Variant report

Variant	rs13017143
Chromosome Location	chr2:86466549-86466550
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 78 )
Associated
traits (count: 11 )

rSNPs within LD-proxies of this variant (count:57)

rs_ID	r²[population]
rs10186289	0.84[CEU][hapmap]
rs10189492	0.87[CEU][hapmap];0.87[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs10195199	1.00[CHB][hapmap];0.89[JPT][hapmap];0.82[ASN][1000 genomes]
rs10200186	0.87[AMR][1000 genomes]
rs10200526	0.88[CEU][hapmap];0.87[AMR][1000 genomes]
rs10200619	0.81[CEU][hapmap]
rs10520415	0.88[CEU][hapmap];0.93[GIH][hapmap];0.81[MEX][hapmap];0.87[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs11127026	0.88[CEU][hapmap];0.91[GIH][hapmap];0.81[MEX][hapmap];0.87[AMR][1000 genomes]
rs11127028	0.85[AMR][1000 genomes]
rs11127029	0.88[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[ASN][1000 genomes]
rs11685863	0.80[CEU][hapmap]
rs11691122	0.96[ASN][1000 genomes]
rs12469233	0.87[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs12472390	0.88[CEU][hapmap];0.87[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs12472676	0.88[CEU][hapmap];0.87[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs12476706	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[AMR][1000 genomes];0.92[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12478575	0.88[CEU][hapmap];0.85[AMR][1000 genomes]
rs12478653	0.84[CEU][hapmap];0.81[GIH][hapmap];0.81[MEX][hapmap];0.85[AMR][1000 genomes]
rs12620833	0.88[CEU][hapmap];0.85[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs12622200	0.88[CEU][hapmap];0.93[GIH][hapmap];0.81[MEX][hapmap];0.87[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs12714178	1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[ASN][1000 genomes]
rs12714179	0.92[CEU][hapmap];0.87[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs12714180	0.88[CEU][hapmap];0.87[AMR][1000 genomes]
rs12999029	1.00[ASW][hapmap];0.88[CEU][hapmap];0.93[GIH][hapmap];0.81[MEX][hapmap];0.81[MKK][hapmap];0.87[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs13007807	0.86[CHB][hapmap];1.00[JPT][hapmap];0.96[ASN][1000 genomes]
rs13015186	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13017338	0.88[CEU][hapmap];0.87[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs13018801	0.88[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs13020869	0.87[AMR][1000 genomes]
rs13023154	1.00[ASW][hapmap];0.96[CEU][hapmap];1.00[CHB][hapmap];0.89[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.88[MKK][hapmap];1.00[TSI][hapmap];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs13024964	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs13421310	0.88[CEU][hapmap];0.87[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs17737955	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs17738096	0.88[CEU][hapmap];0.93[GIH][hapmap];0.81[MEX][hapmap];0.87[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs1863051	0.81[CEU][hapmap]
rs1863052	0.81[CEU][hapmap]
rs1863059	0.83[GIH][hapmap]
rs1863063	0.81[CEU][hapmap]
rs2278105	0.92[CEU][hapmap];0.98[GIH][hapmap];0.81[MEX][hapmap];0.81[MKK][hapmap];0.88[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs2367233	0.88[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[ASN][1000 genomes]
rs34048420	0.87[AMR][1000 genomes]
rs34069316	0.86[AMR][1000 genomes]
rs35160687	0.87[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs35281683	0.87[AMR][1000 genomes]
rs35370705	0.87[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs35762338	0.87[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs6547673	0.81[CEU][hapmap]
rs6547674	1.00[ASW][hapmap];0.88[CEU][hapmap];1.00[CHB][hapmap];0.84[CHD][hapmap];0.81[GIH][hapmap];1.00[JPT][hapmap];0.85[MEX][hapmap];0.96[ASN][1000 genomes]
rs6713456	0.88[CEU][hapmap];0.85[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs6714362	0.88[CEU][hapmap];0.93[GIH][hapmap];0.81[MEX][hapmap];0.87[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs67407963	0.87[AMR][1000 genomes]
rs6746198	0.81[CEU][hapmap]
rs67903513	0.87[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs7422930	1.00[CHB][hapmap];0.90[CHD][hapmap];0.89[JPT][hapmap];0.82[ASN][1000 genomes]
rs7563887	0.84[CEU][hapmap]
rs7571424	0.88[CEU][hapmap];0.81[MEX][hapmap]
rs7593440	0.81[CEU][hapmap]

Variant overlapped rSNPs/rCNVs (count:21 , 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	nsv531380	chr2:86253552-86469217	Enhancers Active TSS Weak transcription Flanking Active TSS Strong transcription Genic enhancers ZNF genes & repeats 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
3	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
4	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
5	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
6	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
7	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
8	nsv1003207	chr2:86286314-86496732	Genic enhancers Strong transcription Weak transcription Flanking Active TSS Active TSS Enhancers ZNF genes & repeats 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
9	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
10	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
11	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
12	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
13	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
14	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
15	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
16	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
17	nsv531381	chr2:86301091-86478346	Active TSS Strong transcription Enhancers Weak transcription Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	47 gene(s)	inside rSNPs	diseases
18	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
19	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
20	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
21	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:11)

SNP	Gene	Cis/trans	Tissue	Source
rs13017143	C2orf23	cis	multi-tissue	Pritchard
rs13017143	DNAH6	cis	parietal	SCAN
rs13017143	IMMT	cis	cerebellum	SCAN
rs13017143	VAMP5	cis	parietal	SCAN
rs13017143	MRPL35	cis	cerebellum	SCAN
rs13017143	MRPL35	cis	parietal	SCAN
rs13017143	MRPL35	Cis_1M	lymphoblastoid	RTeQTL
rs13017143	IMMT	Cis_1M	lymphoblastoid	RTeQTL
rs13017143	IMMT	cis	lymphoblastoid	seeQTL
rs13017143	IMMT	cis	Whole Blood	GTEx
rs13017143	REEP1	cis	parietal	SCAN

Chromatin state (count:49 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:86450800-86476400	Weak transcription	Fetal Brain Male	brain
2	chr2:86452400-86467400	Weak transcription	Brain Inferior Temporal Lobe	brain
3	chr2:86452400-86477400	Weak transcription	Brain Angular Gyrus	brain
4	chr2:86453200-86467600	Weak transcription	Spleen	Spleen
5	chr2:86453200-86468400	Weak transcription	Gastric	stomach
6	chr2:86453200-86475800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
7	chr2:86453400-86470400	Weak transcription	Aorta	Aorta
8	chr2:86459800-86471200	Weak transcription	Fetal Intestine Large	intestine
9	chr2:86459800-86479200	Weak transcription	Esophagus	oesophagus
10	chr2:86460200-86467800	Weak transcription	Fetal Intestine Small	intestine
11	chr2:86460800-86479400	Weak transcription	Brain Anterior Caudate	brain
12	chr2:86461000-86468200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
13	chr2:86462000-86470600	Weak transcription	Colon Smooth Muscle	Colon
14	chr2:86462000-86470600	Weak transcription	Fetal Muscle Leg	muscle
15	chr2:86462600-86467400	Weak transcription	HSMMtube	muscle
16	chr2:86462800-86466600	Weak transcription	Brain Germinal Matrix	brain
17	chr2:86462800-86467200	Weak transcription	Brain Cingulate Gyrus	brain
18	chr2:86462800-86469800	Weak transcription	Rectal Smooth Muscle	rectum
19	chr2:86463000-86466600	Weak transcription	Skeletal Muscle Male	skeletal muscle
20	chr2:86463000-86469200	Weak transcription	Duodenum Smooth Muscle	Duodenum
21	chr2:86463000-86469800	Weak transcription	Skeletal Muscle Female	skeletal muscle
22	chr2:86463000-86470400	Weak transcription	Right Atrium	heart
23	chr2:86463000-86482000	Weak transcription	Psoas Muscle	Psoas
24	chr2:86464400-86469800	Enhancers	Primary B cells from peripheral blood	blood
25	chr2:86464400-86472000	Enhancers	Primary B cells from cord blood	blood
26	chr2:86465400-86466600	Enhancers	Primary T helper naive cells fromperipheralblood	blood
27	chr2:86465400-86466600	Enhancers	Primary T helper cells PMA-I stimulated	--
28	chr2:86465400-86466800	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
29	chr2:86465400-86467000	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
30	chr2:86465400-86467000	Bivalent Enhancer	Primary hematopoietic stem cells G-CSF-mobilized Male	--
31	chr2:86465600-86466800	Enhancers	Primary T cells fromperipheralblood	blood
32	chr2:86465600-86467000	Enhancers	Primary hematopoietic stem cells short term culture	blood
33	chr2:86465600-86467200	Enhancers	Primary hematopoietic stem cells	blood
34	chr2:86465600-86469000	Strong transcription	Stomach Smooth Muscle	stomach
35	chr2:86465600-86471400	Strong transcription	Fetal Brain Female	brain
36	chr2:86465800-86466800	Enhancers	Fetal Thymus	thymus
37	chr2:86465800-86467000	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
38	chr2:86466000-86466600	Enhancers	H9 Cell Line	embryonic stem cell
39	chr2:86466000-86466600	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
40	chr2:86466000-86466600	Enhancers	GM12878-XiMat	blood
41	chr2:86466000-86467200	Weak transcription	Right Ventricle	heart
42	chr2:86466000-86469800	Weak transcription	Left Ventricle	heart
43	chr2:86466000-86471600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
44	chr2:86466200-86466600	Enhancers	Dnd41	blood
45	chr2:86466200-86467600	Enhancers	Primary T cells from cord blood	blood
46	chr2:86466200-86469200	Weak transcription	Fetal Heart	heart
47	chr2:86466400-86466600	Enhancers	HUES6 Cell Line	embryonic stem cell
48	chr2:86466400-86466800	Enhancers	H1 Cell Line	embryonic stem cell
49	chr2:86466400-86466800	Enhancers	Fetal Muscle Trunk	muscle

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