Variant report

Variant	rs13017338
Chromosome Location	chr2:86501553-86501554
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 91 )
Associated
traits (count: 5 )

rSNPs within LD-proxies of this variant (count:74)

rs_ID	r²[population]
rs10186289	0.85[CEU][hapmap];0.84[CHB][hapmap];0.85[EUR][1000 genomes]
rs10189492	1.00[CEU][hapmap];0.82[CHB][hapmap];0.94[JPT][hapmap];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs10200186	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs10200526	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs10200619	0.93[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[YRI][hapmap];0.86[AFR][1000 genomes];0.92[ASN][1000 genomes]
rs10201457	0.81[CHB][hapmap];1.00[JPT][hapmap]
rs10520415	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]
rs11127026	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];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11127028	0.93[AFR][1000 genomes];0.97[AMR][1000 genomes];0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs11127029	0.85[CEU][hapmap]
rs11675942	0.82[JPT][hapmap]
rs11681689	0.83[CEU][hapmap];0.84[JPT][hapmap]
rs11685863	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[YRI][hapmap];0.86[AFR][1000 genomes];0.93[ASN][1000 genomes]
rs11691726	0.93[CHB][hapmap];0.84[JPT][hapmap]
rs11691807	0.82[CEU][hapmap];0.82[JPT][hapmap]
rs12052607	0.84[JPT][hapmap]
rs12466728	0.83[CEU][hapmap];0.84[JPT][hapmap]
rs12469233	1.00[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs12472390	1.00[CEU][hapmap];0.81[CHB][hapmap];0.94[JPT][hapmap];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.84[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];0.94[ASN][1000 genomes]
rs12476706	0.92[CEU][hapmap];0.91[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs12476826	0.84[JPT][hapmap]
rs12478575	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[YRI][hapmap];0.98[AFR][1000 genomes];0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12478653	0.96[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];0.94[ASN][1000 genomes]
rs12620833	1.00[CEU][hapmap];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs12622200	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]
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];0.94[ASN][1000 genomes]
rs12714180	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12988844	0.82[CEU][hapmap];0.82[JPT][hapmap]
rs12999029	1.00[CEU][hapmap];1.00[CHB][hapmap];0.93[JPT][hapmap];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs13015186	0.92[CEU][hapmap];0.87[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs13017143	0.88[CEU][hapmap];0.87[AMR][1000 genomes];0.82[EUR][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];0.94[ASN][1000 genomes]
rs13023154	0.92[CEU][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];0.94[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[JPT][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1863051	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[ASN][1000 genomes]
rs1863052	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[YRI][hapmap];0.83[AFR][1000 genomes];0.92[ASN][1000 genomes]
rs1863059	0.82[JPT][hapmap]
rs1863063	0.92[CEU][hapmap];0.83[CHB][hapmap];0.85[EUR][1000 genomes]
rs2278105	0.96[CEU][hapmap];0.82[CHB][hapmap];1.00[JPT][hapmap];0.99[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs2367233	0.85[CEU][hapmap]
rs34048420	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs34069316	0.98[AFR][1000 genomes];0.99[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs35160687	1.00[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs35281683	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs35370705	1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs35762338	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4392258	0.86[AFR][1000 genomes];0.93[ASN][1000 genomes]
rs4832031	0.82[CEU][hapmap];0.82[JPT][hapmap]
rs4832033	0.84[JPT][hapmap]
rs4832261	0.82[CEU][hapmap];0.82[JPT][hapmap]
rs4832262	0.82[CEU][hapmap];0.82[JPT][hapmap]
rs4832269	0.82[CHB][hapmap];0.83[JPT][hapmap]
rs4832270	0.82[JPT][hapmap]
rs6547668	0.84[JPT][hapmap]
rs6547673	0.86[CEU][hapmap];0.84[CHB][hapmap];0.83[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs6547674	0.84[CEU][hapmap]
rs6713456	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6714362	1.00[CEU][hapmap];0.82[CHB][hapmap];1.00[JPT][hapmap];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs6725234	0.89[CHB][hapmap];0.83[JPT][hapmap]
rs67407963	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.92[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6745235	0.84[JPT][hapmap]
rs6746198	0.93[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[YRI][hapmap];0.86[AFR][1000 genomes];0.93[ASN][1000 genomes]
rs67903513	1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7560886	0.82[JPT][hapmap]
rs7563887	0.85[CEU][hapmap];0.84[CHB][hapmap];0.83[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs7571424	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[AMR][1000 genomes];0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7593440	0.93[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[YRI][hapmap];0.86[AFR][1000 genomes];0.93[ASN][1000 genomes]
rs9677502	0.82[CEU][hapmap];0.82[JPT][hapmap]

Variant overlapped rSNPs/rCNVs (count:17 , 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	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
5	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
6	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
7	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
8	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
9	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
10	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
11	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
12	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
13	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
14	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
15	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
16	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
17	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:5)

SNP	Gene	Cis/trans	Tissue	Source
rs13017338	REEP1	cis	multi-tissue	Pritchard
rs13017338	MRPL35	Cis_1M	lymphoblastoid	RTeQTL
rs13017338	IMMT	cis	Whole Blood	GTEx
rs13017338	IMMT	Cis_1M	lymphoblastoid	RTeQTL
rs13017338	MRPL35	cis	uninvolved skin	skin_eQTL

Chromatin state (count:44 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:86483200-86501800	Weak transcription	Left Ventricle	heart
2	chr2:86499000-86510800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
3	chr2:86499200-86502000	Weak transcription	Pancreas	Pancrea
4	chr2:86499200-86503000	Weak transcription	Fetal Stomach	stomach
5	chr2:86499200-86503200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
6	chr2:86499200-86509600	Weak transcription	Aorta	Aorta
7	chr2:86499800-86501600	Weak transcription	HMEC	breast
8	chr2:86499800-86502000	Weak transcription	Fetal Muscle Trunk	muscle
9	chr2:86499800-86507200	Weak transcription	Brain Inferior Temporal Lobe	brain
10	chr2:86500000-86507400	Weak transcription	Brain Angular Gyrus	brain
11	chr2:86500000-86517400	Weak transcription	Pancreatic Islets	Pancreatic Islet
12	chr2:86500200-86506800	Weak transcription	Fetal Brain Male	brain
13	chr2:86500400-86504000	Strong transcription	Fetal Brain Female	brain
14	chr2:86500800-86503600	Enhancers	GM12878-XiMat	blood
15	chr2:86501200-86501800	Weak transcription	Brain Germinal Matrix	brain
16	chr2:86501200-86502200	Enhancers	Fetal Adrenal Gland	Adrenal Gland
17	chr2:86501200-86502200	Enhancers	HUVEC	blood vessel
18	chr2:86501200-86502200	Enhancers	NHDF-Ad	bronchial
19	chr2:86501200-86502400	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
20	chr2:86501200-86502400	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
21	chr2:86501200-86502400	Enhancers	A549	lung
22	chr2:86501200-86502600	Enhancers	HSMMtube	muscle
23	chr2:86501200-86502800	Enhancers	Fetal Muscle Leg	muscle
24	chr2:86501200-86502800	Enhancers	Small Intestine	intestine
25	chr2:86501200-86502800	Enhancers	HSMM	muscle
26	chr2:86501200-86503600	Enhancers	Skeletal Muscle Male	skeletal muscle
27	chr2:86501200-86503800	Enhancers	Rectal Mucosa Donor 31	rectum
28	chr2:86501200-86503800	Enhancers	Skeletal Muscle Female	skeletal muscle
29	chr2:86501200-86504000	Enhancers	Fetal Intestine Large	intestine
30	chr2:86501200-86504000	Enhancers	Psoas Muscle	Psoas
31	chr2:86501400-86502000	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
32	chr2:86501400-86502000	Enhancers	Sigmoid Colon	Sigmoid Colon
33	chr2:86501400-86502200	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
34	chr2:86501400-86502200	Enhancers	Muscle Satellite Cultured Cells	--
35	chr2:86501400-86502400	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
36	chr2:86501400-86502400	Enhancers	NH-A	brain
37	chr2:86501400-86502600	Enhancers	Stomach Smooth Muscle	stomach
38	chr2:86501400-86502800	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
39	chr2:86501400-86502800	Enhancers	Colon Smooth Muscle	Colon
40	chr2:86501400-86502800	Enhancers	Duodenum Smooth Muscle	Duodenum
41	chr2:86501400-86502800	Enhancers	Hela-S3	cervix
42	chr2:86501400-86503000	Enhancers	Fetal Intestine Small	intestine
43	chr2:86501400-86503200	Enhancers	Stomach Mucosa	stomach
44	chr2:86501400-86503600	Enhancers	Right Ventricle	heart

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