Variant report

Variant	rs12123722
Chromosome Location	chr1:85873950-85873951
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr1:85872823..85874492-chr1:85874813..85877121,2	MCF-7	breast:

Extended variants
information (count: 28 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:24)

rs_ID	r²[population]
rs10873700	1.00[AFR][1000 genomes];0.89[AMR][1000 genomes];0.94[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs11161595	0.85[EUR][1000 genomes]
rs11161604	1.00[CEU][hapmap];0.87[AMR][1000 genomes]
rs11161613	0.89[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11590830	0.87[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs12116463	1.00[AFR][1000 genomes];0.89[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12122154	0.82[EUR][1000 genomes]
rs12126355	1.00[CEU][hapmap];1.00[EUR][1000 genomes]
rs12131258	1.00[ASN][1000 genomes]
rs12136295	1.00[CEU][hapmap];0.91[JPT][hapmap];0.89[AMR][1000 genomes];0.82[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs12143626	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]
rs12717764	0.92[CHB][hapmap]
rs1523998	1.00[CEU][hapmap]
rs17127201	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][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]
rs17127231	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.87[AFR][1000 genomes];0.89[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17127399	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17127565	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[AMR][1000 genomes];0.91[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2235990	0.89[AMR][1000 genomes];0.82[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2284798	1.00[CEU][hapmap];0.92[CHB][hapmap];1.00[JPT][hapmap];0.89[AMR][1000 genomes];0.85[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs28816748	0.87[AMR][1000 genomes];0.91[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs56888838	0.87[AMR][1000 genomes];0.91[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs57996130	0.99[ASN][1000 genomes]
rs593728	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs7553530	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[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:49 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:85862200-85874600	Weak transcription	Pancreas	Pancrea
2	chr1:85864400-85874600	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
3	chr1:85864800-85876800	Weak transcription	iPS-20b Cell Line	embryonic stem cell
4	chr1:85869800-85874400	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
5	chr1:85870200-85874800	Enhancers	Osteobl	bone
6	chr1:85871400-85874000	Enhancers	HSMM	muscle
7	chr1:85871400-85878400	Weak transcription	Fetal Muscle Leg	muscle
8	chr1:85871600-85876600	Weak transcription	HUES6 Cell Line	embryonic stem cell
9	chr1:85871800-85877000	Weak transcription	Ovary	ovary
10	chr1:85872000-85877200	Weak transcription	Skeletal Muscle Female	skeletal muscle
11	chr1:85872400-85874000	Enhancers	Fetal Lung	lung
12	chr1:85872600-85874000	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
13	chr1:85872800-85874000	Enhancers	iPS-15b Cell Line	embryonic stem cell
14	chr1:85872800-85874200	Enhancers	Colon Smooth Muscle	Colon
15	chr1:85872800-85874400	Enhancers	Stomach Smooth Muscle	stomach
16	chr1:85872800-85874400	Enhancers	HepG2	liver
17	chr1:85872800-85874800	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
18	chr1:85873000-85875400	Enhancers	Brain Anterior Caudate	brain
19	chr1:85873200-85874000	Enhancers	Duodenum Smooth Muscle	Duodenum
20	chr1:85873200-85874000	Enhancers	Stomach Mucosa	stomach
21	chr1:85873200-85874000	Enhancers	NHLF	lung
22	chr1:85873200-85876000	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
23	chr1:85873200-85879600	Weak transcription	Brain Cingulate Gyrus	brain
24	chr1:85873400-85874000	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
25	chr1:85873400-85874000	Enhancers	NHDF-Ad	bronchial
26	chr1:85873400-85874400	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
27	chr1:85873400-85874400	Enhancers	NH-A	brain
28	chr1:85873400-85874600	Enhancers	HSMMtube	muscle
29	chr1:85873400-85874800	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
30	chr1:85873400-85874800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
31	chr1:85873400-85875400	Enhancers	Cortex derived primary cultured neurospheres	brain
32	chr1:85873400-85876800	Weak transcription	HUES64 Cell Line	embryonic stem cell
33	chr1:85873400-85876800	Weak transcription	iPS-18 Cell Line	embryonic stem cell
34	chr1:85873400-85882800	Weak transcription	Skeletal Muscle Male	skeletal muscle
35	chr1:85873600-85874000	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
36	chr1:85873600-85875000	Enhancers	HUVEC	blood vessel
37	chr1:85873600-85885000	Weak transcription	Fetal Intestine Large	intestine
38	chr1:85873800-85874000	Flanking Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
39	chr1:85873800-85874000	Enhancers	Rectal Smooth Muscle	rectum
40	chr1:85873800-85874200	Genic enhancers	Muscle Satellite Cultured Cells	--
41	chr1:85873800-85874400	Weak transcription	Aorta	Aorta
42	chr1:85873800-85874600	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
43	chr1:85873800-85875400	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
44	chr1:85873800-85875400	Enhancers	Liver	Liver
45	chr1:85873800-85876600	Weak transcription	HUES48 Cell Line	embryonic stem cell
46	chr1:85873800-85876800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
47	chr1:85873800-85882000	Weak transcription	Fetal Intestine Small	intestine
48	chr1:85873800-85885400	Weak transcription	Fetal Stomach	stomach
49	chr1:85873800-85887600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast

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