Variant report

Variant	rs9379774
Chromosome Location	chr6:25597043-25597044
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 49 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:48)

rs_ID	r²[population]
rs10456322	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[YRI][hapmap];0.83[AFR][1000 genomes];0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs10456323	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[YRI][hapmap];0.81[AFR][1000 genomes];0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs12191432	1.00[JPT][hapmap]
rs12192331	0.85[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[AMR][1000 genomes];0.94[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs12192342	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[YRI][hapmap];0.87[AFR][1000 genomes];0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12195457	1.00[JPT][hapmap]
rs12201249	0.81[ASN][1000 genomes]
rs12207668	0.93[AFR][1000 genomes];0.98[AMR][1000 genomes];0.88[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs12207791	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12208868	1.00[JPT][hapmap]
rs12214693	0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1410443	1.00[JPT][hapmap]
rs150533	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[AMR][1000 genomes];0.94[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs184202	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs1884575	1.00[JPT][hapmap]
rs212927	0.91[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[AMR][1000 genomes];0.94[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs212929	1.00[JPT][hapmap]
rs212931	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[AMR][1000 genomes];0.94[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs212932	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[AMR][1000 genomes];0.94[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs212935	1.00[JPT][hapmap]
rs212937	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[AMR][1000 genomes];0.94[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs212939	1.00[JPT][hapmap]
rs212940	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs301376	0.86[AMR][1000 genomes];0.92[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs301377	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs301388	0.91[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs3827502	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];0.96[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs441472	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs443641	0.90[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs453181	1.00[JPT][hapmap]
rs485567	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[AMR][1000 genomes];0.94[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs55633691	0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs55883446	0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs56285037	0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs56383372	0.87[AFR][1000 genomes];0.96[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6902158	0.84[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs6918563	0.81[ASN][1000 genomes]
rs6927384	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[YRI][hapmap];0.80[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs6931843	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[YRI][hapmap];0.85[AFR][1000 genomes];0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs72839082	0.90[AFR][1000 genomes];0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72839085	0.90[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72839087	0.92[AFR][1000 genomes];0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72839088	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72839089	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7738866	0.92[AMR][1000 genomes];0.88[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7742338	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.93[AFR][1000 genomes];0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9348685	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.93[AFR][1000 genomes];0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9461190	1.00[JPT][hapmap]

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	nsv883488	chr6:25592489-25731691	Enhancers Flanking Active TSS Weak transcription Bivalent/Poised TSS Strong transcription Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	16 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs9379774	LRRC16	cis	lesional skin	skin_eQTL

Chromatin state (count:73 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:25471600-25597200	Weak transcription	Gastric	stomach
2	chr6:25516800-25606400	Weak transcription	Lung	lung
3	chr6:25541600-25612000	Weak transcription	HUES64 Cell Line	embryonic stem cell
4	chr6:25547200-25600600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
5	chr6:25556200-25618000	Weak transcription	Primary B cells from cord blood	blood
6	chr6:25572000-25622200	Weak transcription	HSMMtube	muscle
7	chr6:25577200-25603400	Weak transcription	Fetal Brain Female	brain
8	chr6:25577200-25624800	Weak transcription	Adipose Nuclei	Adipose
9	chr6:25577600-25597200	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
10	chr6:25579200-25604600	Weak transcription	Fetal Brain Male	brain
11	chr6:25580200-25597800	Weak transcription	Hela-S3	cervix
12	chr6:25580200-25599000	Weak transcription	NHEK	skin
13	chr6:25580600-25608600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
14	chr6:25580600-25610200	Weak transcription	Primary T cells fromperipheralblood	blood
15	chr6:25580800-25599600	Weak transcription	Small Intestine	intestine
16	chr6:25581200-25622800	Weak transcription	Colonic Mucosa	Colon
17	chr6:25582000-25611400	Weak transcription	Brain Anterior Caudate	brain
18	chr6:25582000-25626800	Weak transcription	iPS-15b Cell Line	embryonic stem cell
19	chr6:25582400-25622200	Weak transcription	Duodenum Smooth Muscle	Duodenum
20	chr6:25583200-25600600	Weak transcription	Placenta	Placenta
21	chr6:25583600-25598600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
22	chr6:25583600-25623200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
23	chr6:25583800-25623200	Weak transcription	Esophagus	oesophagus
24	chr6:25584400-25597400	Weak transcription	NHDF-Ad	bronchial
25	chr6:25585000-25627000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
26	chr6:25585200-25599600	Weak transcription	Fetal Kidney	kidney
27	chr6:25585200-25629400	Weak transcription	Pancreas	Pancrea
28	chr6:25587400-25622400	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
29	chr6:25587600-25599200	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
30	chr6:25587800-25598200	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
31	chr6:25589000-25603000	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
32	chr6:25589000-25604600	Weak transcription	Fetal Thymus	thymus
33	chr6:25589200-25623400	Weak transcription	HMEC	breast
34	chr6:25590800-25618000	Weak transcription	Brain Inferior Temporal Lobe	brain
35	chr6:25591000-25601600	Strong transcription	Primary T cells from cord blood	blood
36	chr6:25592400-25602400	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
37	chr6:25592400-25625600	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
38	chr6:25592800-25598000	Strong transcription	HUES48 Cell Line	embryonic stem cell
39	chr6:25593200-25600000	Weak transcription	Placenta Amnion	Placenta Amnion
40	chr6:25593200-25608800	Weak transcription	iPS-20b Cell Line	embryonic stem cell
41	chr6:25593400-25609600	Weak transcription	Primary T helper cells fromperipheralblood	blood
42	chr6:25593600-25618600	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
43	chr6:25593800-25602200	Weak transcription	Muscle Satellite Cultured Cells	--
44	chr6:25594200-25629200	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
45	chr6:25594400-25597200	Weak transcription	Fetal Intestine Small	intestine
46	chr6:25594400-25600800	Weak transcription	Fetal Intestine Large	intestine
47	chr6:25594400-25618200	Weak transcription	Primary hematopoietic stem cells	blood
48	chr6:25594400-25627200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
49	chr6:25594600-25606400	Weak transcription	Sigmoid Colon	Sigmoid Colon
50	chr6:25594600-25607200	Weak transcription	Aorta	Aorta

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links