Variant report

Variant	rs7545642
Chromosome Location	chr1:57022324-57022325
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 15 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:14)

rs_ID	r²[population]
rs1041604	0.86[MEX][hapmap]
rs10736393	1.00[ASW][hapmap];1.00[CEU][hapmap];0.90[CHB][hapmap];0.95[GIH][hapmap];0.94[JPT][hapmap];0.97[LWK][hapmap];1.00[MKK][hapmap];0.95[TSI][hapmap];0.96[YRI][hapmap];0.91[AFR][1000 genomes];0.86[AMR][1000 genomes];0.89[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10888980	1.00[CEU][hapmap];0.90[CHB][hapmap];0.94[JPT][hapmap];0.88[YRI][hapmap];0.91[AFR][1000 genomes];0.86[AMR][1000 genomes];0.89[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12568800	0.94[AFR][1000 genomes];0.92[AMR][1000 genomes];0.85[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1759751	0.91[AFR][1000 genomes];0.83[AMR][1000 genomes];0.89[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1777275	0.84[MEX][hapmap]
rs1777280	1.00[CEU][hapmap];0.90[CHB][hapmap];0.94[JPT][hapmap];1.00[YRI][hapmap];0.92[AFR][1000 genomes];0.86[AMR][1000 genomes];0.89[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1777281	1.00[CEU][hapmap];0.90[CHB][hapmap];0.94[JPT][hapmap];0.96[YRI][hapmap];0.91[AFR][1000 genomes];0.86[AMR][1000 genomes];0.89[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1777282	1.00[CEU][hapmap];0.90[CHB][hapmap];0.94[JPT][hapmap];0.95[YRI][hapmap];0.91[AFR][1000 genomes];0.86[AMR][1000 genomes];0.89[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2065553	0.86[MEX][hapmap]
rs2065555	0.86[MEX][hapmap]
rs2404983	0.86[MEX][hapmap]
rs7543448	0.97[AFR][1000 genomes];0.98[AMR][1000 genomes];0.95[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7553307	1.00[CEU][hapmap];0.81[CHB][hapmap];0.94[JPT][hapmap];0.84[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:1 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv869295	chr1:56894955-57656562	Weak transcription Strong transcription Genic enhancers Active TSS Flanking Active TSS Bivalent/Poised TSS Enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	20 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:76 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:57007400-57028400	Weak transcription	Sigmoid Colon	Sigmoid Colon
2	chr1:57009600-57028000	Weak transcription	Fetal Kidney	kidney
3	chr1:57014000-57026000	Weak transcription	Fetal Intestine Large	intestine
4	chr1:57016000-57038600	Weak transcription	HSMMtube	muscle
5	chr1:57016800-57023400	Weak transcription	Fetal Intestine Small	intestine
6	chr1:57017400-57025000	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
7	chr1:57017400-57035400	Weak transcription	Esophagus	oesophagus
8	chr1:57017400-57035400	Weak transcription	Fetal Thymus	thymus
9	chr1:57017400-57039400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
10	chr1:57017600-57025600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
11	chr1:57017800-57023400	Weak transcription	Duodenum Smooth Muscle	Duodenum
12	chr1:57017800-57028200	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
13	chr1:57017800-57028600	Weak transcription	Pancreas	Pancrea
14	chr1:57017800-57040800	Enhancers	Cortex derived primary cultured neurospheres	brain
15	chr1:57019200-57023600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
16	chr1:57019200-57026000	Weak transcription	H1 Cell Line	embryonic stem cell
17	chr1:57019200-57027800	Weak transcription	Fetal Brain Female	brain
18	chr1:57019200-57028400	Weak transcription	Aorta	Aorta
19	chr1:57019200-57030400	Weak transcription	HSMM	muscle
20	chr1:57019400-57023200	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
21	chr1:57019400-57023400	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
22	chr1:57019400-57024000	Weak transcription	Fetal Muscle Leg	muscle
23	chr1:57019400-57027400	Weak transcription	Lung	lung
24	chr1:57019400-57027600	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
25	chr1:57019400-57030000	Weak transcription	Osteobl	bone
26	chr1:57019400-57030200	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
27	chr1:57019600-57022800	Weak transcription	Brain Angular Gyrus	brain
28	chr1:57019600-57023600	Weak transcription	Right Ventricle	heart
29	chr1:57019600-57027000	Weak transcription	Skeletal Muscle Male	skeletal muscle
30	chr1:57019600-57027400	Weak transcription	Skeletal Muscle Female	skeletal muscle
31	chr1:57019600-57027800	Weak transcription	Fetal Brain Male	brain
32	chr1:57019600-57028000	Weak transcription	Fetal Lung	lung
33	chr1:57019600-57028400	Enhancers	Liver	Liver
34	chr1:57019800-57022400	Weak transcription	Ovary	ovary
35	chr1:57019800-57023800	Weak transcription	HepG2	liver
36	chr1:57019800-57031400	Weak transcription	Placenta Amnion	Placenta Amnion
37	chr1:57020000-57028000	Weak transcription	Colon Smooth Muscle	Colon
38	chr1:57020000-57028800	Weak transcription	Stomach Mucosa	stomach
39	chr1:57020200-57031800	Weak transcription	Placenta	Placenta
40	chr1:57020400-57029000	Weak transcription	Fetal Stomach	stomach
41	chr1:57020600-57023800	Enhancers	HUES6 Cell Line	embryonic stem cell
42	chr1:57020800-57022600	Enhancers	Spleen	Spleen
43	chr1:57021000-57023000	Weak transcription	iPS-15b Cell Line	embryonic stem cell
44	chr1:57021000-57023200	Weak transcription	Brain Cingulate Gyrus	brain
45	chr1:57021000-57024200	Weak transcription	Fetal Muscle Trunk	muscle
46	chr1:57021200-57022400	Enhancers	HUES48 Cell Line	embryonic stem cell
47	chr1:57021200-57027800	Weak transcription	NHLF	lung
48	chr1:57021400-57022600	Enhancers	Left Ventricle	heart
49	chr1:57021400-57023000	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
50	chr1:57021400-57023400	Weak transcription	Right Atrium	heart

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