Variant report

Variant	rs3001006
Chromosome Location	chr6:53700093-53700094
allele	C/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:46)

rs_ID	r²[population]
rs10948787	0.81[EUR][1000 genomes]
rs11759220	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12661475	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12661938	0.90[AFR][1000 genomes];0.84[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs12663216	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1883632	0.94[CHB][hapmap]
rs3001004	0.94[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs3001005	0.84[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3001007	0.83[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs3001008	0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs3003488	0.81[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs3003490	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs3003492	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs3003494	0.94[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs3003498	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs35081045	0.80[ASN][1000 genomes]
rs3813850	0.80[CHB][hapmap];0.81[JPT][hapmap]
rs4254992	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4478409	0.85[JPT][hapmap]
rs4486000	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4540263	0.83[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4582388	0.91[ASN][1000 genomes]
rs4618525	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4640878	0.83[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4645422	0.80[EUR][1000 genomes]
rs4715427	0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4715428	0.82[ASN][1000 genomes]
rs4715429	0.89[ASN][1000 genomes]
rs60467893	0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs62397076	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs62397090	0.99[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs6905323	0.90[AMR][1000 genomes];0.99[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs6905563	1.00[CEU][hapmap];0.93[CHB][hapmap];0.94[JPT][hapmap];0.85[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6906326	0.94[CHB][hapmap];0.89[JPT][hapmap]
rs6909040	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6909094	0.86[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6925391	0.89[ASN][1000 genomes]
rs7750173	0.95[EUR][1000 genomes]
rs9296720	0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9463983	0.95[AFR][1000 genomes];0.85[AMR][1000 genomes];0.95[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs9463988	0.89[ASN][1000 genomes]
rs9463996	0.94[JPT][hapmap]
rs9463997	0.82[CHB][hapmap];0.88[JPT][hapmap]
rs9474643	0.81[CHB][hapmap];0.87[JPT][hapmap]
rs9474661	0.85[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9474665	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[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
rs3001006	LRRC1	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:50 , 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	chr6:53684000-53710200	Weak transcription	Primary T cells from cord blood	blood
3	chr6:53687600-53702000	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
4	chr6:53692600-53702600	Weak transcription	Aorta	Aorta
5	chr6:53693400-53700800	Weak transcription	Pancreas	Pancrea
6	chr6:53693400-53701400	Weak transcription	HSMM	muscle
7	chr6:53693400-53720000	Weak transcription	Left Ventricle	heart
8	chr6:53694000-53708400	Weak transcription	Fetal Thymus	thymus
9	chr6:53695000-53702600	Weak transcription	Gastric	stomach
10	chr6:53695000-53705600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
11	chr6:53695000-53710000	Weak transcription	H9 Cell Line	embryonic stem cell
12	chr6:53695000-53719800	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
13	chr6:53695000-53743200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
14	chr6:53695600-53700800	Weak transcription	H1 Cell Line	embryonic stem cell
15	chr6:53696000-53701400	Enhancers	Brain Hippocampus Middle	brain
16	chr6:53696200-53702600	Weak transcription	iPS-18 Cell Line	embryonic stem cell
17	chr6:53696400-53708400	Weak transcription	Sigmoid Colon	Sigmoid Colon
18	chr6:53696600-53702600	Weak transcription	HUES48 Cell Line	embryonic stem cell
19	chr6:53697000-53700200	Weak transcription	Brain Cingulate Gyrus	brain
20	chr6:53697200-53718600	Weak transcription	Duodenum Mucosa	Duodenum
21	chr6:53698000-53700800	Weak transcription	Rectal Smooth Muscle	rectum
22	chr6:53698000-53702200	Weak transcription	Colon Smooth Muscle	Colon
23	chr6:53698000-53702600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
24	chr6:53698000-53715600	Weak transcription	Rectal Mucosa Donor 31	rectum
25	chr6:53698200-53702200	Weak transcription	Thymus	Thymus
26	chr6:53698200-53702600	Weak transcription	Duodenum Smooth Muscle	Duodenum
27	chr6:53698200-53702800	Weak transcription	HSMMtube	muscle
28	chr6:53698200-53702800	Weak transcription	HUVEC	blood vessel
29	chr6:53698400-53702600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
30	chr6:53698600-53702600	Weak transcription	HMEC	breast
31	chr6:53698800-53700600	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
32	chr6:53699000-53700200	Weak transcription	Cortex derived primary cultured neurospheres	brain
33	chr6:53699000-53704800	Weak transcription	Fetal Intestine Small	intestine
34	chr6:53699200-53700800	Weak transcription	Brain Germinal Matrix	brain
35	chr6:53699200-53700800	Weak transcription	Brain Substantia Nigra	brain
36	chr6:53699200-53702000	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
37	chr6:53699200-53702000	Weak transcription	Pancreatic Islets	Pancreatic Islet
38	chr6:53699200-53702600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
39	chr6:53699200-53703400	Weak transcription	HUES64 Cell Line	embryonic stem cell
40	chr6:53699400-53702000	Weak transcription	NHEK	skin
41	chr6:53699400-53702200	Weak transcription	Brain Anterior Caudate	brain
42	chr6:53699400-53702400	Weak transcription	Fetal Heart	heart
43	chr6:53699400-53702600	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
44	chr6:53699400-53702600	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
45	chr6:53699400-53709200	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
46	chr6:53699800-53700200	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
47	chr6:53700000-53700400	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
48	chr6:53700000-53700400	Enhancers	Brain Angular Gyrus	brain
49	chr6:53700000-53701200	Enhancers	Brain Inferior Temporal Lobe	brain
50	chr6:53700000-53704800	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived

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