Variant report

Variant	rs12070247
Chromosome Location	chr1:57028050-57028051
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 31 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:30)

rs_ID	r²[population]
rs10493212	0.80[YRI][hapmap]
rs11206845	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11206846	1.00[YRI][hapmap];0.94[AFR][1000 genomes]
rs11800865	0.87[AFR][1000 genomes]
rs11800883	0.95[AFR][1000 genomes]
rs11805547	0.81[ASN][1000 genomes]
rs11810635	1.00[AFR][1000 genomes]
rs12058459	0.85[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12058536	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12059747	1.00[ASW][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12059843	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12070557	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12090895	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12096715	0.80[MKK][hapmap];0.80[YRI][hapmap]
rs12098117	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.89[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1418521	0.85[YRI][hapmap]
rs1572058	0.90[ASW][hapmap];0.87[LWK][hapmap];0.94[MKK][hapmap];0.85[YRI][hapmap];0.81[AFR][1000 genomes]
rs17114119	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.89[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs17114125	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[TSI][hapmap];0.89[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs17114126	0.90[YRI][hapmap]
rs1953114	1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs28365912	0.89[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs28673510	1.00[AFR][1000 genomes]
rs41446844	1.00[ASW][hapmap];0.94[LWK][hapmap];0.94[MKK][hapmap];0.95[YRI][hapmap];0.95[AFR][1000 genomes]
rs56332336	0.97[AFR][1000 genomes]
rs6661359	1.00[AFR][1000 genomes]
rs6687908	0.89[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6702052	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72903425	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.89[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7539051	0.90[ASW][hapmap];1.00[LWK][hapmap];0.94[MKK][hapmap];0.90[YRI][hapmap];0.84[AFR][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:83 , 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	chr1:57016000-57038600	Weak transcription	HSMMtube	muscle
3	chr1:57017400-57035400	Weak transcription	Esophagus	oesophagus
4	chr1:57017400-57035400	Weak transcription	Fetal Thymus	thymus
5	chr1:57017400-57039400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
6	chr1:57017800-57028200	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
7	chr1:57017800-57028600	Weak transcription	Pancreas	Pancrea
8	chr1:57017800-57040800	Enhancers	Cortex derived primary cultured neurospheres	brain
9	chr1:57019200-57028400	Weak transcription	Aorta	Aorta
10	chr1:57019200-57030400	Weak transcription	HSMM	muscle
11	chr1:57019400-57030000	Weak transcription	Osteobl	bone
12	chr1:57019400-57030200	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
13	chr1:57019600-57028400	Enhancers	Liver	Liver
14	chr1:57019800-57031400	Weak transcription	Placenta Amnion	Placenta Amnion
15	chr1:57020000-57028800	Weak transcription	Stomach Mucosa	stomach
16	chr1:57020200-57031800	Weak transcription	Placenta	Placenta
17	chr1:57020400-57029000	Weak transcription	Fetal Stomach	stomach
18	chr1:57021400-57028600	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
19	chr1:57021400-57028600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
20	chr1:57021400-57032800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
21	chr1:57022000-57030400	Weak transcription	Primary B cells from peripheral blood	blood
22	chr1:57022600-57028600	Weak transcription	Spleen	Spleen
23	chr1:57023800-57028600	Enhancers	HepG2	liver
24	chr1:57023800-57030400	Enhancers	iPS-18 Cell Line	embryonic stem cell
25	chr1:57023800-57033000	Enhancers	Brain Hippocampus Middle	brain
26	chr1:57024200-57028200	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
27	chr1:57024200-57029000	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
28	chr1:57024200-57030000	Weak transcription	Primary neutrophils fromperipheralblood	blood
29	chr1:57024200-57030600	Weak transcription	Breast Myoepithelial Primary Cells	Breast
30	chr1:57024200-57030600	Weak transcription	Fetal Muscle Leg	muscle
31	chr1:57024200-57030800	Weak transcription	Duodenum Smooth Muscle	Duodenum
32	chr1:57025000-57028200	Weak transcription	Brain Angular Gyrus	brain
33	chr1:57025400-57028600	Enhancers	iPS-20b Cell Line	embryonic stem cell
34	chr1:57025600-57029800	Enhancers	HUES48 Cell Line	embryonic stem cell
35	chr1:57025600-57030600	Enhancers	ES-I3 Cell Line	embryonic stem cell
36	chr1:57025600-57040000	Weak transcription	Fetal Muscle Trunk	muscle
37	chr1:57026000-57028600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
38	chr1:57026000-57033200	Enhancers	Fetal Intestine Large	intestine
39	chr1:57026200-57032200	Enhancers	Ovary	ovary
40	chr1:57026200-57033000	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
41	chr1:57026400-57028400	Weak transcription	Right Atrium	heart
42	chr1:57026400-57029200	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
43	chr1:57026800-57033000	Enhancers	Fetal Intestine Small	intestine
44	chr1:57027000-57028400	Weak transcription	Duodenum Mucosa	Duodenum
45	chr1:57027000-57034200	Genic enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
46	chr1:57027400-57028600	Enhancers	NHDF-Ad	bronchial
47	chr1:57027400-57029200	Enhancers	Right Ventricle	heart
48	chr1:57027400-57029400	Enhancers	Skeletal Muscle Female	skeletal muscle
49	chr1:57027400-57030800	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
50	chr1:57027400-57032000	Enhancers	Fetal Adrenal Gland	Adrenal Gland

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