Variant report

Variant	rs12758237
Chromosome Location	chr1:85870783-85870784
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 51 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:47)

rs_ID	r²[population]
rs10158674	0.94[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs10782550	0.92[ASN][1000 genomes]
rs11161597	0.91[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs11161599	0.95[CEU][hapmap];1.00[CHB][hapmap];0.88[JPT][hapmap];0.91[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs11161614	0.85[CEU][hapmap];0.87[EUR][1000 genomes]
rs11801146	0.89[ASN][1000 genomes]
rs12118950	1.00[CEU][hapmap];0.92[CHB][hapmap];1.00[JPT][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12120551	0.83[AMR][1000 genomes];0.92[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs12122816	0.92[ASN][1000 genomes]
rs12123745	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12125900	0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12128907	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12129502	1.00[CEU][hapmap];0.91[CHB][hapmap];1.00[JPT][hapmap];0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12130145	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[AMR][1000 genomes];0.92[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12130380	0.86[CEU][hapmap];0.86[EUR][1000 genomes]
rs12130591	0.89[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[AMR][1000 genomes];0.80[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12131926	0.89[EUR][1000 genomes]
rs12132677	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12133722	1.00[CEU][hapmap];0.92[CHB][hapmap];1.00[JPT][hapmap];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12135333	1.00[CHB][hapmap];0.82[JPT][hapmap];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12138621	0.90[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12138852	1.00[CEU][hapmap];0.92[CHB][hapmap];1.00[JPT][hapmap];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12139958	1.00[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs12140170	0.90[CEU][hapmap];0.92[CHB][hapmap];1.00[JPT][hapmap];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12140272	0.91[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12140457	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12140935	1.00[JPT][hapmap];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12717763	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[AMR][1000 genomes];0.92[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12724823	0.89[CEU][hapmap];0.92[CHB][hapmap];1.00[JPT][hapmap];0.85[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs12736004	0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12743049	1.00[CEU][hapmap];0.92[CHB][hapmap];1.00[JPT][hapmap];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12758768	0.87[AMR][1000 genomes];0.98[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1498374	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1608536	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17384381	0.95[CEU][hapmap];0.92[CHB][hapmap];1.00[JPT][hapmap];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs17388521	1.00[CEU][hapmap];0.92[CHB][hapmap];1.00[JPT][hapmap];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2076699	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[AMR][1000 genomes];0.92[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2300639	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[AMR][1000 genomes];0.92[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2300640	0.87[AMR][1000 genomes];0.92[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs28529751	0.82[AMR][1000 genomes];0.80[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs34561661	0.84[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs35193119	0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35240561	0.86[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs35761966	0.97[ASN][1000 genomes]
rs36110608	0.91[AFR][1000 genomes];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs3768223	0.83[AMR][1000 genomes];0.92[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs71652696	0.87[AMR][1000 genomes];0.90[EUR][1000 genomes];0.92[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 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
4	esv3393958	chr1:85857980-85874598	Enhancers Weak transcription Active TSS Flanking Active TSS ZNF genes & repeats Strong transcription Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	n/a

No data

Chromatin state (count:46 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:85856000-85872800	Weak transcription	Fetal Intestine Small	intestine
2	chr1:85862200-85874600	Weak transcription	Pancreas	Pancrea
3	chr1:85864000-85872600	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
4	chr1:85864400-85871000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
5	chr1:85864400-85871800	Weak transcription	NH-A	brain
6	chr1:85864400-85872200	Weak transcription	Skeletal Muscle Male	skeletal muscle
7	chr1:85864400-85873000	Weak transcription	iPS-18 Cell Line	embryonic stem cell
8	chr1:85864400-85874600	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
9	chr1:85864800-85876800	Weak transcription	iPS-20b Cell Line	embryonic stem cell
10	chr1:85865200-85871200	Weak transcription	Skeletal Muscle Female	skeletal muscle
11	chr1:85865400-85870800	Weak transcription	NHDF-Ad	bronchial
12	chr1:85865400-85871200	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
13	chr1:85865400-85871400	Weak transcription	Fetal Lung	lung
14	chr1:85865400-85871400	Weak transcription	HSMM	muscle
15	chr1:85865400-85872800	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
16	chr1:85865600-85870800	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
17	chr1:85865600-85871600	Weak transcription	Rectal Smooth Muscle	rectum
18	chr1:85866200-85870800	Weak transcription	HUES64 Cell Line	embryonic stem cell
19	chr1:85866200-85871000	Weak transcription	HUES48 Cell Line	embryonic stem cell
20	chr1:85866200-85871000	Weak transcription	HUES6 Cell Line	embryonic stem cell
21	chr1:85866200-85871600	Weak transcription	Adipose Nuclei	Adipose
22	chr1:85868600-85870800	Flanking Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
23	chr1:85868600-85872800	Enhancers	Liver	Liver
24	chr1:85869000-85871200	Enhancers	Muscle Satellite Cultured Cells	--
25	chr1:85869000-85872800	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
26	chr1:85869200-85870800	Flanking Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
27	chr1:85869200-85871000	Enhancers	HUVEC	blood vessel
28	chr1:85869200-85873200	Weak transcription	Duodenum Smooth Muscle	Duodenum
29	chr1:85869400-85872200	Weak transcription	Fetal Kidney	kidney
30	chr1:85869800-85871600	Enhancers	Aorta	Aorta
31	chr1:85869800-85871800	Enhancers	Colon Smooth Muscle	Colon
32	chr1:85869800-85874400	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
33	chr1:85870000-85871200	Weak transcription	Brain Substantia Nigra	brain
34	chr1:85870000-85871800	Enhancers	Ovary	ovary
35	chr1:85870000-85873000	Enhancers	HSMMtube	muscle
36	chr1:85870200-85871000	Weak transcription	Brain Anterior Caudate	brain
37	chr1:85870200-85871000	Weak transcription	Sigmoid Colon	Sigmoid Colon
38	chr1:85870200-85872600	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
39	chr1:85870200-85874800	Enhancers	Osteobl	bone
40	chr1:85870400-85870800	Weak transcription	Cortex derived primary cultured neurospheres	brain
41	chr1:85870400-85872800	Weak transcription	Placenta Amnion	Placenta Amnion
42	chr1:85870400-85872800	Weak transcription	Stomach Smooth Muscle	stomach
43	chr1:85870600-85871400	Enhancers	Fetal Muscle Leg	muscle
44	chr1:85870600-85871800	Enhancers	Fetal Stomach	stomach
45	chr1:85870600-85872800	Weak transcription	Brain Cingulate Gyrus	brain
46	chr1:85870600-85872800	Weak transcription	Rectal Mucosa Donor 31	rectum

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