Variant report

Variant	rs10520415
Chromosome Location	chr2:86498738-86498739
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 95 )
Associated
traits (count: 9 )

rSNPs within LD-proxies of this variant (count:77)

rs_ID	r²[population]
rs10186289	0.92[CEU][hapmap];0.83[CHB][hapmap];0.85[EUR][1000 genomes]
rs10189492	1.00[CEU][hapmap];0.82[CHB][hapmap];1.00[JPT][hapmap];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs10200186	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10200526	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10200619	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[YRI][hapmap];0.86[AFR][1000 genomes];0.94[ASN][1000 genomes]
rs10201457	0.81[CHB][hapmap];0.86[CHD][hapmap];1.00[JPT][hapmap]
rs11127026	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];0.87[LWK][hapmap];1.00[MEX][hapmap];0.86[MKK][hapmap];1.00[TSI][hapmap];0.92[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11127028	0.93[AFR][1000 genomes];0.97[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11127029	0.84[CEU][hapmap]
rs11674249	0.81[ASN][1000 genomes]
rs11675942	0.82[JPT][hapmap]
rs11681689	0.82[CEU][hapmap];0.82[JPT][hapmap]
rs11685863	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[YRI][hapmap];0.86[AFR][1000 genomes];0.96[ASN][1000 genomes]
rs11691726	0.93[CHB][hapmap];0.82[JPT][hapmap]
rs11691807	0.82[CEU][hapmap];0.82[JPT][hapmap]
rs12052607	0.82[JPT][hapmap];0.80[ASN][1000 genomes]
rs12466728	0.82[CEU][hapmap];0.82[JPT][hapmap]
rs12469233	1.00[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs12472390	1.00[CEU][hapmap];0.81[CHB][hapmap];1.00[JPT][hapmap];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs12472676	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12476706	0.92[CEU][hapmap];0.91[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs12476826	0.82[JPT][hapmap]
rs12478575	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[YRI][hapmap];0.98[AFR][1000 genomes];0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12478653	1.00[ASW][hapmap];0.96[CEU][hapmap];1.00[CHB][hapmap];0.94[CHD][hapmap];0.87[GIH][hapmap];1.00[JPT][hapmap];0.87[LWK][hapmap];1.00[MEX][hapmap];0.86[MKK][hapmap];0.95[TSI][hapmap];0.92[YRI][hapmap];0.98[AFR][1000 genomes];0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12620833	1.00[CEU][hapmap];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs12622200	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.94[LWK][hapmap];1.00[MEX][hapmap];0.91[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]
rs12714179	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12714180	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12988844	0.82[CEU][hapmap];0.82[JPT][hapmap]
rs12999029	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.93[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13015186	0.92[CEU][hapmap];0.87[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs13017143	0.88[CEU][hapmap];0.93[GIH][hapmap];0.81[MEX][hapmap];0.87[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs13017338	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];0.97[ASN][1000 genomes]
rs13018801	0.83[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs13020869	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs13023154	0.92[CEU][hapmap];0.98[GIH][hapmap];0.81[MEX][hapmap];0.91[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs13024964	0.96[CEU][hapmap];0.91[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs13421310	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs17438687	0.82[CEU][hapmap];0.82[JPT][hapmap]
rs17737955	0.92[CEU][hapmap];0.87[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs17738096	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.94[LWK][hapmap];1.00[MEX][hapmap];0.91[MKK][hapmap];1.00[TSI][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1863051	0.92[CEU][hapmap];1.00[CHB][hapmap];0.83[CHD][hapmap];0.85[GIH][hapmap];1.00[JPT][hapmap];0.82[MEX][hapmap];0.81[TSI][hapmap];0.92[ASN][1000 genomes]
rs1863052	1.00[ASW][hapmap];0.92[CEU][hapmap];1.00[CHB][hapmap];0.89[CHD][hapmap];0.85[GIH][hapmap];1.00[JPT][hapmap];0.82[MEX][hapmap];0.81[TSI][hapmap];0.85[YRI][hapmap];0.83[AFR][1000 genomes];0.94[ASN][1000 genomes]
rs1863059	0.81[GIH][hapmap];0.82[JPT][hapmap]
rs1863063	0.92[CEU][hapmap];0.83[CHB][hapmap];0.95[MEX][hapmap];0.85[EUR][1000 genomes]
rs2278105	0.96[CEU][hapmap];0.82[CHB][hapmap];0.83[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.81[MKK][hapmap];1.00[TSI][hapmap];0.99[AMR][1000 genomes];0.95[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2367233	0.84[CEU][hapmap]
rs34048420	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs34069316	0.98[AFR][1000 genomes];0.99[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs35160687	1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs35281683	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs35370705	1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs35494267	0.80[ASN][1000 genomes]
rs35762338	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4392258	0.86[AFR][1000 genomes];0.96[ASN][1000 genomes]
rs4832031	0.82[CEU][hapmap];0.82[JPT][hapmap]
rs4832033	0.82[JPT][hapmap];0.80[ASN][1000 genomes]
rs4832261	0.82[CEU][hapmap];0.82[JPT][hapmap]
rs4832262	0.82[CEU][hapmap];0.82[JPT][hapmap]
rs4832269	0.82[CHB][hapmap];0.81[JPT][hapmap]
rs4832270	0.82[JPT][hapmap]
rs6547668	0.82[JPT][hapmap]
rs6547673	0.92[CEU][hapmap];0.83[CHB][hapmap];0.83[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs6547674	0.84[CEU][hapmap];0.83[GIH][hapmap]
rs6713456	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6714362	1.00[CEU][hapmap];0.82[CHB][hapmap];0.89[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.81[LWK][hapmap];1.00[MEX][hapmap];0.91[MKK][hapmap];1.00[TSI][hapmap];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs6725234	0.88[CHB][hapmap];0.81[JPT][hapmap];0.80[ASN][1000 genomes]
rs6738585	0.80[ASN][1000 genomes]
rs67407963	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.92[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6745235	0.82[JPT][hapmap]
rs6746198	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[YRI][hapmap];0.86[AFR][1000 genomes];0.96[ASN][1000 genomes]
rs67903513	1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7560886	0.81[JPT][hapmap];0.80[ASN][1000 genomes]
rs7563887	0.92[CEU][hapmap];0.83[CHB][hapmap];0.83[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs7571424	1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[CHD][hapmap];0.83[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.98[TSI][hapmap];0.89[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7593440	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[YRI][hapmap];0.86[AFR][1000 genomes];0.96[ASN][1000 genomes]
rs9677502	0.82[CEU][hapmap];0.82[JPT][hapmap]

Variant overlapped rSNPs/rCNVs (count:18 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv2751903	chr2:86253542-86505453	Active TSS Genic enhancers Weak transcription Strong transcription Enhancers ZNF genes & repeats Flanking Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	47 gene(s)	inside rSNPs	diseases
2	nsv1007474	chr2:86281967-86505453	Enhancers Flanking Active TSS Strong transcription Weak transcription Transcr. at gene 5' and 3' Genic enhancers Active TSS Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	47 gene(s)	inside rSNPs	diseases
3	nsv997563	chr2:86281967-86506132	Genic enhancers Weak transcription Strong transcription Flanking Active TSS Enhancers Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	47 gene(s)	inside rSNPs	diseases
4	nsv1008924	chr2:86282722-86499402	Genic enhancers Strong transcription Weak transcription ZNF genes & repeats Enhancers Active TSS Flanking Active TSS Bivalent Enhancer 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	47 gene(s)	inside rSNPs	diseases
5	nsv999956	chr2:86285944-86505453	Active TSS Weak transcription Enhancers Flanking Active TSS Strong transcription Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	47 gene(s)	inside rSNPs	diseases
6	nsv1012768	chr2:86285944-86506132	Strong transcription Weak transcription Genic enhancers Flanking Active TSS Enhancers ZNF genes & repeats Active TSS Bivalent Enhancer 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	47 gene(s)	inside rSNPs	diseases
7	nsv1000441	chr2:86286314-86508168	Enhancers Weak transcription Strong transcription Genic enhancers Active TSS Flanking Active TSS Transcr. at gene 5' and 3' 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	47 gene(s)	inside rSNPs	diseases
8	nsv535808	chr2:86286314-86508168	Genic enhancers Weak transcription Flanking Active TSS Strong transcription Enhancers Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	47 gene(s)	inside rSNPs	diseases
9	nsv1004442	chr2:86286480-86506132	Flanking Active TSS Weak transcription Transcr. at gene 5' and 3' Active TSS Genic enhancers Strong transcription Enhancers ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	47 gene(s)	inside rSNPs	diseases
10	nsv916616	chr2:86289130-86509326	Weak transcription Strong transcription Enhancers Flanking Active TSS Genic enhancers Active TSS 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	47 gene(s)	inside rSNPs	diseases
11	nsv458563	chr2:86292341-86507688	Weak transcription Enhancers Strong transcription Flanking Active TSS Transcr. at gene 5' and 3' Active TSS ZNF genes & repeats Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	47 gene(s)	inside rSNPs	diseases
12	nsv582370	chr2:86292341-86507688	Flanking Active TSS Active TSS Strong transcription Weak transcription Enhancers Genic enhancers Transcr. at gene 5' and 3' 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	47 gene(s)	inside rSNPs	diseases
13	nsv1009140	chr2:86294939-86506132	Weak transcription Strong transcription Enhancers Genic enhancers ZNF genes & repeats Active TSS Transcr. at gene 5' and 3' Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	47 gene(s)	inside rSNPs	diseases
14	nsv582371	chr2:86296566-86507688	Weak transcription Strong transcription Enhancers Flanking Active TSS Genic enhancers Bivalent Enhancer 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	47 gene(s)	inside rSNPs	diseases
15	nsv1001157	chr2:86301440-86508168	Strong transcription Enhancers Weak transcription Flanking Active TSS Genic enhancers Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	47 gene(s)	inside rSNPs	diseases
16	esv3412938	chr2:86370969-86867936	Strong transcription Enhancers Genic enhancers Weak transcription Flanking Bivalent TSS/Enh Active TSS Flanking Active TSS ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	77 gene(s)	inside rSNPs	diseases
17	nsv458574	chr2:86385728-86507688	Enhancers Flanking Active TSS Genic enhancers Weak transcription ZNF genes & repeats Strong transcription Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	36 gene(s)	inside rSNPs	diseases
18	nsv582372	chr2:86385728-86507688	Enhancers Genic enhancers Weak transcription Strong transcription Active TSS Flanking Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	36 gene(s)	inside rSNPs	diseases

mRNA abundance (count:9)

SNP	Gene	Cis/trans	Tissue	Source
rs10520415	IMMT	cis	Whole Blood	GTEx
rs10520415	IMMT	cis	cerebellum	SCAN
rs10520415	MRPL35	cis	cerebellum	SCAN
rs10520415	VAMP5	cis	parietal	SCAN
rs10520415	REEP1	cis	lymphoblastoid	seeQTL
rs10520415	MRPL35	cis	parietal	SCAN
rs10520415	REEP1	cis	parietal	SCAN
rs10520415	MRPL35	cis	uninvolved skin	skin_eQTL
rs10520415	ZNF384	trans	parietal	SCAN

Chromatin state (count:14 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:86483200-86501800	Weak transcription	Left Ventricle	heart
2	chr2:86488600-86501400	Weak transcription	Stomach Smooth Muscle	stomach
3	chr2:86490200-86501200	Weak transcription	Skeletal Muscle Male	skeletal muscle
4	chr2:86497200-86499600	ZNF genes & repeats	Fetal Intestine Small	intestine
5	chr2:86497200-86501400	Weak transcription	Stomach Mucosa	stomach
6	chr2:86497600-86500400	ZNF genes & repeats	Fetal Brain Female	brain
7	chr2:86497800-86499000	ZNF genes & repeats	Colon Smooth Muscle	Colon
8	chr2:86497800-86499800	ZNF genes & repeats	Brain Germinal Matrix	brain
9	chr2:86497800-86499800	ZNF genes & repeats	Duodenum Smooth Muscle	Duodenum
10	chr2:86498000-86499400	Weak transcription	Fetal Brain Male	brain
11	chr2:86498400-86499000	ZNF genes & repeats	Brain Dorsolateral Prefrontal Cortex	brain
12	chr2:86498600-86499000	ZNF genes & repeats	Skeletal Muscle Female	skeletal muscle
13	chr2:86498600-86499000	ZNF genes & repeats	HSMMtube	muscle
14	chr2:86498600-86500000	ZNF genes & repeats	Brain Angular Gyrus	brain

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