Variant report

Variant	rs12148786
Chromosome Location	chr15:76800362-76800363
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 92 )
Associated
traits (count: 11 )

rSNPs within LD-proxies of this variant (count:88)

rs_ID	r²[population]
rs11072599	0.94[CHB][hapmap];1.00[JPT][hapmap];0.83[ASN][1000 genomes]
rs11072603	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[AMR][1000 genomes];0.85[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs1117367	0.96[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.84[AMR][1000 genomes];0.86[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs1125932	0.93[CHB][hapmap];1.00[JPT][hapmap]
rs12148805	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[YRI][hapmap];0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12437627	0.95[CHB][hapmap];0.84[CHD][hapmap];1.00[JPT][hapmap]
rs12438077	0.94[CHB][hapmap];1.00[JPT][hapmap]
rs12439484	0.83[JPT][hapmap]
rs12441433	1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];0.95[LWK][hapmap];1.00[MEX][hapmap];0.97[TSI][hapmap];0.87[AMR][1000 genomes];0.88[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs12441550	0.94[CHB][hapmap];1.00[JPT][hapmap]
rs12443137	0.92[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];0.85[AMR][1000 genomes];0.89[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs12592171	0.88[CHB][hapmap];1.00[JPT][hapmap];0.83[ASN][1000 genomes]
rs12593751	0.84[ASN][1000 genomes]
rs12594212	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12594541	0.84[AMR][1000 genomes];0.88[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs12594577	0.94[CHB][hapmap];1.00[JPT][hapmap]
rs12898430	0.85[AMR][1000 genomes];0.86[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs12899871	0.95[CHB][hapmap];1.00[JPT][hapmap];0.85[ASN][1000 genomes]
rs12900494	0.95[CHB][hapmap];1.00[JPT][hapmap]
rs12902174	0.93[CHB][hapmap];1.00[JPT][hapmap]
rs12902414	0.91[ASN][1000 genomes]
rs12907805	0.95[CHB][hapmap];0.84[CHD][hapmap];0.81[GIH][hapmap];1.00[JPT][hapmap]
rs12911987	0.93[CHB][hapmap];0.93[JPT][hapmap]
rs12914005	0.85[ASN][1000 genomes]
rs12915248	0.95[CHB][hapmap];0.83[CHD][hapmap];1.00[JPT][hapmap];0.85[ASN][1000 genomes]
rs12916573	0.95[CHB][hapmap];0.81[CHD][hapmap];1.00[JPT][hapmap];0.91[ASN][1000 genomes]
rs1587381	0.95[CHB][hapmap];0.84[CHD][hapmap];1.00[JPT][hapmap];0.85[ASN][1000 genomes]
rs1588961	0.85[ASN][1000 genomes]
rs17361504	0.83[JPT][hapmap]
rs17362383	0.95[CHB][hapmap];0.84[CHD][hapmap];0.81[GIH][hapmap];1.00[JPT][hapmap]
rs17363713	0.84[ASN][1000 genomes]
rs17364076	0.95[CHB][hapmap];0.84[CHD][hapmap];0.84[GIH][hapmap];1.00[JPT][hapmap];0.85[ASN][1000 genomes]
rs17364330	0.95[CHB][hapmap];0.84[CHD][hapmap];1.00[JPT][hapmap];0.85[ASN][1000 genomes]
rs17460201	0.95[CHB][hapmap];0.84[CHD][hapmap];0.81[GIH][hapmap];1.00[JPT][hapmap]
rs17461634	0.85[ASN][1000 genomes]
rs1838050	0.81[EUR][1000 genomes]
rs1867197	0.95[CHB][hapmap];0.84[CHD][hapmap];1.00[JPT][hapmap]
rs1874944	0.94[CHB][hapmap];1.00[JPT][hapmap]
rs1965492	0.82[ASN][1000 genomes]
rs2056544	0.87[AMR][1000 genomes];0.89[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2083762	0.92[CEU][hapmap];0.94[CHB][hapmap];0.97[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.83[EUR][1000 genomes]
rs2117369	0.94[CHB][hapmap];1.00[JPT][hapmap];0.85[ASN][1000 genomes]
rs2120107	1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.97[TSI][hapmap];0.86[AMR][1000 genomes];0.86[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2120108	0.95[CHB][hapmap];0.84[CHD][hapmap];0.84[GIH][hapmap];1.00[JPT][hapmap]
rs2164101	0.85[ASN][1000 genomes]
rs2304920	0.95[CHB][hapmap];1.00[JPT][hapmap]
rs2404740	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[YRI][hapmap];0.83[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2404741	0.82[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2454454	0.82[GIH][hapmap];0.91[MEX][hapmap];0.80[TSI][hapmap]
rs2461870	0.82[GIH][hapmap];0.91[MEX][hapmap];0.80[TSI][hapmap]
rs284895	0.95[CHB][hapmap];0.84[CHD][hapmap];0.83[GIH][hapmap];1.00[JPT][hapmap];0.85[ASN][1000 genomes]
rs2896954	0.83[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs3816266	0.95[CHB][hapmap];1.00[JPT][hapmap]
rs3866543	0.95[CHB][hapmap];0.81[CHD][hapmap];0.88[JPT][hapmap]
rs4079681	0.89[CHB][hapmap];1.00[JPT][hapmap]
rs437131	0.84[GIH][hapmap]
rs4633676	0.95[CHB][hapmap];0.81[CHD][hapmap];1.00[JPT][hapmap];0.82[ASN][1000 genomes]
rs4886495	0.82[GIH][hapmap]
rs4886496	0.95[CHB][hapmap];1.00[JPT][hapmap]
rs4886799	0.95[CHB][hapmap];0.81[CHD][hapmap];1.00[JPT][hapmap]
rs4886801	0.95[CHB][hapmap];0.81[CHD][hapmap];1.00[JPT][hapmap]
rs4886805	0.81[GIH][hapmap]
rs4886813	0.95[CHB][hapmap];0.84[CHD][hapmap];1.00[JPT][hapmap]
rs4886817	0.89[CHB][hapmap];0.84[CHD][hapmap];0.86[GIH][hapmap];0.94[JPT][hapmap]
rs4886818	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[AMR][1000 genomes];0.86[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs4886825	0.95[CHB][hapmap];0.81[CHD][hapmap];1.00[JPT][hapmap]
rs56089215	0.82[ASN][1000 genomes]
rs6495206	0.86[AMR][1000 genomes];0.86[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs66986092	0.91[ASN][1000 genomes]
rs67232575	0.84[ASN][1000 genomes]
rs67263359	0.91[ASN][1000 genomes]
rs67888330	0.84[ASN][1000 genomes]
rs67920045	0.91[ASN][1000 genomes]
rs7162455	0.82[ASN][1000 genomes]
rs7163946	0.95[CHB][hapmap];1.00[JPT][hapmap];0.85[ASN][1000 genomes]
rs7164060	0.95[CHB][hapmap];1.00[JPT][hapmap]
rs7164813	0.95[CHB][hapmap];0.84[CHD][hapmap];0.84[GIH][hapmap];1.00[JPT][hapmap]
rs7165025	0.85[ASN][1000 genomes]
rs7174953	0.94[CHB][hapmap];1.00[JPT][hapmap]
rs7179142	0.84[CHB][hapmap];1.00[JPT][hapmap]
rs7342603	0.95[CHB][hapmap];1.00[JPT][hapmap]
rs7350777	0.95[CHB][hapmap];0.84[CHD][hapmap];1.00[JPT][hapmap]
rs7403276	0.95[CHB][hapmap];1.00[JPT][hapmap]
rs8025134	0.85[ASN][1000 genomes]
rs8030411	0.94[CHB][hapmap];0.84[CHD][hapmap];0.81[GIH][hapmap];1.00[JPT][hapmap]
rs8036703	0.94[CHB][hapmap];0.83[CHD][hapmap];1.00[JPT][hapmap]
rs8039545	0.95[CHB][hapmap];1.00[JPT][hapmap]
rs8043474	0.95[CHB][hapmap];1.00[JPT][hapmap]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv542438	chr15:76697056-76892157	Weak transcription Strong transcription ZNF genes & repeats Enhancers Flanking Active TSS Genic enhancers Active TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA	3 gene(s)	inside rSNPs	diseases
2	nsv542439	chr15:76762161-77196336	Enhancers Weak transcription Strong transcription ZNF genes & repeats Flanking Active TSS Active TSS Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA	9 gene(s)	inside rSNPs	diseases
3	esv3440794	chr15:76764595-77571114	Weak transcription Enhancers Strong transcription Active TSS Flanking Active TSS Genic enhancers ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	25 gene(s)	inside rSNPs	diseases
4	nsv904400	chr15:76772062-77085283	Strong transcription Weak transcription Genic enhancers ZNF genes & repeats Enhancers Active TSS Flanking Active TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA	4 gene(s)	inside rSNPs	diseases

mRNA abundance (count:11)

SNP	Gene	Cis/trans	Tissue	Source
rs12148786	TBC1D2B	cis	parietal	SCAN
rs12148786	SCAPER	cis	lung	GTEx
rs12148786	GRAMD2	cis	cerebellum	SCAN
rs12148786	SCAPER	cis	cerebellum	SCAN
rs12148786	ZNF291	cis	multi-tissue	Pritchard
rs12148786	SCAPER	Cis_1M	lymphoblastoid	RTeQTL
rs12148786	SCAPER	cis	Artery Tibial	GTEx
rs12148786	SCAPER	cis	Nerve Tibial	GTEx
rs12148786	SCAPER	cis	Thyroid	GTEx
rs12148786	NRG4	cis	parietal	SCAN
rs12148786	SCAPER	cis	parietal	SCAN

Chromatin state (count:20 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:76725800-76812600	Weak transcription	Left Ventricle	heart
2	chr15:76788400-76813600	Weak transcription	Primary T cells fromperipheralblood	blood
3	chr15:76790000-76802000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
4	chr15:76791200-76806200	Weak transcription	Fetal Muscle Leg	muscle
5	chr15:76792600-76801800	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
6	chr15:76794000-76810400	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
7	chr15:76794200-76806400	Weak transcription	Gastric	stomach
8	chr15:76794800-76801200	Weak transcription	Right Ventricle	heart
9	chr15:76795200-76806800	Weak transcription	Brain Inferior Temporal Lobe	brain
10	chr15:76795800-76810600	Weak transcription	Sigmoid Colon	Sigmoid Colon
11	chr15:76796400-76805200	Weak transcription	Fetal Intestine Large	intestine
12	chr15:76796800-76806400	Weak transcription	Breast Myoepithelial Primary Cells	Breast
13	chr15:76797000-76805000	Weak transcription	Stomach Smooth Muscle	stomach
14	chr15:76797000-76806400	Weak transcription	Rectal Mucosa Donor 29	rectum
15	chr15:76797200-76803600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
16	chr15:76797200-76804800	Weak transcription	Primary T cells from cord blood	blood
17	chr15:76797200-76806400	Weak transcription	Liver	Liver
18	chr15:76797400-76825000	Weak transcription	Primary B cells from cord blood	blood
19	chr15:76799400-76800400	Enhancers	Duodenum Mucosa	Duodenum
20	chr15:76799800-76804800	Weak transcription	Fetal Intestine Small	intestine

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