Variant report

Variant	rs7175129
Chromosome Location	chr15:44030018-44030019
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 133 )
Associated
traits (count: 7 )

rSNPs within LD-proxies of this variant (count:119)

rs_ID	r²[population]
rs10163054	0.95[CHB][hapmap];0.95[JPT][hapmap];0.90[ASN][1000 genomes]
rs10438303	1.00[CHB][hapmap];1.00[JPT][hapmap];0.99[ASN][1000 genomes]
rs1053492	1.00[CEU][hapmap];0.91[EUR][1000 genomes]
rs11070407	0.94[ASN][1000 genomes]
rs11070408	1.00[CHB][hapmap];0.95[JPT][hapmap];1.00[ASN][1000 genomes]
rs11070410	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.83[AFR][1000 genomes];0.87[AMR][1000 genomes];0.94[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs11070412	0.81[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs11638972	1.00[CEU][hapmap];0.81[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs11852840	0.86[ASN][1000 genomes]
rs11856795	1.00[CHB][hapmap]
rs12101756	0.87[ASN][1000 genomes]
rs12437808	0.99[ASN][1000 genomes]
rs12440573	1.00[CHB][hapmap];0.95[JPT][hapmap]
rs12441127	1.00[CHB][hapmap];0.95[JPT][hapmap];0.99[ASN][1000 genomes]
rs12441861	1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[ASN][1000 genomes]
rs12441984	1.00[CHB][hapmap];0.90[JPT][hapmap]
rs12442129	0.86[ASN][1000 genomes]
rs12443102	0.89[CHB][hapmap];0.94[JPT][hapmap]
rs12702	1.00[CHB][hapmap];0.95[JPT][hapmap]
rs12908467	0.89[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs13380397	0.82[ASN][1000 genomes]
rs16950562	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs16963953	0.84[ASN][1000 genomes]
rs16965120	1.00[CHB][hapmap];0.95[JPT][hapmap]
rs16977724	1.00[CHB][hapmap];0.89[JPT][hapmap]
rs16977798	1.00[CHB][hapmap];0.89[JPT][hapmap]
rs1975364	0.81[EUR][1000 genomes]
rs2277531	1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[ASN][1000 genomes]
rs2411284	0.86[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs2412810	1.00[ASN][1000 genomes]
rs2412823	0.82[CEU][hapmap]
rs2439	0.95[CHB][hapmap];0.95[JPT][hapmap]
rs2447193	1.00[CHB][hapmap];0.95[JPT][hapmap]
rs2447196	0.95[CHB][hapmap];0.95[JPT][hapmap]
rs2447208	1.00[CHB][hapmap];0.95[JPT][hapmap]
rs2447210	0.83[EUR][1000 genomes]
rs2447215	0.83[EUR][1000 genomes]
rs2467402	0.95[CHB][hapmap];1.00[JPT][hapmap];0.98[ASN][1000 genomes]
rs2470120	0.82[EUR][1000 genomes]
rs2470121	1.00[CHB][hapmap];0.95[JPT][hapmap]
rs2470135	0.94[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs2614811	1.00[CHB][hapmap];0.95[JPT][hapmap]
rs2614819	1.00[CHB][hapmap];0.89[JPT][hapmap]
rs2788	1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[ASN][1000 genomes]
rs28366727	0.80[EUR][1000 genomes]
rs28433760	0.94[ASN][1000 genomes]
rs28495368	0.95[CHB][hapmap];0.95[JPT][hapmap]
rs28502289	0.97[ASN][1000 genomes]
rs28504496	0.99[ASN][1000 genomes]
rs28509275	1.00[CHB][hapmap];0.89[JPT][hapmap]
rs28513374	1.00[CHB][hapmap]
rs28542007	0.97[ASN][1000 genomes]
rs28578041	0.92[ASN][1000 genomes]
rs28578398	0.87[ASN][1000 genomes]
rs28595038	0.94[ASN][1000 genomes]
rs28636829	1.00[CHB][hapmap];0.95[JPT][hapmap]
rs28678901	0.85[ASN][1000 genomes]
rs28684672	1.00[CHB][hapmap];0.95[JPT][hapmap]
rs28718261	0.94[ASN][1000 genomes]
rs28891769	0.87[ASN][1000 genomes]
rs2920781	0.90[CHB][hapmap];0.95[JPT][hapmap]
rs2920782	0.83[EUR][1000 genomes]
rs2927071	0.95[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.81[EUR][1000 genomes]
rs2927072	1.00[CHB][hapmap];0.95[JPT][hapmap]
rs2927085	0.87[CEU][hapmap];0.91[AMR][1000 genomes]
rs2955969	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.87[EUR][1000 genomes]
rs2957636	0.83[EUR][1000 genomes]
rs2957639	0.81[EUR][1000 genomes]
rs3087657	1.00[CEU][hapmap];0.82[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs3099045	0.81[EUR][1000 genomes]
rs3101443	1.00[CHB][hapmap];0.95[JPT][hapmap]
rs35457073	0.98[ASN][1000 genomes]
rs35654783	0.99[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs35866764	0.81[EUR][1000 genomes]
rs3736180	1.00[CHB][hapmap];0.95[JPT][hapmap]
rs3742982	1.00[CHB][hapmap]
rs3759790	1.00[CHB][hapmap];0.89[JPT][hapmap]
rs3759791	0.95[CHB][hapmap];0.95[JPT][hapmap]
rs3816792	0.95[CHB][hapmap];0.89[JPT][hapmap]
rs3825783	1.00[CHB][hapmap];0.95[JPT][hapmap]
rs3862142	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs4332723	0.95[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4617832	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs4924720	0.91[AFR][1000 genomes];0.99[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs4924722	0.84[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs4997480	1.00[CHB][hapmap];1.00[JPT][hapmap];0.98[ASN][1000 genomes]
rs524908	1.00[CEU][hapmap];1.00[CHB][hapmap]
rs533143	1.00[CEU][hapmap];1.00[CHB][hapmap]
rs575082	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.87[EUR][1000 genomes]
rs60883262	0.86[ASN][1000 genomes]
rs62018947	0.97[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs62018952	0.83[AFR][1000 genomes];0.82[AMR][1000 genomes];0.92[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs663214	1.00[CEU][hapmap];0.84[EUR][1000 genomes]
rs667476	0.88[CEU][hapmap];0.95[CHB][hapmap]
rs686666	0.95[CEU][hapmap]
rs688009	0.95[CEU][hapmap];1.00[CHB][hapmap];0.90[JPT][hapmap]
rs693919	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.86[EUR][1000 genomes]
rs694461	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.88[EUR][1000 genomes]
rs7168158	0.88[ASN][1000 genomes]
rs7169322	1.00[CHB][hapmap];0.89[JPT][hapmap]
rs7169988	0.90[CHB][hapmap];0.95[JPT][hapmap]
rs7170167	0.84[ASN][1000 genomes]
rs7171750	1.00[CHB][hapmap];0.94[JPT][hapmap];0.99[ASN][1000 genomes]
rs7174208	1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[ASN][1000 genomes]
rs7174732	0.85[AMR][1000 genomes];0.88[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7175032	1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[ASN][1000 genomes]
rs7178343	0.96[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs7180818	0.81[AMR][1000 genomes];0.92[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs8023458	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs8023508	1.00[CHB][hapmap]
rs8023696	0.98[ASN][1000 genomes]
rs8029210	0.98[ASN][1000 genomes]
rs8030169	0.96[ASN][1000 genomes]
rs8032649	1.00[CHB][hapmap];0.89[JPT][hapmap]
rs8033846	0.90[AFR][1000 genomes];0.90[AMR][1000 genomes];0.85[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs8034451	0.80[EUR][1000 genomes]
rs8042868	1.00[CHB][hapmap];0.95[JPT][hapmap]
rs9944216	1.00[CHB][hapmap]
rs9989313	1.00[CHB][hapmap];0.89[JPT][hapmap]

Variant overlapped rSNPs/rCNVs (count:14 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv1846172	chr15:43632138-44116986	Bivalent Enhancer Weak transcription Genic enhancers Strong transcription Active TSS Enhancers Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	101 gene(s)	inside rSNPs	diseases
2	esv1846701	chr15:43759774-44116986	Strong transcription Weak transcription Active TSS Flanking Active TSS Enhancers Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	90 gene(s)	inside rSNPs	diseases
3	esv2758379	chr15:43823158-44148641	Strong transcription Enhancers Weak transcription Transcr. at gene 5' and 3' Flanking Active TSS Active TSS Bivalent/Poised TSS Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	84 gene(s)	inside rSNPs	diseases
4	esv2760028	chr15:43823158-44148641	Genic enhancers Enhancers Active TSS Transcr. at gene 5' and 3' Weak transcription Strong transcription Flanking Active TSS ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	84 gene(s)	inside rSNPs	diseases
5	nsv427960	chr15:43823158-44148641	Flanking Active TSS Active TSS Strong transcription Weak transcription Transcr. at gene 5' and 3' ZNF genes & repeats Enhancers Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	84 gene(s)	inside rSNPs	diseases
6	esv2757598	chr15:43831923-44058634	Enhancers Weak transcription Flanking Active TSS Active TSS Strong transcription ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	31 gene(s)	inside rSNPs	diseases
7	nsv904150	chr15:43836478-44040965	Flanking Active TSS Enhancers Weak transcription Active TSS Strong transcription ZNF genes & repeats Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	31 gene(s)	inside rSNPs	diseases
8	nsv904158	chr15:43852043-44053617	Strong transcription Flanking Active TSS Active TSS Enhancers Weak transcription ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	31 gene(s)	inside rSNPs	diseases
9	nsv1037786	chr15:43888926-44318587	Weak transcription Flanking Active TSS Strong transcription Transcr. at gene 5' and 3' Enhancers Active TSS Genic enhancers Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	90 gene(s)	inside rSNPs	diseases
10	nsv542370	chr15:43888926-44318587	Weak transcription Genic enhancers Flanking Active TSS Active TSS Enhancers Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	90 gene(s)	inside rSNPs	diseases
11	nsv431387	chr15:43929378-44862930	Weak transcription Strong transcription Active TSS ZNF genes & repeats Enhancers Flanking Active TSS Bivalent/Poised TSS Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	158 gene(s)	inside rSNPs	diseases
12	nsv976928	chr15:43948866-44040886	Active TSS Enhancers Flanking Active TSS Bivalent Enhancer Weak transcription Transcr. at gene 5' and 3' Strong transcription Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	28 gene(s)	inside rSNPs	diseases
13	nsv931051	chr15:43988761-44833518	Strong transcription Enhancers Weak transcription Active TSS Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	154 gene(s)	inside rSNPs	diseases
14	esv33661	chr15:44016519-44064420	Weak transcription Enhancers Strong transcription Flanking Active TSS Active TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	19 gene(s)	inside rSNPs	diseases

mRNA abundance (count:7)

SNP	Gene	Cis/trans	Tissue	Source
rs7175129	TGM5	cis	Lymphoblastoid	GTEx
rs7175129	ZSCAN29	cis	Thyroid	GTEx
rs7175129	STRCP1	cis	Thyroid	GTEx
rs7175129	ELL3	cis	multi-tissue	Pritchard
rs7175129	AC011330.5	cis	Artery Tibial	GTEx
rs7175129	AC011330.5	cis	Thyroid	GTEx
rs7175129	CKMT1A	cis	Esophagus Mucosa	GTEx

Chromatin state (count:3 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:44013400-44037400	Weak transcription	Fetal Intestine Small	intestine
2	chr15:44020000-44038000	Weak transcription	Brain Cingulate Gyrus	brain
3	chr15:44028000-44038000	Weak transcription	HSMMtube	muscle

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