Variant report

Variant	rs12207791
Chromosome Location	chr6:25580821-25580822
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr6:25577394..25580689-chr6:25580776..25585685,6	MCF-7	breast:
2	chr6:25566255..25568302-chr6:25580219..25582911,2	MCF-7	breast:

Extended variants
information (count: 54 )
Associated
traits (count: 1 )

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

rs_ID	r²[population]
rs10456322	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[YRI][hapmap];0.84[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs10456323	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[YRI][hapmap];0.86[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs11759560	1.00[JPT][hapmap]
rs12191432	1.00[JPT][hapmap]
rs12192331	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs12192342	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[YRI][hapmap];0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12195457	1.00[JPT][hapmap]
rs12201249	0.81[ASN][1000 genomes]
rs12203031	1.00[JPT][hapmap]
rs12207668	0.98[AFR][1000 genomes];0.94[AMR][1000 genomes];0.88[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs12208868	1.00[JPT][hapmap]
rs12211739	1.00[JPT][hapmap]
rs12214693	0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1410443	1.00[JPT][hapmap]
rs150533	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[AMR][1000 genomes];0.99[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs184202	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs1884575	1.00[JPT][hapmap]
rs212927	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[AMR][1000 genomes];0.99[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs212929	1.00[JPT][hapmap]
rs212931	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[AMR][1000 genomes];0.99[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs212932	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[AMR][1000 genomes];0.99[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs212935	1.00[JPT][hapmap]
rs212937	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[AMR][1000 genomes];0.99[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs212939	1.00[JPT][hapmap]
rs212940	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2762357	0.82[EUR][1000 genomes]
rs301376	0.90[AMR][1000 genomes];0.97[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs301377	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs301388	0.95[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs3827502	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs441472	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs443641	0.94[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs453181	1.00[JPT][hapmap]
rs485567	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[AMR][1000 genomes];0.99[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs55633691	0.92[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs55883446	0.90[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs56285037	0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs56383372	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6902158	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs6918563	0.81[ASN][1000 genomes]
rs6927384	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[YRI][hapmap];0.84[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs6931843	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[YRI][hapmap];0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs716796	1.00[JPT][hapmap]
rs72839082	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72839085	0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72839087	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72839088	1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72839089	0.97[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7738866	0.81[AFR][1000 genomes];0.88[AMR][1000 genomes];0.87[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7742338	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9348685	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9379774	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]
rs9461151	1.00[JPT][hapmap]
rs9461190	1.00[JPT][hapmap]

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs12207791	LRRC16	cis	lesional skin	skin_eQTL

Chromatin state (count:61 , 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	chr6:25522400-25588600	Weak transcription	HMEC	breast
4	chr6:25530800-25584200	Weak transcription	Fetal Intestine Small	intestine
5	chr6:25538600-25592800	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
6	chr6:25539200-25582000	Weak transcription	Rectal Mucosa Donor 29	rectum
7	chr6:25541600-25584400	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
8	chr6:25541600-25612000	Weak transcription	HUES64 Cell Line	embryonic stem cell
9	chr6:25544000-25593600	Weak transcription	Fetal Lung	lung
10	chr6:25547200-25600600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
11	chr6:25556200-25618000	Weak transcription	Primary B cells from cord blood	blood
12	chr6:25557200-25591400	Weak transcription	Ovary	ovary
13	chr6:25564200-25582600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
14	chr6:25565400-25583400	Weak transcription	Rectal Mucosa Donor 31	rectum
15	chr6:25565800-25581400	Weak transcription	Fetal Intestine Large	intestine
16	chr6:25566000-25581400	Weak transcription	Breast Myoepithelial Primary Cells	Breast
17	chr6:25566400-25581000	Weak transcription	Aorta	Aorta
18	chr6:25566400-25581600	Weak transcription	Duodenum Mucosa	Duodenum
19	chr6:25568000-25581400	Weak transcription	Primary T cells from cord blood	blood
20	chr6:25571200-25581600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
21	chr6:25572000-25622200	Weak transcription	HSMMtube	muscle
22	chr6:25574200-25594200	Weak transcription	H9 Cell Line	embryonic stem cell
23	chr6:25577000-25590600	Weak transcription	Brain Angular Gyrus	brain
24	chr6:25577200-25592000	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
25	chr6:25577200-25594200	Weak transcription	Brain Substantia Nigra	brain
26	chr6:25577200-25603400	Weak transcription	Fetal Brain Female	brain
27	chr6:25577200-25624800	Weak transcription	Adipose Nuclei	Adipose
28	chr6:25577400-25581400	Weak transcription	Sigmoid Colon	Sigmoid Colon
29	chr6:25577400-25582000	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
30	chr6:25577600-25581200	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
31	chr6:25577600-25597200	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
32	chr6:25578600-25581200	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
33	chr6:25578600-25583200	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
34	chr6:25579000-25581200	Weak transcription	Cortex derived primary cultured neurospheres	brain
35	chr6:25579200-25604600	Weak transcription	Fetal Brain Male	brain
36	chr6:25579600-25588600	Weak transcription	Primary hematopoietic stem cells	blood
37	chr6:25579600-25593200	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
38	chr6:25579800-25581000	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
39	chr6:25580000-25581000	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
40	chr6:25580000-25581000	Enhancers	Primary T helper cells PMA-I stimulated	--
41	chr6:25580000-25583000	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
42	chr6:25580000-25588400	Weak transcription	iPS-20b Cell Line	embryonic stem cell
43	chr6:25580000-25590000	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
44	chr6:25580200-25581000	Flanking Active TSS	Dnd41	blood
45	chr6:25580200-25584200	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
46	chr6:25580200-25585000	Weak transcription	HUES48 Cell Line	embryonic stem cell
47	chr6:25580200-25597800	Weak transcription	Hela-S3	cervix
48	chr6:25580200-25599000	Weak transcription	NHEK	skin
49	chr6:25580400-25584600	Weak transcription	Fetal Kidney	kidney
50	chr6:25580400-25592600	Weak transcription	Primary T helper naive cells fromperipheralblood	blood

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