Variant report

Variant	rs2958132
Chromosome Location	chr12:57144533-57144534
allele	C/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	SPI1	chr12:57144473-57144668	K562	blood:	n/a	chr12:57144567-57144576 chr12:57144566-57144579 chr12:57144565-57144578 chr12:57144568-57144575
2	SPI1	chr12:57144480-57144628	K562	blood:	n/a	chr12:57144567-57144576 chr12:57144566-57144579 chr12:57144565-57144578 chr12:57144568-57144575
3	SPI1	chr12:57144347-57144783	HL-60	blood:	n/a	chr12:57144567-57144576 chr12:57144566-57144579 chr12:57144565-57144578 chr12:57144568-57144575

No.	Distal block	Cell Line	Cell type
1	chr12:57143938..57146732-chr12:57482240..57484256,2	MCF-7	breast:
2	chr12:57144483..57147144-chr12:57389426..57391985,2	MCF-7	breast:
3	chr12:57144135..57146956-chr12:57408791..57411536,2	MCF-7	breast:
4	chr12:57079557..57083885-chr12:57143480..57147449,6	MCF-7	breast:
5	chr12:57130157..57132110-chr12:57143416..57145525,2	MCF-7	breast:
6	chr12:57028905..57032364-chr12:57143305..57146712,4	K562	blood:
7	chr12:57117372..57120851-chr12:57140459..57146973,9	MCF-7	breast:
8	chr12:57080587..57084416-chr12:57143537..57149136,7	MCF-7	breast:
9	chr12:57136854..57139921-chr12:57143326..57145629,3	MCF-7	breast:
10	chr12:57116864..57121762-chr12:57140480..57149366,20	K562	blood:
11	chr12:57143195..57148502-chr12:57480974..57485182,5	K562	blood:
12	chr12:57080423..57083977-chr12:57143486..57147763,4	K562	blood:
13	chr12:57037903..57040646-chr12:57144102..57147965,5	K562	blood:
14	chr12:57028481..57030405-chr12:57144099..57146089,2	K562	blood:
15	chr12:57143341..57145088-chr12:57231516..57233756,2	K562	blood:
16	chr12:57111474..57114081-chr12:57143216..57146135,2	MCF-7	breast:
17	chr12:57142485..57145559-chr12:57478493..57481424,3	MCF-7	breast:
18	chr12:57117044..57122605-chr12:57141917..57149366,15	K562	blood:
19	chr12:57037775..57040917-chr12:57144043..57146588,3	MCF-7	breast:
20	chr12:57039548..57041575-chr12:57144187..57146304,2	K562	blood:

Variant related genes	Relation type
HSD17B6	TF binding region
ENSG00000198056	Chromatin interaction
ENSG00000110955	Chromatin interaction
ENSG00000258442	Chromatin interaction
ENSG00000166863	Chromatin interaction
ENSG00000076108	Chromatin interaction
ENSG00000196531	Chromatin interaction
ENSG00000166886	Chromatin interaction
ENSG00000207031	Chromatin interaction
ENSG00000166881	Chromatin interaction
ENSG00000110958	Chromatin interaction
ENSG00000268162	Chromatin interaction

Extended variants
information (count: 41 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:39)

rs_ID	r²[population]
rs1026565	0.93[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10459246	0.91[AMR][1000 genomes];0.92[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs10747770	0.89[AFR][1000 genomes];0.96[AMR][1000 genomes];0.93[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs10783796	0.96[AFR][1000 genomes];0.97[AMR][1000 genomes];0.91[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10876918	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11171951	0.91[AFR][1000 genomes];0.96[AMR][1000 genomes];0.89[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11171956	0.89[AMR][1000 genomes];0.90[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1131514	0.98[AFR][1000 genomes];0.97[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12227117	0.86[ASN][1000 genomes]
rs12828563	0.95[AMR][1000 genomes];0.89[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1466382	0.93[AMR][1000 genomes];0.90[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1975875	0.93[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1979325	0.94[ASN][1000 genomes]
rs2035081	0.96[AFR][1000 genomes];0.97[AMR][1000 genomes];0.90[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2035082	0.90[AMR][1000 genomes];0.89[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2290894	0.93[AMR][1000 genomes];0.89[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2926741	0.85[AMR][1000 genomes];0.87[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2926743	0.94[ASN][1000 genomes]
rs2926747	0.93[AMR][1000 genomes];0.89[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2926748	0.88[AFR][1000 genomes];0.97[AMR][1000 genomes];0.90[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2958127	0.91[AFR][1000 genomes];0.97[AMR][1000 genomes];0.91[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2958130	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2958134	1.00[AFR][1000 genomes];0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2958138	0.81[AMR][1000 genomes]
rs2958148	0.90[AMR][1000 genomes];0.89[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2958149	0.90[ASN][1000 genomes]
rs3214051	0.93[AMR][1000 genomes];0.89[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4759256	0.94[ASN][1000 genomes]
rs4788	0.93[ASN][1000 genomes]
rs4902	0.88[AFR][1000 genomes];0.97[AMR][1000 genomes];0.90[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7137749	0.81[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs7295862	0.87[AMR][1000 genomes];0.90[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs7313074	0.94[ASN][1000 genomes]
rs7966391	0.93[AMR][1000 genomes];0.92[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7967600	0.90[AFR][1000 genomes];0.96[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7978685	0.93[ASN][1000 genomes]
rs7980317	0.90[AFR][1000 genomes];0.96[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs898609	0.90[AFR][1000 genomes];0.97[AMR][1000 genomes];0.90[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs898611	0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[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	nsv1040850	chr12:57055011-57679209	Strong transcription Weak transcription Flanking Active TSS Enhancers Bivalent Enhancer Active TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	181 gene(s)	inside rSNPs	diseases
2	esv1794914	chr12:57119236-57195379	Active TSS Strong transcription Weak transcription Flanking Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Enhancers Genic enhancers Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	36 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:121 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:57119400-57145000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
2	chr12:57119800-57144600	Weak transcription	Pancreatic Islets	Pancreatic Islet
3	chr12:57119800-57144800	Weak transcription	NHLF	lung
4	chr12:57119800-57145000	Weak transcription	Colonic Mucosa	Colon
5	chr12:57119800-57145000	Weak transcription	Right Ventricle	heart
6	chr12:57120000-57144600	Weak transcription	NHDF-Ad	bronchial
7	chr12:57120000-57144800	Weak transcription	Fetal Heart	heart
8	chr12:57120000-57144800	Weak transcription	Fetal Kidney	kidney
9	chr12:57120000-57144800	Weak transcription	NH-A	brain
10	chr12:57120000-57145000	Weak transcription	Colon Smooth Muscle	Colon
11	chr12:57120000-57145200	Weak transcription	Aorta	Aorta
12	chr12:57120200-57144800	Weak transcription	Osteobl	bone
13	chr12:57120200-57145000	Weak transcription	Rectal Smooth Muscle	rectum
14	chr12:57120600-57144800	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
15	chr12:57121400-57144600	Strong transcription	HUES64 Cell Line	embryonic stem cell
16	chr12:57127000-57145000	Weak transcription	Psoas Muscle	Psoas
17	chr12:57130800-57145000	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
18	chr12:57131000-57145000	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
19	chr12:57131000-57145200	Weak transcription	Pancreas	Pancrea
20	chr12:57131400-57145200	Weak transcription	Small Intestine	intestine
21	chr12:57132000-57145200	Weak transcription	Spleen	Spleen
22	chr12:57133400-57144800	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
23	chr12:57133600-57144800	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
24	chr12:57133600-57145000	Weak transcription	HSMM	muscle
25	chr12:57134400-57144800	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
26	chr12:57135000-57145000	Weak transcription	Esophagus	oesophagus
27	chr12:57135000-57145600	Weak transcription	Lung	lung
28	chr12:57135200-57145000	Weak transcription	Brain Inferior Temporal Lobe	brain
29	chr12:57135400-57144800	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
30	chr12:57135400-57145000	Weak transcription	Brain Cingulate Gyrus	brain
31	chr12:57135400-57145000	Weak transcription	Left Ventricle	heart
32	chr12:57136000-57145000	Weak transcription	Stomach Smooth Muscle	stomach
33	chr12:57136200-57144800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
34	chr12:57136200-57145000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
35	chr12:57136400-57144600	Weak transcription	Fetal Intestine Small	intestine
36	chr12:57137400-57144600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
37	chr12:57138000-57145000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
38	chr12:57138600-57144800	Weak transcription	Duodenum Smooth Muscle	Duodenum
39	chr12:57138600-57145200	Weak transcription	Ovary	ovary
40	chr12:57138800-57144600	Weak transcription	HMEC	breast
41	chr12:57139200-57145000	Weak transcription	Placenta Amnion	Placenta Amnion
42	chr12:57139600-57144800	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
43	chr12:57139600-57144800	Weak transcription	Fetal Lung	lung
44	chr12:57139600-57144800	Weak transcription	NHEK	skin
45	chr12:57139600-57145200	Weak transcription	Brain Substantia Nigra	brain
46	chr12:57139600-57145200	Weak transcription	Gastric	stomach
47	chr12:57140000-57145000	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
48	chr12:57140400-57144800	Weak transcription	Primary T helper naive cells from peripheral blood	blood
49	chr12:57140600-57145000	Weak transcription	Skeletal Muscle Male	skeletal muscle
50	chr12:57140800-57144800	Weak transcription	Muscle Satellite Cultured Cells	--

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