Variant report

Variant	rs6909094
Chromosome Location	chr6:53712327-53712328
allele	A/G
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:45)

rs_ID	r²[population]
rs10948787	0.81[EUR][1000 genomes]
rs11759220	0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12661475	0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12661938	0.81[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs12663216	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1883632	0.88[CHB][hapmap]
rs3001004	0.84[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs3001005	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs3001006	0.86[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs3001007	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs3001008	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs3003488	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs3003490	0.86[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs3003492	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs3003494	0.84[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs3003498	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs3813850	0.82[CEU][hapmap];0.81[CHB][hapmap];0.85[JPT][hapmap]
rs4254992	0.86[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4478409	0.90[JPT][hapmap]
rs4486000	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4540263	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4582388	0.92[ASN][1000 genomes]
rs4618525	0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4640878	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4645422	0.80[EUR][1000 genomes]
rs4715427	0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4715428	0.83[ASN][1000 genomes]
rs4715429	0.90[ASN][1000 genomes]
rs60467893	0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs62397076	0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs62397090	0.99[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs6905323	0.87[AMR][1000 genomes];0.99[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs6905563	1.00[CEU][hapmap];0.94[CHB][hapmap];0.92[JPT][hapmap];0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6906326	0.94[CHB][hapmap];0.86[JPT][hapmap]
rs6909040	0.86[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6925391	0.90[ASN][1000 genomes]
rs7750173	0.95[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs9296720	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9463983	0.81[AFR][1000 genomes];0.82[AMR][1000 genomes];0.95[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs9463988	0.90[ASN][1000 genomes]
rs9463996	0.93[JPT][hapmap]
rs9463997	0.92[JPT][hapmap]
rs9474643	0.81[CHB][hapmap];0.92[JPT][hapmap]
rs9474661	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9474665	0.86[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1034955	chr6:53447607-53931055	Enhancers Bivalent Enhancer Weak transcription Flanking Active TSS Flanking Bivalent TSS/Enh Active TSS Strong transcription Bivalent/Poised TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	35 gene(s)	inside rSNPs	diseases
2	nsv1021506	chr6:53600338-53770482	Flanking Active TSS Weak transcription Enhancers Active TSS Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Strong transcription Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	diseases
3	nsv830664	chr6:53698021-53825270	Enhancers Weak transcription Strong transcription ZNF genes & repeats Genic enhancers Flanking Active TSS Active TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	5 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs6909094	LRRC1	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:47 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:53680400-53721600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
2	chr6:53693400-53720000	Weak transcription	Left Ventricle	heart
3	chr6:53695000-53719800	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
4	chr6:53695000-53743200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
5	chr6:53697200-53718600	Weak transcription	Duodenum Mucosa	Duodenum
6	chr6:53698000-53715600	Weak transcription	Rectal Mucosa Donor 31	rectum
7	chr6:53703000-53718600	Weak transcription	Pancreas	Pancrea
8	chr6:53703200-53720000	Weak transcription	HSMMtube	muscle
9	chr6:53703200-53720200	Weak transcription	Aorta	Aorta
10	chr6:53703200-53726400	Weak transcription	Fetal Stomach	stomach
11	chr6:53703800-53717200	Weak transcription	Primary hematopoietic stem cells	blood
12	chr6:53703800-53727600	Weak transcription	Stomach Smooth Muscle	stomach
13	chr6:53705400-53718800	Weak transcription	NHEK	skin
14	chr6:53706000-53720200	Weak transcription	Esophagus	oesophagus
15	chr6:53706000-53722400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
16	chr6:53706200-53722000	Weak transcription	H1 Cell Line	embryonic stem cell
17	chr6:53706400-53714400	Weak transcription	Fetal Muscle Trunk	muscle
18	chr6:53706400-53720200	Weak transcription	Fetal Muscle Leg	muscle
19	chr6:53707600-53718800	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
20	chr6:53707800-53712800	Weak transcription	Placenta	Placenta
21	chr6:53707800-53718800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
22	chr6:53708000-53712400	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
23	chr6:53708600-53712400	Weak transcription	Small Intestine	intestine
24	chr6:53709400-53718600	Weak transcription	Gastric	stomach
25	chr6:53709600-53719800	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
26	chr6:53709800-53719800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
27	chr6:53709800-53762200	Weak transcription	Primary B cells from cord blood	blood
28	chr6:53710200-53713200	Enhancers	Brain Cingulate Gyrus	brain
29	chr6:53710400-53713000	Enhancers	Brain Substantia Nigra	brain
30	chr6:53710400-53720400	Weak transcription	Rectal Mucosa Donor 29	rectum
31	chr6:53710600-53712800	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
32	chr6:53710600-53713000	Enhancers	Brain Inferior Temporal Lobe	brain
33	chr6:53710800-53712400	Genic enhancers	Dnd41	blood
34	chr6:53710800-53712800	Enhancers	Brain Angular Gyrus	brain
35	chr6:53710800-53713000	Enhancers	Brain Anterior Caudate	brain
36	chr6:53711000-53712400	Weak transcription	Colon Smooth Muscle	Colon
37	chr6:53711000-53715600	Weak transcription	Fetal Intestine Small	intestine
38	chr6:53711200-53712400	Weak transcription	Primary T cells from cord blood	blood
39	chr6:53711200-53712400	Weak transcription	Sigmoid Colon	Sigmoid Colon
40	chr6:53711200-53718800	Weak transcription	Fetal Intestine Large	intestine
41	chr6:53711200-53719800	Weak transcription	Rectal Smooth Muscle	rectum
42	chr6:53711200-53720400	Weak transcription	Cortex derived primary cultured neurospheres	brain
43	chr6:53711400-53712400	Weak transcription	Fetal Thymus	thymus
44	chr6:53711400-53719600	Weak transcription	Thymus	Thymus
45	chr6:53711800-53713400	Enhancers	HepG2	liver
46	chr6:53712200-53712600	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
47	chr6:53712200-53713200	Enhancers	Brain Hippocampus Middle	brain

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