Variant report

Variant	rs11161614
Chromosome Location	chr1:85898160-85898161
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 48 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:46)

rs_ID	r²[population]
rs10158674	0.81[CEU][hapmap];0.84[GIH][hapmap]
rs11161599	0.81[CEU][hapmap]
rs11161615	0.81[CEU][hapmap]
rs11161616	0.82[ASW][hapmap];0.90[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.90[GIH][hapmap];1.00[JPT][hapmap];0.86[MEX][hapmap];0.87[AMR][1000 genomes];0.83[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11161617	0.82[ASW][hapmap];0.90[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.80[GIH][hapmap];0.86[MEX][hapmap];0.86[AMR][1000 genomes];0.83[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs11802390	1.00[YRI][hapmap]
rs11809826	1.00[YRI][hapmap]
rs11809833	1.00[YRI][hapmap]
rs12033170	1.00[YRI][hapmap]
rs12049529	0.87[AMR][1000 genomes];0.83[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12118950	0.86[CEU][hapmap];0.87[EUR][1000 genomes]
rs12120551	0.81[EUR][1000 genomes]
rs12123745	0.86[CEU][hapmap];0.89[EUR][1000 genomes]
rs12125900	0.84[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs12128907	0.90[CEU][hapmap];0.84[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs12129013	0.91[CEU][hapmap];0.87[MEX][hapmap];0.86[AMR][1000 genomes]
rs12129502	0.89[CEU][hapmap];0.82[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs12130145	0.81[CEU][hapmap];0.81[EUR][1000 genomes]
rs12130380	1.00[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12130591	0.82[ASW][hapmap];0.85[GIH][hapmap];1.00[MKK][hapmap]
rs12131926	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12132677	0.86[CEU][hapmap];0.87[EUR][1000 genomes]
rs12133722	0.86[CEU][hapmap];0.95[GIH][hapmap];0.80[MEX][hapmap];0.86[TSI][hapmap];0.87[EUR][1000 genomes]
rs12135333	1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.85[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs12138852	0.86[CEU][hapmap];0.87[EUR][1000 genomes]
rs12139958	0.87[EUR][1000 genomes]
rs12140170	0.87[EUR][1000 genomes]
rs12140457	0.86[CEU][hapmap];0.86[EUR][1000 genomes]
rs12140935	0.87[EUR][1000 genomes]
rs12717763	0.81[CEU][hapmap];0.84[GIH][hapmap];0.81[EUR][1000 genomes]
rs12724823	0.85[GIH][hapmap]
rs12736004	0.81[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs12743049	0.86[CEU][hapmap];0.82[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs12758237	0.85[CEU][hapmap];0.87[EUR][1000 genomes]
rs12758768	0.85[EUR][1000 genomes]
rs1498374	0.81[CEU][hapmap];0.84[GIH][hapmap]
rs1608536	0.85[CEU][hapmap];0.87[EUR][1000 genomes]
rs17384381	0.82[ASW][hapmap];0.81[CEU][hapmap];0.95[GIH][hapmap];0.86[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.85[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs17388521	0.86[CEU][hapmap];0.95[GIH][hapmap];0.93[MEX][hapmap];0.86[TSI][hapmap];0.82[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs2076699	0.81[CEU][hapmap];0.84[GIH][hapmap];0.81[EUR][1000 genomes]
rs2300639	0.81[CEU][hapmap];0.81[EUR][1000 genomes]
rs2300640	0.81[EUR][1000 genomes]
rs35193119	0.87[EUR][1000 genomes]
rs36110608	0.87[EUR][1000 genomes]
rs3768223	0.81[EUR][1000 genomes]
rs986639	0.86[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1006994	chr1:85454304-86327679	Active TSS Enhancers Weak transcription Flanking Active TSS Strong transcription Flanking Bivalent TSS/Enh Genic enhancers ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	72 gene(s)	inside rSNPs	diseases
2	nsv830470	chr1:85820775-86014080	Enhancers Weak transcription Genic enhancers Flanking Active TSS ZNF genes & repeats Strong transcription Active TSS Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs11161614	BCL10	cis	parietal	SCAN

Chromatin state (count:27 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:85874000-85903800	Weak transcription	NHLF	lung
2	chr1:85874200-85903600	Weak transcription	Muscle Satellite Cultured Cells	--
3	chr1:85874400-85903600	Weak transcription	HepG2	liver
4	chr1:85874400-85904200	Weak transcription	NH-A	brain
5	chr1:85886400-85899000	Weak transcription	NHDF-Ad	bronchial
6	chr1:85886400-85903800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
7	chr1:85886400-85914200	Weak transcription	HSMMtube	muscle
8	chr1:85886800-85903800	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
9	chr1:85887600-85902200	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
10	chr1:85887600-85903400	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
11	chr1:85890400-85902200	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
12	chr1:85892200-85906200	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
13	chr1:85893800-85906200	Weak transcription	Rectal Smooth Muscle	rectum
14	chr1:85893800-85916800	Weak transcription	Breast Myoepithelial Primary Cells	Breast
15	chr1:85894400-85903600	Weak transcription	Skeletal Muscle Female	skeletal muscle
16	chr1:85894600-85903600	Weak transcription	Adipose Nuclei	Adipose
17	chr1:85894600-85903800	Weak transcription	HUVEC	blood vessel
18	chr1:85894600-85904200	Weak transcription	Fetal Intestine Small	intestine
19	chr1:85896400-85899400	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
20	chr1:85897000-85899200	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
21	chr1:85897000-85899400	Strong transcription	HSMM	muscle
22	chr1:85897000-85904200	Weak transcription	Fetal Intestine Large	intestine
23	chr1:85897200-85899200	Strong transcription	Osteobl	bone
24	chr1:85897400-85900400	Weak transcription	Fetal Brain Female	brain
25	chr1:85897800-85904200	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
26	chr1:85897800-85904800	Weak transcription	Cortex derived primary cultured neurospheres	brain
27	chr1:85898000-85902200	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin

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