Variant report

Variant	rs1543356
Chromosome Location	chr6:53788361-53788362
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr6:53649451..53651865-chr6:53788090..53790923,2	MCF-7	breast:

Extended variants
information (count: 39 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:37)

rs_ID	r²[population]
rs10498795	0.87[AMR][1000 genomes]
rs12196155	0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs16884427	0.82[AFR][1000 genomes];0.95[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs2223617	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs2473599	0.90[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2473601	0.93[EUR][1000 genomes]
rs2473603	0.95[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs2494087	0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2494089	0.93[EUR][1000 genomes]
rs2494090	0.87[AMR][1000 genomes];0.96[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2494091	0.89[AMR][1000 genomes];0.93[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2745460	0.96[EUR][1000 genomes]
rs2820217	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.94[TSI][hapmap];0.90[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs2820218	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs2894816	0.83[EUR][1000 genomes]
rs4077760	0.82[CHB][hapmap];1.00[JPT][hapmap]
rs4272222	0.90[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs4276504	1.00[CHB][hapmap]
rs4357137	1.00[CEU][hapmap];1.00[JPT][hapmap]
rs4380749	0.82[AMR][1000 genomes]
rs4397225	0.87[AMR][1000 genomes]
rs4476827	1.00[CEU][hapmap];0.82[CHB][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.92[TSI][hapmap]
rs4580851	0.82[AMR][1000 genomes]
rs6903532	0.87[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs6905927	1.00[CEU][hapmap];0.82[CHB][hapmap];1.00[JPT][hapmap];0.82[AMR][1000 genomes]
rs6908101	0.91[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs6925165	0.87[AMR][1000 genomes]
rs761135	0.85[ASW][hapmap];0.89[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.80[MKK][hapmap];1.00[TSI][hapmap];0.87[YRI][hapmap];0.85[AFR][1000 genomes];0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs761136	0.85[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs763814	0.85[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7752800	0.84[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7772783	0.84[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs9382261	0.87[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs9382262	0.87[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs9382264	0.85[EUR][1000 genomes]
rs9464005	0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs9474672	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.94[TSI][hapmap];0.93[AMR][1000 genomes];0.91[EUR][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	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:4)

SNP	Gene	Cis/trans	Tissue	Source
rs1543356	LRRC1	cis	parietal	SCAN
rs1543356	C6orf142	cis	cerebellum	SCAN
rs1543356	COL21A1	cis	cerebellum	SCAN
rs1543356	FBXO9	cis	parietal	SCAN

Chromatin state (count:87 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:53759200-53794400	Weak transcription	Right Ventricle	heart
2	chr6:53759600-53789800	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
3	chr6:53760400-53789400	Weak transcription	Stomach Mucosa	stomach
4	chr6:53760400-53791200	Weak transcription	Hela-S3	cervix
5	chr6:53760600-53793600	Weak transcription	Pancreatic Islets	Pancreatic Islet
6	chr6:53761400-53791200	Weak transcription	Colon Smooth Muscle	Colon
7	chr6:53761600-53790800	Weak transcription	Fetal Heart	heart
8	chr6:53762000-53791200	Weak transcription	Muscle Satellite Cultured Cells	--
9	chr6:53762000-53791600	Weak transcription	Fetal Lung	lung
10	chr6:53768800-53796000	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
11	chr6:53769200-53790400	Weak transcription	Placenta Amnion	Placenta Amnion
12	chr6:53770000-53795800	Weak transcription	Primary hematopoietic stem cells short term culture	blood
13	chr6:53772000-53803000	Weak transcription	Lung	lung
14	chr6:53776000-53790600	Weak transcription	Brain Germinal Matrix	brain
15	chr6:53776600-53789200	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
16	chr6:53776800-53791000	Weak transcription	HUVEC	blood vessel
17	chr6:53777600-53790600	Strong transcription	Fetal Thymus	thymus
18	chr6:53778000-53791800	Weak transcription	Small Intestine	intestine
19	chr6:53779600-53791400	Weak transcription	Placenta	Placenta
20	chr6:53780200-53790400	Weak transcription	Gastric	stomach
21	chr6:53781000-53789200	Weak transcription	Primary B cells from peripheral blood	blood
22	chr6:53781000-53791200	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
23	chr6:53782400-53789400	Weak transcription	Brain Inferior Temporal Lobe	brain
24	chr6:53782400-53790400	Weak transcription	Brain Cingulate Gyrus	brain
25	chr6:53783000-53791400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
26	chr6:53783200-53789400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
27	chr6:53783400-53789800	Genic enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
28	chr6:53783600-53790800	Weak transcription	Cortex derived primary cultured neurospheres	brain
29	chr6:53784000-53790200	Weak transcription	Brain Substantia Nigra	brain
30	chr6:53784400-53790400	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
31	chr6:53784600-53789000	Weak transcription	Monocytes-CD14+_RO01746	blood
32	chr6:53784600-53791600	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
33	chr6:53784600-53794200	Weak transcription	Primary monocytes fromperipheralblood	blood
34	chr6:53784800-53794000	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
35	chr6:53785600-53791400	Weak transcription	Primary hematopoietic stem cells	blood
36	chr6:53785600-53794400	Weak transcription	Thymus	Thymus
37	chr6:53786000-53791800	Weak transcription	Fetal Stomach	stomach
38	chr6:53786000-53794200	Weak transcription	Left Ventricle	heart
39	chr6:53786200-53789000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
40	chr6:53786200-53791000	Weak transcription	NHEK	skin
41	chr6:53786400-53788400	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
42	chr6:53786600-53789000	Weak transcription	Primary neutrophils fromperipheralblood	blood
43	chr6:53786600-53791200	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
44	chr6:53786600-53791400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
45	chr6:53786600-53791600	Weak transcription	Rectal Smooth Muscle	rectum
46	chr6:53786800-53789000	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
47	chr6:53786800-53791400	Weak transcription	Fetal Kidney	kidney
48	chr6:53786800-53794400	Weak transcription	Stomach Smooth Muscle	stomach
49	chr6:53787000-53789400	Weak transcription	Rectal Mucosa Donor 31	rectum
50	chr6:53787000-53791200	Weak transcription	Colonic Mucosa	Colon

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