Variant report

Variant	rs3001005
Chromosome Location	chr6:53698649-53698650
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 51 )
Associated
traits (count: 1 )

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

rs_ID	r²[population]
rs10948787	0.81[EUR][1000 genomes]
rs11759220	0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12661475	0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[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];0.99[ASN][1000 genomes]
rs1883632	0.89[CHB][hapmap]
rs3001004	0.86[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs3001006	0.84[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3001007	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs3001008	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs3003488	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs3003490	0.84[AFR][1000 genomes];0.97[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];0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs3003494	0.86[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs3003498	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];1.00[TSI][hapmap];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs35081045	0.80[ASN][1000 genomes]
rs3813850	0.81[CEU][hapmap];0.82[CHB][hapmap];0.91[GIH][hapmap];0.83[JPT][hapmap];0.86[TSI][hapmap]
rs4254992	0.84[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4273680	0.85[CHD][hapmap];0.80[JPT][hapmap]
rs4478409	0.86[JPT][hapmap]
rs4486000	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.97[LWK][hapmap];0.88[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4540263	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4582388	0.91[ASN][1000 genomes]
rs4618525	0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4640878	0.95[AFR][1000 genomes];1.00[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	0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs62397076	0.92[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	0.87[AMR][1000 genomes];0.99[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs6905563	1.00[CEU][hapmap];0.94[CHB][hapmap];0.94[JPT][hapmap];0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6906326	0.94[CHB][hapmap];0.89[JPT][hapmap]
rs6909040	0.84[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6909094	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6925391	0.89[ASN][1000 genomes]
rs6928222	0.91[YRI][hapmap]
rs7750173	0.95[EUR][1000 genomes]
rs9296720	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9463983	0.82[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	0.84[CHD][hapmap];0.89[JPT][hapmap]
rs9474643	0.82[CHB][hapmap];0.89[JPT][hapmap]
rs9474661	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9474665	0.84[AFR][1000 genomes];0.97[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
rs3001005	LRRC1	cis	multi-tissue	Pritchard

Chromatin state (count:55 , 50 per page) page: 1 2

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	chr6:53689400-53699400	Enhancers	Fetal Intestine Large	intestine
5	chr6:53690000-53699000	Enhancers	Fetal Intestine Small	intestine
6	chr6:53692600-53702600	Weak transcription	Aorta	Aorta
7	chr6:53693400-53700800	Weak transcription	Pancreas	Pancrea
8	chr6:53693400-53701400	Weak transcription	HSMM	muscle
9	chr6:53693400-53720000	Weak transcription	Left Ventricle	heart
10	chr6:53693600-53698800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
11	chr6:53694000-53699000	Weak transcription	Right Atrium	heart
12	chr6:53694000-53708400	Weak transcription	Fetal Thymus	thymus
13	chr6:53695000-53702600	Weak transcription	Gastric	stomach
14	chr6:53695000-53705600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
15	chr6:53695000-53710000	Weak transcription	H9 Cell Line	embryonic stem cell
16	chr6:53695000-53719800	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
17	chr6:53695000-53743200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
18	chr6:53695600-53698800	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
19	chr6:53695600-53700800	Weak transcription	H1 Cell Line	embryonic stem cell
20	chr6:53696000-53701400	Enhancers	Brain Hippocampus Middle	brain
21	chr6:53696200-53702600	Weak transcription	iPS-18 Cell Line	embryonic stem cell
22	chr6:53696400-53699000	Weak transcription	HepG2	liver
23	chr6:53696400-53708400	Weak transcription	Sigmoid Colon	Sigmoid Colon
24	chr6:53696600-53702600	Weak transcription	HUES48 Cell Line	embryonic stem cell
25	chr6:53696800-53698800	Weak transcription	HUES64 Cell Line	embryonic stem cell
26	chr6:53696800-53699400	Enhancers	NHEK	skin
27	chr6:53696800-53699800	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
28	chr6:53697000-53700200	Weak transcription	Brain Cingulate Gyrus	brain
29	chr6:53697200-53699000	Weak transcription	Brain Inferior Temporal Lobe	brain
30	chr6:53697200-53699400	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
31	chr6:53697200-53699400	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
32	chr6:53697200-53718600	Weak transcription	Duodenum Mucosa	Duodenum
33	chr6:53697600-53698800	Enhancers	Brain Anterior Caudate	brain
34	chr6:53697800-53698800	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
35	chr6:53697800-53698800	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
36	chr6:53697800-53699200	Enhancers	Brain Germinal Matrix	brain
37	chr6:53697800-53699600	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
38	chr6:53698000-53698800	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
39	chr6:53698000-53699000	Enhancers	Cortex derived primary cultured neurospheres	brain
40	chr6:53698000-53699400	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
41	chr6:53698000-53700800	Weak transcription	Rectal Smooth Muscle	rectum
42	chr6:53698000-53702200	Weak transcription	Colon Smooth Muscle	Colon
43	chr6:53698000-53702600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
44	chr6:53698000-53715600	Weak transcription	Rectal Mucosa Donor 31	rectum
45	chr6:53698200-53699200	Weak transcription	Placenta Amnion	Placenta Amnion
46	chr6:53698200-53702200	Weak transcription	Thymus	Thymus
47	chr6:53698200-53702600	Weak transcription	Duodenum Smooth Muscle	Duodenum
48	chr6:53698200-53702800	Weak transcription	HSMMtube	muscle
49	chr6:53698200-53702800	Weak transcription	HUVEC	blood vessel
50	chr6:53698400-53699200	Enhancers	Brain Substantia Nigra	brain

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