK][hapmap];0.85[YRI][hapmap]
rs10519444	1.00[CHB][hapmap];1.00[CHD][hapmap];0.85[GIH][hapmap];0.92[JPT][hapmap]
rs11241379	1.00[CHB][hapmap];0.91[JPT][hapmap];0.91[ASN][1000 genomes]
rs11951682	0.84[CHB][hapmap]
rs11954350	0.85[CHB][hapmap]
rs11955144	0.85[CHB][hapmap]
rs11955906	0.85[CHB][hapmap]
rs11956927	0.82[ASW][hapmap];0.85[CEU][hapmap];0.84[LWK][hapmap];0.83[MKK][hapmap]
rs11957382	0.85[CHB][hapmap];0.90[CHD][hapmap]
rs11958276	0.82[CEU][hapmap];0.83[AFR][1000 genomes]
rs11958647	0.92[CHB][hapmap]
rs12522977	0.84[CHB][hapmap]
rs13362436	1.00[CHB][hapmap];1.00[CHD][hapmap];0.92[JPT][hapmap];0.91[ASN][1000 genomes]
rs1396484	0.85[CHB][hapmap];0.90[CHD][hapmap]
rs1396486	0.85[CHB][hapmap];0.90[CHD][hapmap]
rs1508870	0.84[CHB][hapmap]
rs1508873	0.85[CHB][hapmap];0.90[CHD][hapmap]
rs1543952	0.85[CHB][hapmap]
rs1567331	0.82[CEU][hapmap];1.00[CHB][hapmap];0.82[JPT][hapmap]
rs1567338	0.85[CHB][hapmap]
rs1567339	0.85[CHB][hapmap];0.90[CHD][hapmap]
rs17138834	0.85[CEU][hapmap];1.00[CHB][hapmap];0.90[CHD][hapmap];1.00[GIH][hapmap];0.83[JPT][hapmap];1.00[MEX][hapmap];0.85[TSI][hapmap]
rs17138841	0.85[CEU][hapmap];0.92[CHB][hapmap];0.90[CHD][hapmap];0.92[GIH][hapmap];0.83[JPT][hapmap];1.00[MEX][hapmap];0.83[MKK][hapmap];0.85[TSI][hapmap]
rs17138848	0.85[CEU][hapmap];1.00[CHB][hapmap];0.83[JPT][hapmap]
rs17138861	0.85[CHB][hapmap]
rs17138879	0.85[CEU][hapmap];1.00[CHB][hapmap];0.93[CHD][hapmap];1.00[GIH][hapmap];0.92[JPT][hapmap];1.00[MEX][hapmap];0.85[MKK][hapmap];0.92[TSI][hapmap]
rs17139198	0.85[CEU][hapmap];0.85[YRI][hapmap];0.90[AFR][1000 genomes]
rs17139333	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.97[LWK][hapmap];0.96[MKK][hapmap];1.00[TSI][hapmap];0.96[YRI][hapmap];0.83[AFR][1000 genomes];0.90[EUR][1000 genomes]
rs17139366	0.83[JPT][hapmap]
rs17139455	0.83[JPT][hapmap]
rs1876672	0.85[CHB][hapmap];0.90[CHD][hapmap]
rs1876676	0.85[CHB][hapmap]
rs2136213	0.85[CEU][hapmap];1.00[CHB][hapmap];0.92[JPT][hapmap]
rs2161321	0.85[CHB][hapmap];0.90[CHD][hapmap]
rs2174996	0.85[CHB][hapmap];0.90[CHD][hapmap]
rs2416434	0.85[CHB][hapmap];0.90[CHD][hapmap]
rs28558935	0.90[EUR][1000 genomes]
rs3087832	0.82[CEU][hapmap]
rs3946989	0.85[CEU][hapmap];1.00[CHB][hapmap];0.83[JPT][hapmap]
rs4260709	0.91[CHB][hapmap]
rs4301260	0.85[CHB][hapmap]
rs4484468	0.85[CHB][hapmap];0.90[CHD][hapmap]
rs4507525	0.83[CHB][hapmap]
rs4593303	0.85[CHB][hapmap];0.90[CHD][hapmap]
rs4921070	0.86[ASN][1000 genomes]
rs4921071	1.00[CEU][hapmap];0.88[CHB][hapmap];0.82[JPT][hapmap];1.00[YRI][hapmap];0.80[AFR][1000 genomes];0.86[AMR][1000 genomes];1.00[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs4921073	0.85[CEU][hapmap];0.85[MKK][hapmap]
rs4921076	0.85[CHB][hapmap]
rs4921078	0.85[CHB][hapmap];0.90[CHD][hapmap]
rs4921085	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.84[AFR][1000 genomes];0.82[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs56038821	0.88[EUR][1000 genomes]
rs56322212	0.86[ASN][1000 genomes]
rs56324813	0.86[ASN][1000 genomes]
rs56327109	0.81[AFR][1000 genomes]
rs56659474	0.82[AFR][1000 genomes];0.82[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs57484726	0.86[ASN][1000 genomes]
rs57907464	0.86[AMR][1000 genomes];1.00[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs57999994	0.83[AFR][1000 genomes]
rs58244621	0.90[AFR][1000 genomes]
rs58404617	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.92[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs58484280	0.85[EUR][1000 genomes]
rs58889682	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.92[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs58914490	0.85[EUR][1000 genomes]
rs59543587	0.87[AFR][1000 genomes];0.86[AMR][1000 genomes];0.92[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs59710673	0.83[AFR][1000 genomes];0.86[AMR][1000 genomes];1.00[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs60264648	0.86[ASN][1000 genomes]
rs6859442	0.85[CEU][hapmap]
rs6859670	0.85[CHB][hapmap]
rs6860662	0.85[CEU][hapmap];0.89[MKK][hapmap]
rs6874458	0.85[CHB][hapmap]
rs6874747	1.00[CHB][hapmap];0.91[JPT][hapmap];0.91[ASN][1000 genomes]
rs6876214	1.00[CEU][hapmap];1.00[CHB][hapmap];0.91[JPT][hapmap];0.81[YRI][hapmap];0.85[EUR][1000 genomes]
rs6878530	0.91[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.96[CHD][hapmap];1.00[GIH][hapmap];0.92[JPT][hapmap];0.95[LWK][hapmap];1.00[MEX][hapmap];0.98[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.80[AFR][1000 genomes];0.82[AMR][1000 genomes];0.92[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs6878871	0.85[CHB][hapmap];0.90[CHD][hapmap]
rs6879075	0.85[CHB][hapmap]
rs6887275	0.85[CHB][hapmap];0.90[CHD][hapmap]
rs6887852	0.85[CHB][hapmap];0.90[CHD][hapmap]
rs6888823	1.00[CEU][hapmap];0.92[JPT][hapmap];0.96[YRI][hapmap];0.82[AFR][1000 genomes];0.88[EUR][1000 genomes]
rs6890263	0.85[CEU][hapmap];1.00[CHB][hapmap];0.90[CHD][hapmap];1.00[GIH][hapmap];0.83[JPT][hapmap];1.00[MEX][hapmap]
rs6894471	0.85[CHB][hapmap];0.87[CHD][hapmap]
rs6898524	1.00[CEU][hapmap];1.00[CHB][hapmap];0.92[JPT][hapmap];0.85[EUR][1000 genomes]
rs73257219	0.82[AFR][1000 genomes];0.86[AMR][1000 genomes];0.92[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs73257238	0.87[AFR][1000 genomes];0.86[AMR][1000 genomes];0.92[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs73257269	0.82[AFR][1000 genomes]
rs73257286	0.91[ASN][1000 genomes]
rs73257302	0.91[ASN][1000 genomes]
rs73261018	0.84[AFR][1000 genomes];0.82[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs73780898	0.83[AFR][1000 genomes]
rs73780900	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7449449	0.85[CHB][hapmap]
rs7701174	0.85[CEU][hapmap]
rs7701736	1.00[CHB][hapmap];0.83[JPT][hapmap];0.86[ASN][1000 genomes]
rs7702152	1.00[CHB][hapmap]
rs7703978	0.85[CEU][hapmap];1.00[CHB][hapmap];0.83[JPT][hapmap]
rs7707191	0.85[CHB][hapmap]
rs7711861	1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];0.92[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7718026	0.83[AFR][1000 genomes];0.88[EUR][1000 genomes]
rs7718843	0.85[CHB][hapmap];0.90[CHD][hapmap]
rs7719318	0.85[CHB][hapmap]
rs7720518	0.84[CHB][hapmap]
rs7721510	0.85[CHB][hapmap]
rs7723648	0.85[CHB][hapmap]
rs7726794	1.00[CHB][hapmap];0.82[JPT][hapmap]
rs7728055	1.00[CHB][hapmap]
rs7730943	0.85[CHB][hapmap]
rs7733187	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.92[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.87[AFR][1000 genomes];0.86[AMR][1000 genomes];0.89[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7734614	0.85[CHB][hapmap]
rs7736793	0.91[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.92[JPT][hapmap];0.97[LWK][hapmap];1.00[MEX][hapmap];0.98[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.80[AFR][1000 genomes];0.86[AMR][1000 genomes];0.94[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs9326997	0.85[CHB][hapmap]
rs9686231	0.85[CHB][hapmap];0.90[CHD][hapmap]
rs9686686	0.85[CHB][hapmap]
rs9687350	0.85[CHB][hapmap]

Variant overlapped rSNPs/rCNVs (count:26 , 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	nsv1032531	chr5:115489694-115583800	Enhancers ZNF genes & repeats Weak transcription Strong transcription Active TSS Genic enhancers Bivalent/Poised TSS Flanking Active TSS	TF binding region Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
4	nsv882742	chr5:115489770-115584159	ZNF genes & repeats Enhancers Weak transcription Strong transcription Active TSS Flanking Active TSS Bivalent/Poised TSS Genic enhancers	TF binding region Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
5	nsv882743	chr5:115501792-115634127	Enhancers Weak transcription ZNF genes & repeats Strong transcription Flanking Active TSS Active TSS Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
6	nsv524812	chr5:115517238-115584159	Weak transcription Flanking Active TSS Enhancers ZNF genes & repeats Strong transcription Active TSS Bivalent/Poised TSS	TF binding region Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
7	nsv1019540	chr5:115526349-115610020	Weak transcription ZNF genes & repeats Enhancers Strong transcription Bivalent/Poised TSS Flanking Active TSS Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
8	esv2752058	chr5:115533065-115605198	Weak transcription Enhancers ZNF genes & repeats Bivalent/Poised TSS Flanking Active TSS Strong transcription Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
9	nsv1016585	chr5:115533065-115605455	Strong transcription Enhancers Weak transcription ZNF genes & repeats Active TSS Flanking Active TSS Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
10	nsv1032799	chr5:115533065-115609552	Weak transcription Strong transcription Flanking Active TSS ZNF genes & repeats Enhancers Bivalent/Poised TSS Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
11	nsv1016924	chr5:115533065-115610020	Weak transcription Enhancers Flanking Active TSS ZNF genes & repeats Strong transcription Bivalent/Poised TSS Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
12	nsv599481	chr5:115540041-115609552	Enhancers ZNF genes & repeats Weak transcription Strong transcription Flanking Active TSS Bivalent/Poised TSS Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
13	nsv1028663	chr5:115540586-115586834	Enhancers Weak transcription ZNF genes & repeats Strong transcription Flanking Active TSS Bivalent/Poised TSS Active TSS	TF binding region Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
14	nsv1024670	chr5:115540586-115615459	Weak transcription Enhancers ZNF genes & repeats Strong transcription Bivalent/Poised TSS Flanking Active TSS Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
15	nsv519321	chr5:115541563-115584159	Strong transcription Weak transcription Flanking Active TSS ZNF genes & repeats Bivalent/Poised TSS Enhancers Active TSS	TF binding region Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
16	nsv462401	chr5:115541563-115609552	Strong transcription Weak transcription ZNF genes & repeats Enhancers Bivalent/Poised TSS Flanking Active TSS Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
17	nsv599482	chr5:115541563-115609552	Enhancers Weak transcription Strong transcription ZNF genes & repeats Flanking Active TSS Bivalent/Poised TSS Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
18	nsv521050	chr5:115541563-115617297	Weak transcription Enhancers ZNF genes & repeats Strong transcription Flanking Active TSS Active TSS Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
19	nsv599483	chr5:115561128-115609552	Enhancers Weak transcription ZNF genes & repeats Bivalent/Poised TSS Strong transcription Flanking Active TSS	Chromatin interactive region	n/a	inside rSNPs	diseases
20	nsv882744	chr5:115561128-115609552	Enhancers Weak transcription Strong transcription ZNF genes & repeats Flanking Active TSS Bivalent/Poised TSS	Chromatin interactive region	n/a	inside rSNPs	diseases
21	nsv882745	chr5:115561128-115616288	ZNF genes & repeats Enhancers Weak transcription Flanking Active TSS Strong transcription Bivalent/Poised TSS	Chromatin interactive region	n/a	inside rSNPs	diseases
22	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
23	nsv882747	chr5:115566636-115662510	Weak transcription ZNF genes & repeats Strong transcription Active TSS Enhancers Flanking Active TSS Bivalent/Poised TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
24	esv34428	chr5:115575513-115626966	Weak transcription Enhancers Bivalent/Poised TSS ZNF genes & repeats Strong transcription Flanking Active TSS Active TSS	TF binding region CpG island Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
25	esv2753795	chr5:115576026-115626966	Enhancers ZNF genes & repeats Weak transcription Flanking Active TSS Strong transcription Bivalent/Poised TSS Active TSS	TF binding region CpG island Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
26	esv2755740	chr5:115576139-115633474	ZNF genes & repeats Strong transcription Weak transcription Enhancers Bivalent/Poised TSS Flanking Active TSS Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs17139253	COMMD10	cis	lymphoblastoid	seeQTL

Chromatin state (count:16 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:115551800-115576400	Weak transcription	Primary T helper cells fromperipheralblood	blood
2	chr5:115557400-115580800	Weak transcription	Primary T helper cells PMA-I stimulated	--
3	chr5:115557400-115583200	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
4	chr5:115559200-115578400	Weak transcription	Fetal Lung	lung
5	chr5:115560400-115581000	Weak transcription	Primary T cells from cord blood	blood
6	chr5:115560400-115610600	Weak transcription	Left Ventricle	heart
7	chr5:115561400-115580000	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
8	chr5:115561800-115586400	Weak transcription	Monocytes-CD14+_RO01746	blood
9	chr5:115562400-115589000	Weak transcription	Ovary	ovary
10	chr5:115568400-115578800	Weak transcription	Primary T helper naive cells from peripheral blood	blood
11	chr5:115569600-115577600	Weak transcription	Fetal Kidney	kidney
12	chr5:115569800-115582200	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
13	chr5:115572000-115580400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
14	chr5:115573000-115578800	Weak transcription	Primary B cells from cord blood	blood
15	chr5:115574000-115580000	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
16	chr5:115575000-115578200	Weak transcription	Colon Smooth Muscle	Colon

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