Variant report

Variant	rs11752017
Chromosome Location	chr6:25372665-25372666
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 41 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:36)

rs_ID	r²[population]
rs10456322	1.00[JPT][hapmap]
rs10456323	1.00[JPT][hapmap]
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];0.87[EUR][1000 genomes]
rs12154021	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs12192331	1.00[JPT][hapmap]
rs12203031	1.00[JPT][hapmap];1.00[YRI][hapmap]
rs12203442	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]
rs12211739	1.00[JPT][hapmap];1.00[YRI][hapmap]
rs1410443	1.00[JPT][hapmap]
rs150533	1.00[JPT][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]
rs301377	1.00[JPT][hapmap]
rs441472	1.00[JPT][hapmap]
rs453181	1.00[JPT][hapmap]
rs485567	1.00[JPT][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]
rs7752524	1.00[JPT][hapmap]
rs7762537	1.00[JPT][hapmap]
rs7764258	1.00[JPT][hapmap]
rs9348685	1.00[JPT][hapmap]
rs9461151	0.89[CEU][hapmap];1.00[JPT][hapmap];0.87[EUR][1000 genomes]
rs9467496	0.89[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
rs11752017	LRRC16	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:19 , 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	chr6:25368200-25375400	Weak transcription	Primary B cells from cord blood	blood
3	chr6:25370400-25374000	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
4	chr6:25370400-25377200	Weak transcription	Right Atrium	heart
5	chr6:25370400-25378400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
6	chr6:25370800-25377200	Weak transcription	Gastric	stomach
7	chr6:25370800-25388800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
8	chr6:25371000-25373800	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
9	chr6:25371000-25377000	Weak transcription	Pancreas	Pancrea
10	chr6:25371000-25377400	Weak transcription	Aorta	Aorta
11	chr6:25371200-25374000	Weak transcription	Small Intestine	intestine
12	chr6:25371400-25378400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
13	chr6:25371600-25373800	Enhancers	Primary T helper naive cells fromperipheralblood	blood
14	chr6:25371600-25373800	Enhancers	Primary T helper cells PMA-I stimulated	--
15	chr6:25371600-25377000	Weak transcription	Fetal Intestine Small	intestine
16	chr6:25371800-25377400	Weak transcription	Thymus	Thymus
17	chr6:25372000-25375600	Weak transcription	HUES48 Cell Line	embryonic stem cell
18	chr6:25372400-25372800	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
19	chr6:25372400-25375200	Weak transcription	Primary T helper cells fromperipheralblood	blood

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