Variant report

Variant	rs4254992
Chromosome Location	chr6:53696752-53696753
allele	A/C
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:47)

rs_ID	r²[population]
rs10948787	0.81[EUR][1000 genomes]
rs11759220	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12661475	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[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];0.98[ASN][1000 genomes]
rs1883632	0.89[CHB][hapmap]
rs3001004	0.94[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs3001005	0.84[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs3001006	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs3001007	0.83[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs3001008	0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs3003488	0.81[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3003490	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[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];1.00[ASN][1000 genomes]
rs3003494	0.94[AFR][1000 genomes];0.98[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];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs35081045	0.81[ASN][1000 genomes]
rs3813850	0.82[CHB][hapmap];0.83[JPT][hapmap]
rs4273680	0.80[JPT][hapmap]
rs4478409	0.87[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];0.99[ASN][1000 genomes]
rs4540263	0.83[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4582388	0.90[ASN][1000 genomes]
rs4618525	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4640878	0.83[AFR][1000 genomes];0.97[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];0.91[ASN][1000 genomes]
rs4715428	0.81[ASN][1000 genomes]
rs4715429	0.88[ASN][1000 genomes]
rs60467893	0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs62397076	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs62397090	0.99[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs6905323	0.90[AMR][1000 genomes];0.99[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs6905563	1.00[CEU][hapmap];0.94[CHB][hapmap];0.94[JPT][hapmap];0.85[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6906326	0.94[CHB][hapmap];0.90[JPT][hapmap]
rs6909040	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6909094	0.86[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6925391	0.88[ASN][1000 genomes]
rs7750173	0.95[EUR][1000 genomes]
rs9296720	0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9463983	0.95[AFR][1000 genomes];0.85[AMR][1000 genomes];0.95[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs9463988	0.88[ASN][1000 genomes]
rs9463996	0.95[JPT][hapmap]
rs9463997	0.89[JPT][hapmap]
rs9474643	0.82[CHB][hapmap];0.89[JPT][hapmap]
rs9474661	0.85[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9474665	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 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

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs4254992	LRRC1	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:58 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:53676200-53697800	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
2	chr6:53680400-53721600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
3	chr6:53684000-53710200	Weak transcription	Primary T cells from cord blood	blood
4	chr6:53684600-53697000	Enhancers	Brain Substantia Nigra	brain
5	chr6:53687600-53702000	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
6	chr6:53689400-53699400	Enhancers	Fetal Intestine Large	intestine
7	chr6:53689800-53697200	Enhancers	Colon Smooth Muscle	Colon
8	chr6:53690000-53699000	Enhancers	Fetal Intestine Small	intestine
9	chr6:53690400-53697200	Enhancers	Brain Anterior Caudate	brain
10	chr6:53691200-53697800	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
11	chr6:53691400-53697400	Enhancers	Rectal Mucosa Donor 31	rectum
12	chr6:53692400-53697800	Weak transcription	Brain Germinal Matrix	brain
13	chr6:53692600-53702600	Weak transcription	Aorta	Aorta
14	chr6:53693400-53696800	Weak transcription	HSMMtube	muscle
15	chr6:53693400-53697200	Enhancers	Duodenum Mucosa	Duodenum
16	chr6:53693400-53697800	Weak transcription	Thymus	Thymus
17	chr6:53693400-53700800	Weak transcription	Pancreas	Pancrea
18	chr6:53693400-53701400	Weak transcription	HSMM	muscle
19	chr6:53693400-53720000	Weak transcription	Left Ventricle	heart
20	chr6:53693600-53698800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
21	chr6:53694000-53696800	Enhancers	HUES64 Cell Line	embryonic stem cell
22	chr6:53694000-53697000	Enhancers	iPS-15b Cell Line	embryonic stem cell
23	chr6:53694000-53698600	Enhancers	Pancreatic Islets	Pancreatic Islet
24	chr6:53694000-53699000	Weak transcription	Right Atrium	heart
25	chr6:53694000-53708400	Weak transcription	Fetal Thymus	thymus
26	chr6:53694400-53696800	Enhancers	Rectal Smooth Muscle	rectum
27	chr6:53694600-53697800	Weak transcription	HUVEC	blood vessel
28	chr6:53694800-53696800	Enhancers	Small Intestine	intestine
29	chr6:53694800-53697400	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
30	chr6:53695000-53697800	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
31	chr6:53695000-53697800	Weak transcription	HMEC	breast
32	chr6:53695000-53698000	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
33	chr6:53695000-53702600	Weak transcription	Gastric	stomach
34	chr6:53695000-53705600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
35	chr6:53695000-53710000	Weak transcription	H9 Cell Line	embryonic stem cell
36	chr6:53695000-53719800	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
37	chr6:53695000-53743200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
38	chr6:53695200-53696800	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
39	chr6:53695200-53697000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
40	chr6:53695200-53698600	Weak transcription	Brain Angular Gyrus	brain
41	chr6:53695400-53697200	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
42	chr6:53695400-53698000	Weak transcription	Cortex derived primary cultured neurospheres	brain
43	chr6:53695600-53696800	Weak transcription	NHEK	skin
44	chr6:53695600-53697800	Weak transcription	Hela-S3	cervix
45	chr6:53695600-53698800	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
46	chr6:53695600-53700800	Weak transcription	H1 Cell Line	embryonic stem cell
47	chr6:53695800-53697000	Enhancers	Brain Cingulate Gyrus	brain
48	chr6:53696000-53701400	Enhancers	Brain Hippocampus Middle	brain
49	chr6:53696200-53697200	Enhancers	Brain Inferior Temporal Lobe	brain
50	chr6:53696200-53702600	Weak transcription	iPS-18 Cell Line	embryonic stem cell

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