Variant report

Variant	rs12203442
Chromosome Location	chr6:25377798-25377799
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr6:25375050..25376557-chr6:25376841..25379401,2	K562	blood:

Extended variants
information (count: 55 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:50)

rs_ID	r²[population]
rs10456322	1.00[JPT][hapmap]
rs10456323	1.00[JPT][hapmap]
rs11752017	1.00[CEU][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11759560	1.00[JPT][hapmap];1.00[YRI][hapmap]
rs11759648	1.00[CEU][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.88[AFR][1000 genomes];0.94[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs12154021	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs12192331	1.00[JPT][hapmap]
rs12203031	1.00[JPT][hapmap];1.00[YRI][hapmap]
rs12211739	1.00[JPT][hapmap];1.00[YRI][hapmap]
rs1410443	1.00[JPT][hapmap]
rs150533	1.00[JPT][hapmap]
rs1810471	1.00[CHB][hapmap]
rs184202	1.00[JPT][hapmap]
rs212927	1.00[JPT][hapmap]
rs212929	1.00[JPT][hapmap]
rs212931	1.00[JPT][hapmap]
rs212932	1.00[JPT][hapmap]
rs212935	1.00[JPT][hapmap]
rs212937	1.00[JPT][hapmap]
rs212939	1.00[JPT][hapmap]
rs212940	1.00[JPT][hapmap]
rs2690056	1.00[CHB][hapmap]
rs2690062	1.00[CHB][hapmap]
rs2690066	1.00[CHB][hapmap]
rs2744263	1.00[CHB][hapmap]
rs2744273	1.00[CHB][hapmap]
rs2744274	1.00[CHB][hapmap]
rs2744279	1.00[CHB][hapmap]
rs2744281	1.00[CHB][hapmap]
rs2744286	1.00[CHB][hapmap]
rs301377	1.00[JPT][hapmap]
rs441472	1.00[JPT][hapmap]
rs453181	1.00[JPT][hapmap]
rs4594940	1.00[CHB][hapmap]
rs485567	1.00[JPT][hapmap]
rs6456661	1.00[CHB][hapmap]
rs6902158	1.00[JPT][hapmap]
rs6927384	1.00[JPT][hapmap]
rs6931843	1.00[JPT][hapmap]
rs716796	1.00[JPT][hapmap]
rs760865	1.00[JPT][hapmap]
rs7742338	1.00[JPT][hapmap]
rs7743508	1.00[CHB][hapmap]
rs7743997	1.00[CHB][hapmap]
rs7752524	1.00[JPT][hapmap]
rs7762537	1.00[JPT][hapmap]
rs7764258	1.00[JPT][hapmap]
rs9348685	1.00[JPT][hapmap]
rs9461151	1.00[CEU][hapmap];1.00[JPT][hapmap];0.88[EUR][1000 genomes]
rs9467496	0.86[CEU][hapmap]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv883485	chr6:25259137-25437986	Weak transcription Enhancers Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS Strong transcription Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
2	nsv883486	chr6:25260434-25422369	Weak transcription Enhancers Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats Strong transcription Bivalent/Poised TSS Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
3	nsv883487	chr6:25280119-25508868	Weak transcription Enhancers Flanking Active TSS Strong transcription Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
4	nsv830612	chr6:25342408-25509758	Enhancers Strong transcription Weak transcription Flanking Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Genic enhancers Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
5	nsv601168	chr6:25346334-25393306	Enhancers Weak transcription Flanking Active TSS Bivalent Enhancer Active TSS ZNF genes & repeats Genic enhancers Strong transcription Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region	3 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs12203442	LRRC16	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:16 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:25368000-25378400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
2	chr6:25370400-25378400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
3	chr6:25370800-25388800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
4	chr6:25371400-25378400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
5	chr6:25375800-25378400	Weak transcription	HUES48 Cell Line	embryonic stem cell
6	chr6:25375800-25381200	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
7	chr6:25377000-25377800	Enhancers	Pancreas	Pancrea
8	chr6:25377200-25378800	Enhancers	Right Atrium	heart
9	chr6:25377200-25379000	Enhancers	Fetal Thymus	thymus
10	chr6:25377400-25378600	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
11	chr6:25377400-25378800	Enhancers	Aorta	Aorta
12	chr6:25377400-25379200	Enhancers	Thymus	Thymus
13	chr6:25377400-25410600	Weak transcription	Gastric	stomach
14	chr6:25377600-25377800	ZNF genes & repeats	Fetal Intestine Small	intestine
15	chr6:25377600-25378000	Enhancers	Primary T helper naive cells fromperipheralblood	blood
16	chr6:25377600-25378800	Enhancers	GM12878-XiMat	blood

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