Variant report

Variant	rs2257089
Chromosome Location	chr1:179258507-179258508
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	NR2F2	chr1:179257973-179258607	MCF-7	breast:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr1:179247878..179250453-chr1:179256970..179259849,2	MCF-7	breast:
2	chr1:179258474..179260132-chr1:179334011..179336378,2	MCF-7	breast:
3	chr1:179254343..179259872-chr1:179260262..179264377,6	K562	blood:

Variant related genes	Relation type
SOAT1	TF binding region
ENSG00000162779	Chromatin interaction
ENSG00000057252	Chromatin interaction

Extended variants
information (count: 37 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:36)

rs_ID	r²[population]
rs10798655	0.91[ASN][1000 genomes]
rs12042899	0.80[ASN][1000 genomes]
rs12138973	0.82[ASN][1000 genomes]
rs12725375	0.98[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12749666	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2050450	0.84[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2050451	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2152318	0.92[AFR][1000 genomes];0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2247061	0.95[ASN][1000 genomes]
rs2248979	0.87[AMR][1000 genomes];0.83[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2250352	0.89[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2250477	0.95[AFR][1000 genomes];0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2254214	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2254580	0.81[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2254623	0.89[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2255375	0.89[AFR][1000 genomes]
rs2257100	0.96[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2484440	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2484443	0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2484446	0.92[AFR][1000 genomes];0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2492777	0.87[AFR][1000 genomes];0.87[AMR][1000 genomes];0.83[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2492778	0.88[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2493116	0.98[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2493117	0.97[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2493118	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2493119	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2783391	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2783392	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2783393	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs404818	1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs433722	0.94[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4652364	0.89[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs56371666	0.82[AMR][1000 genomes];0.85[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs61824366	0.85[AMR][1000 genomes];0.92[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs6425530	0.94[AFR][1000 genomes];0.92[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7523431	0.89[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[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	nsv1005278	chr1:179197645-179371395	Weak transcription Active TSS Enhancers Flanking Active TSS Bivalent Enhancer ZNF genes & repeats Genic enhancers Strong transcription Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region miRNA target site	16 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:20 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:179256000-179258600	Enhancers	Fetal Intestine Small	intestine
2	chr1:179256200-179258600	Enhancers	Stomach Mucosa	stomach
3	chr1:179256400-179258800	Enhancers	Fetal Intestine Large	intestine
4	chr1:179256600-179258800	Enhancers	Rectal Mucosa Donor 31	rectum
5	chr1:179256600-179258800	Enhancers	HepG2	liver
6	chr1:179257600-179258600	Enhancers	Gastric	stomach
7	chr1:179257600-179258600	Enhancers	Pancreas	Pancrea
8	chr1:179257800-179258600	Enhancers	Duodenum Mucosa	Duodenum
9	chr1:179257800-179258600	Enhancers	Sigmoid Colon	Sigmoid Colon
10	chr1:179258000-179258600	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
11	chr1:179258000-179258600	Enhancers	Placenta	Placenta
12	chr1:179258000-179258800	Enhancers	Colonic Mucosa	Colon
13	chr1:179258200-179258600	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
14	chr1:179258200-179258600	Enhancers	Fetal Adrenal Gland	Adrenal Gland
15	chr1:179258200-179258600	Enhancers	Rectal Mucosa Donor 29	rectum
16	chr1:179258400-179258600	Enhancers	iPS-18 Cell Line	embryonic stem cell
17	chr1:179258400-179258600	Enhancers	A549	lung
18	chr1:179258400-179261400	Weak transcription	Liver	Liver
19	chr1:179258400-179261400	Weak transcription	Rectal Smooth Muscle	rectum
20	chr1:179258400-179262400	Weak transcription	Fetal Kidney	kidney

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