Variant report

Variant	rs12143626
Chromosome Location	chr1:85921219-85921220
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	chr1:85921195..85924566-chr1:85929657..85932092,3	MCF-7	breast:
2	chr1:85920031..85922123-chr1:85928283..85929923,2	K562	blood:

Variant related genes	Relation type
ENSG00000153904	Chromatin interaction

Extended variants
information (count: 22 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:20)

rs_ID	r²[population]
rs10873700	0.85[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs11161604	1.00[CEU][hapmap]
rs11161613	0.88[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12116463	0.85[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs12123722	1.00[CEU][hapmap];0.93[CHB][hapmap];1.00[JPT][hapmap];0.87[AMR][1000 genomes];0.91[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12126355	1.00[CEU][hapmap];0.91[EUR][1000 genomes]
rs12131258	0.94[ASN][1000 genomes]
rs12136295	1.00[CEU][hapmap];0.91[JPT][hapmap];0.84[ASN][1000 genomes]
rs1523998	1.00[CEU][hapmap]
rs17127201	1.00[CEU][hapmap];0.93[CHB][hapmap];1.00[JPT][hapmap];0.87[AMR][1000 genomes];0.91[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs17127231	1.00[CEU][hapmap];0.93[CHB][hapmap];1.00[JPT][hapmap];0.91[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs17127399	1.00[CEU][hapmap];0.92[CHB][hapmap];1.00[JPT][hapmap];0.87[AMR][1000 genomes];0.91[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs17127565	1.00[CEU][hapmap];0.92[CHB][hapmap];1.00[JPT][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2235990	0.83[ASN][1000 genomes]
rs2284798	1.00[CEU][hapmap];0.84[CHB][hapmap];1.00[JPT][hapmap];0.83[ASN][1000 genomes]
rs28816748	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs56888838	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs57996130	0.87[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs593728	0.93[CHB][hapmap];1.00[JPT][hapmap];0.94[ASN][1000 genomes]
rs7553530	0.87[AMR][1000 genomes];0.85[EUR][1000 genomes];0.91[ASN][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	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

No data

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:85901400-85923000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
2	chr1:85914200-85924800	Weak transcription	Duodenum Mucosa	Duodenum
3	chr1:85915200-85927800	Weak transcription	Sigmoid Colon	Sigmoid Colon
4	chr1:85915600-85925400	Weak transcription	Brain Germinal Matrix	brain
5	chr1:85916400-85921800	Enhancers	Liver	Liver
6	chr1:85917000-85922200	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
7	chr1:85917000-85923000	Weak transcription	Psoas Muscle	Psoas
8	chr1:85917400-85922400	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
9	chr1:85917400-85926400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
10	chr1:85917400-85929400	Weak transcription	Fetal Muscle Leg	muscle
11	chr1:85917400-85929400	Weak transcription	Gastric	stomach
12	chr1:85917400-85929800	Weak transcription	Esophagus	oesophagus
13	chr1:85917600-85921600	Enhancers	Fetal Lung	lung
14	chr1:85917800-85927200	Weak transcription	NH-A	brain
15	chr1:85917800-85928800	Weak transcription	HUES6 Cell Line	embryonic stem cell
16	chr1:85918200-85921400	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
17	chr1:85918800-85923600	Weak transcription	Pancreatic Islets	Pancreatic Islet
18	chr1:85919000-85922000	Enhancers	HUVEC	blood vessel
19	chr1:85919200-85928400	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
20	chr1:85919400-85924800	Weak transcription	Fetal Kidney	kidney
21	chr1:85919400-85927200	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
22	chr1:85919600-85921400	Genic enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
23	chr1:85919600-85928200	Weak transcription	Fetal Brain Female	brain
24	chr1:85919800-85925000	Weak transcription	Adipose Nuclei	Adipose
25	chr1:85920000-85921400	Enhancers	Osteobl	bone
26	chr1:85920000-85922600	Weak transcription	Fetal Intestine Large	intestine
27	chr1:85920000-85923800	Weak transcription	Duodenum Smooth Muscle	Duodenum
28	chr1:85920000-85924800	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
29	chr1:85920000-85925000	Weak transcription	Cortex derived primary cultured neurospheres	brain
30	chr1:85920000-85925000	Weak transcription	Brain Inferior Temporal Lobe	brain
31	chr1:85920000-85929600	Weak transcription	Brain Substantia Nigra	brain
32	chr1:85920200-85921400	Strong transcription	HSMM	muscle
33	chr1:85920200-85922600	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
34	chr1:85920200-85922600	Weak transcription	Fetal Intestine Small	intestine
35	chr1:85920200-85923000	Weak transcription	Pancreas	Pancrea
36	chr1:85920200-85925000	Weak transcription	Aorta	Aorta
37	chr1:85920200-85925400	Weak transcription	Ovary	ovary
38	chr1:85920200-85926400	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
39	chr1:85920200-85928000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
40	chr1:85920400-85926400	Weak transcription	NHLF	lung
41	chr1:85920600-85921600	Enhancers	NHDF-Ad	bronchial
42	chr1:85920600-85922600	Weak transcription	HepG2	liver
43	chr1:85920600-85923000	Enhancers	Small Intestine	intestine
44	chr1:85920600-85923800	Weak transcription	Rectal Smooth Muscle	rectum
45	chr1:85920600-85924800	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
46	chr1:85920600-85925000	Weak transcription	Muscle Satellite Cultured Cells	--
47	chr1:85920800-85923400	Weak transcription	Fetal Stomach	stomach
48	chr1:85920800-85925000	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
49	chr1:85920800-85929000	Weak transcription	HSMMtube	muscle
50	chr1:85921200-85921400	Enhancers	Colon Smooth Muscle	Colon

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