Variant report

Variant	rs485499
Chromosome Location	chr3:159745863-159745864
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-RP11-432B6.3.1-3	chr3:159745703-159746060	ucscGeneNc_uc003fbw_1

Extended variants
information (count: 55 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:54)

rs_ID	r²[population]
rs11708713	0.93[EUR][1000 genomes]
rs11716424	0.93[EUR][1000 genomes]
rs11716451	0.93[EUR][1000 genomes]
rs1651081	1.00[CEU][hapmap];0.93[EUR][1000 genomes]
rs1874886	0.93[EUR][1000 genomes]
rs2366643	1.00[CEU][hapmap];0.93[EUR][1000 genomes]
rs2366644	0.92[EUR][1000 genomes]
rs2647928	0.88[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs2647930	0.93[EUR][1000 genomes]
rs2647931	0.93[EUR][1000 genomes]
rs2914116	1.00[CEU][hapmap];0.93[EUR][1000 genomes]
rs2936302	0.92[EUR][1000 genomes]
rs2936303	0.93[EUR][1000 genomes]
rs4580600	0.92[EUR][1000 genomes]
rs4679867	0.96[CEU][hapmap];1.00[CHB][hapmap];0.91[CHD][hapmap];1.00[JPT][hapmap];0.87[AMR][1000 genomes];0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4680536	0.84[AMR][1000 genomes];0.86[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4680538	0.92[EUR][1000 genomes]
rs480134	0.92[EUR][1000 genomes]
rs480913	1.00[CEU][hapmap];0.93[EUR][1000 genomes]
rs483714	0.93[EUR][1000 genomes]
rs484600	1.00[CEU][hapmap];0.93[EUR][1000 genomes]
rs485789	0.84[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.94[MEX][hapmap];1.00[MKK][hapmap];0.97[TSI][hapmap];1.00[YRI][hapmap];0.90[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs491966	1.00[CEU][hapmap];0.93[EUR][1000 genomes]
rs522127	0.93[EUR][1000 genomes]
rs523886	0.93[EUR][1000 genomes]
rs526734	0.90[EUR][1000 genomes]
rs545143	1.00[CEU][hapmap];0.97[GIH][hapmap];0.93[TSI][hapmap];0.93[EUR][1000 genomes]
rs545232	1.00[CEU][hapmap];0.97[GIH][hapmap];0.93[TSI][hapmap];0.93[EUR][1000 genomes]
rs547875	0.93[EUR][1000 genomes]
rs548018	0.93[EUR][1000 genomes]
rs55740284	0.93[ASN][1000 genomes]
rs564799	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.84[MEX][hapmap];0.97[TSI][hapmap];0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs564976	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs571099	0.93[EUR][1000 genomes]
rs574808	1.00[CEU][hapmap];0.97[GIH][hapmap];0.93[TSI][hapmap];0.93[EUR][1000 genomes]
rs579079	0.94[EUR][1000 genomes]
rs586094	1.00[CEU][hapmap];0.92[EUR][1000 genomes]
rs587422	0.93[EUR][1000 genomes]
rs588998	0.93[EUR][1000 genomes]
rs589446	0.90[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs589545	1.00[CEU][hapmap];0.93[EUR][1000 genomes]
rs600519	1.00[CEU][hapmap];0.93[EUR][1000 genomes]
rs62270441	0.93[EUR][1000 genomes]
rs629209	0.93[EUR][1000 genomes]
rs6441288	1.00[CEU][hapmap]
rs6441289	1.00[CEU][hapmap];0.93[EUR][1000 genomes]
rs6441290	0.93[EUR][1000 genomes]
rs669003	1.00[CEU][hapmap];0.97[GIH][hapmap];0.93[TSI][hapmap];0.93[EUR][1000 genomes]
rs6771363	1.00[CEU][hapmap];0.93[EUR][1000 genomes]
rs6808498	1.00[CEU][hapmap];0.93[EUR][1000 genomes]
rs6808518	0.93[EUR][1000 genomes]
rs7640862	0.92[EUR][1000 genomes]
rs9290051	0.92[EUR][1000 genomes]
rs9845010	0.93[EUR][1000 genomes]

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

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv829769	chr3:159606913-159805282	Enhancers Active TSS Genic enhancers Flanking Active TSS Strong transcription Weak transcription ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	12 gene(s)	inside rSNPs	diseases

Variant related diseases (count:1)

Disease	PMID	Source
Primary biliary cirrhosis	21399635	GWAS catalog

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs485499	SCHIP1	cis	lymphoblastoid	seeQTL
rs485499	IL12A	cis	lymphoblastoid	seeQTL

Chromatin state (count:30 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:159743600-159747400	Enhancers	Primary hematopoietic stem cells	blood
2	chr3:159744000-159747000	Enhancers	Primary hematopoietic stem cells short term culture	blood
3	chr3:159744000-159756200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
4	chr3:159744400-159746000	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
5	chr3:159744600-159746200	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
6	chr3:159744600-159746400	Enhancers	NHDF-Ad	bronchial
7	chr3:159744600-159746400	Enhancers	NHLF	lung
8	chr3:159744800-159746200	Flanking Active TSS	GM12878-XiMat	blood
9	chr3:159745000-159746000	Enhancers	HSMM	muscle
10	chr3:159745000-159746200	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
11	chr3:159745000-159746200	Enhancers	Muscle Satellite Cultured Cells	--
12	chr3:159745200-159746000	Enhancers	ES-I3 Cell Line	embryonic stem cell
13	chr3:159745200-159746000	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
14	chr3:159745200-159746000	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
15	chr3:159745200-159746000	Enhancers	A549	lung
16	chr3:159745200-159746000	Enhancers	Hela-S3	cervix
17	chr3:159745200-159746000	Enhancers	HMEC	breast
18	chr3:159745200-159746200	Enhancers	Primary monocytes fromperipheralblood	blood
19	chr3:159745200-159746200	Enhancers	Monocytes-CD14+_RO01746	blood
20	chr3:159745200-159747000	Enhancers	Primary T regulatory cells fromperipheralblood	blood
21	chr3:159745400-159746000	Enhancers	HUES6 Cell Line	embryonic stem cell
22	chr3:159745400-159746000	Enhancers	HSMMtube	muscle
23	chr3:159745400-159746200	Enhancers	ES-WA7 Cell Line	embryonic stem cell
24	chr3:159745400-159747800	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
25	chr3:159745600-159746400	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
26	chr3:159745600-159746400	Enhancers	Osteobl	bone
27	chr3:159745600-159750000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
28	chr3:159745800-159746200	Enhancers	NH-A	brain
29	chr3:159745800-159746400	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
30	chr3:159745800-159746400	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived

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