Variant report

Variant	rs7540393
Chromosome Location	chr1:85893728-85893729
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 20 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:17)

rs_ID	r²[population]
rs10493764	0.86[CEU][hapmap];0.88[JPT][hapmap];0.82[AFR][1000 genomes];0.90[AMR][1000 genomes];0.92[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12402128	0.82[CEU][hapmap];0.89[CHB][hapmap];1.00[JPT][hapmap];0.84[YRI][hapmap];0.82[AFR][1000 genomes];0.85[AMR][1000 genomes];0.92[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1523993	0.86[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];0.89[AMR][1000 genomes];0.91[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs17387935	0.98[ASN][1000 genomes]
rs17590006	0.88[CHB][hapmap];1.00[JPT][hapmap];0.85[ASN][1000 genomes]
rs35092233	0.90[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs35294786	0.96[AFR][1000 genomes];0.85[AMR][1000 genomes];0.91[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs35876501	0.96[AFR][1000 genomes];0.85[AMR][1000 genomes];0.91[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs35956189	0.82[AFR][1000 genomes];0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs36062892	0.85[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs3768226	0.88[CHB][hapmap];1.00[JPT][hapmap];0.85[ASN][1000 genomes]
rs4475804	0.84[EUR][1000 genomes]
rs61769490	0.81[AMR][1000 genomes];0.91[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs61783046	0.91[AFR][1000 genomes];0.90[AMR][1000 genomes];0.92[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6659486	0.96[AFR][1000 genomes];0.85[AMR][1000 genomes];0.91[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6669293	0.83[ASN][1000 genomes]
rs6673833	0.80[CEU][hapmap];0.88[CHB][hapmap];1.00[JPT][hapmap];0.83[AMR][1000 genomes];0.92[EUR][1000 genomes];0.98[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	nsv1006994	chr1:85454304-86327679	Active TSS Enhancers Weak transcription Flanking Active TSS Strong transcription Flanking Bivalent TSS/Enh Genic enhancers ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	72 gene(s)	inside rSNPs	diseases
2	nsv830470	chr1:85820775-86014080	Enhancers Weak transcription Genic enhancers Flanking Active TSS ZNF genes & repeats Strong transcription Active TSS Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases
3	nsv1008877	chr1:85843238-85897570	Enhancers Weak transcription ZNF genes & repeats Active TSS Strong transcription Genic enhancers Flanking Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:42 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:85874000-85903800	Weak transcription	NHLF	lung
2	chr1:85874200-85903600	Weak transcription	Muscle Satellite Cultured Cells	--
3	chr1:85874400-85903600	Weak transcription	HepG2	liver
4	chr1:85874400-85904200	Weak transcription	NH-A	brain
5	chr1:85886400-85899000	Weak transcription	NHDF-Ad	bronchial
6	chr1:85886400-85903800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
7	chr1:85886400-85914200	Weak transcription	HSMMtube	muscle
8	chr1:85886800-85897200	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
9	chr1:85886800-85903800	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
10	chr1:85887600-85902200	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
11	chr1:85887600-85903400	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
12	chr1:85890000-85894200	Weak transcription	HSMM	muscle
13	chr1:85890400-85902200	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
14	chr1:85891000-85897200	Weak transcription	Fetal Brain Female	brain
15	chr1:85891600-85897200	Weak transcription	Osteobl	bone
16	chr1:85891800-85894000	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
17	chr1:85892200-85906200	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
18	chr1:85892400-85893800	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
19	chr1:85892800-85893800	Enhancers	Rectal Smooth Muscle	rectum
20	chr1:85892800-85894400	Enhancers	Fetal Brain Male	brain
21	chr1:85893000-85893800	Enhancers	HUES48 Cell Line	embryonic stem cell
22	chr1:85893000-85893800	Enhancers	Breast Myoepithelial Primary Cells	Breast
23	chr1:85893000-85894200	Enhancers	Colon Smooth Muscle	Colon
24	chr1:85893000-85894600	Enhancers	Liver	Liver
25	chr1:85893200-85893800	Enhancers	Brain Hippocampus Middle	brain
26	chr1:85893200-85893800	Enhancers	Brain Inferior Temporal Lobe	brain
27	chr1:85893200-85894200	Weak transcription	Fetal Intestine Small	intestine
28	chr1:85893400-85893800	Enhancers	Duodenum Mucosa	Duodenum
29	chr1:85893400-85894200	Enhancers	Rectal Mucosa Donor 29	rectum
30	chr1:85893400-85894400	Enhancers	Aorta	Aorta
31	chr1:85893400-85894400	Enhancers	Psoas Muscle	Psoas
32	chr1:85893400-85894400	Enhancers	Skeletal Muscle Female	skeletal muscle
33	chr1:85893400-85894600	Enhancers	Primary hematopoietic stem cells short term culture	blood
34	chr1:85893400-85894600	Enhancers	Skeletal Muscle Male	skeletal muscle
35	chr1:85893600-85893800	Enhancers	Left Ventricle	heart
36	chr1:85893600-85894000	Weak transcription	HUVEC	blood vessel
37	chr1:85893600-85894400	Enhancers	Brain Anterior Caudate	brain
38	chr1:85893600-85894400	Enhancers	Sigmoid Colon	Sigmoid Colon
39	chr1:85893600-85894600	Genic enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
40	chr1:85893600-85894600	Enhancers	Adipose Nuclei	Adipose
41	chr1:85893600-85894600	Enhancers	Pancreas	Pancrea
42	chr1:85893600-85897000	Weak transcription	Cortex derived primary cultured neurospheres	brain

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