Variant report

Variant	rs6905563
Chromosome Location	chr6:53685743-53685744
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr6:53658699..53661103-chr6:53683402..53686266,2	MCF-7	breast:
2	chr6:53681224..53682761-chr6:53685337..53687008,2	K562	blood:
3	chr6:53680007..53681550-chr6:53684589..53687118,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000137269	Chromatin interaction
ENSG00000228614	Chromatin interaction

Extended variants
information (count: 47 )
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];0.96[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];0.94[CHB][hapmap];0.94[JPT][hapmap];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1883632	0.81[CHB][hapmap]
rs3001004	0.88[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs3001005	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs3001006	0.85[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs3001007	0.95[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	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3003490	0.85[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3003492	1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3003494	0.88[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs3003498	1.00[CEU][hapmap];0.94[CHB][hapmap];0.94[JPT][hapmap];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs35081045	0.81[ASN][1000 genomes]
rs3813850	0.84[CEU][hapmap]
rs4254992	0.85[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4486000	1.00[CEU][hapmap];0.94[CHB][hapmap];0.94[JPT][hapmap];0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4540263	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4582388	0.90[ASN][1000 genomes]
rs4618525	0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4640878	0.98[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];0.91[ASN][1000 genomes]
rs4715428	0.81[ASN][1000 genomes]
rs4715429	0.88[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];0.81[ASN][1000 genomes]
rs6905323	0.87[AMR][1000 genomes];0.99[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs6906326	0.87[CHB][hapmap];0.94[JPT][hapmap]
rs6909040	0.85[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6909094	0.95[AFR][1000 genomes];1.00[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	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9463983	0.81[AFR][1000 genomes];0.82[AMR][1000 genomes];0.95[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs9463988	0.88[ASN][1000 genomes]
rs9463996	0.88[JPT][hapmap]
rs9463997	0.82[JPT][hapmap]
rs9474643	0.81[JPT][hapmap]
rs9474661	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9474665	0.85[AFR][1000 genomes];0.97[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
rs6905563	LRRC1	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:49 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:53661400-53688200	Weak transcription	Right Ventricle	heart
2	chr6:53670200-53686400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
3	chr6:53670800-53693200	Weak transcription	H9 Cell Line	embryonic stem cell
4	chr6:53673400-53687200	Weak transcription	Fetal Muscle Leg	muscle
5	chr6:53676200-53697800	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
6	chr6:53676800-53686800	Weak transcription	Right Atrium	heart
7	chr6:53676800-53687200	Weak transcription	Brain Inferior Temporal Lobe	brain
8	chr6:53678600-53692200	Weak transcription	Esophagus	oesophagus
9	chr6:53680400-53685800	Weak transcription	Brain Angular Gyrus	brain
10	chr6:53680400-53690000	Weak transcription	Fetal Intestine Small	intestine
11	chr6:53680400-53690200	Weak transcription	Fetal Thymus	thymus
12	chr6:53680400-53691800	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
13	chr6:53680400-53692400	Weak transcription	Pancreas	Pancrea
14	chr6:53680400-53721600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
15	chr6:53680600-53687000	Weak transcription	Duodenum Smooth Muscle	Duodenum
16	chr6:53680600-53689400	Weak transcription	Fetal Intestine Large	intestine
17	chr6:53680600-53694400	Weak transcription	iPS-20b Cell Line	embryonic stem cell
18	chr6:53680800-53687200	Weak transcription	Fetal Kidney	kidney
19	chr6:53680800-53689600	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
20	chr6:53681000-53687200	Weak transcription	Aorta	Aorta
21	chr6:53681200-53689800	Weak transcription	Osteobl	bone
22	chr6:53681400-53686800	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
23	chr6:53682200-53687000	Weak transcription	Fetal Brain Female	brain
24	chr6:53682600-53689400	Weak transcription	Breast Myoepithelial Primary Cells	Breast
25	chr6:53683000-53686200	Weak transcription	Rectal Smooth Muscle	rectum
26	chr6:53683600-53689800	Weak transcription	Dnd41	blood
27	chr6:53683800-53687200	Enhancers	Brain Hippocampus Middle	brain
28	chr6:53684000-53685800	Weak transcription	Colon Smooth Muscle	Colon
29	chr6:53684000-53687200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
30	chr6:53684000-53687400	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
31	chr6:53684000-53687600	Weak transcription	Psoas Muscle	Psoas
32	chr6:53684000-53691400	Weak transcription	Hela-S3	cervix
33	chr6:53684000-53692400	Weak transcription	Left Ventricle	heart
34	chr6:53684000-53694000	Weak transcription	iPS-15b Cell Line	embryonic stem cell
35	chr6:53684000-53710200	Weak transcription	Primary T cells from cord blood	blood
36	chr6:53684200-53689400	Weak transcription	Sigmoid Colon	Sigmoid Colon
37	chr6:53684400-53687000	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
38	chr6:53684600-53686800	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
39	chr6:53684600-53690600	Weak transcription	Muscle Satellite Cultured Cells	--
40	chr6:53684600-53697000	Enhancers	Brain Substantia Nigra	brain
41	chr6:53684800-53688200	Enhancers	Brain Cingulate Gyrus	brain
42	chr6:53684800-53689800	Weak transcription	HMEC	breast
43	chr6:53685000-53685800	Enhancers	Stomach Smooth Muscle	stomach
44	chr6:53685000-53689600	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
45	chr6:53685000-53689800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
46	chr6:53685000-53690200	Weak transcription	NHEK	skin
47	chr6:53685200-53688000	Enhancers	Brain Anterior Caudate	brain
48	chr6:53685400-53685800	Weak transcription	Gastric	stomach
49	chr6:53685600-53688400	Enhancers	Pancreatic Islets	Pancreatic Islet

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