Variant report

Variant	rs1026395
Chromosome Location	chr12:123377821-123377822
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:3)
CpG islands
(count:0)
Chromatin interactive
region (count:8)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:3 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	RUNX3	chr12:123377811-123378382	GM12878	blood:	n/a	n/a
2	STAT3	chr12:123377743-123378250	MCF10A-Er-Src	breast:	n/a	chr12:123378124-123378147
3	NFATC1	chr12:123377703-123378302	GM12878	blood:	n/a	n/a

No data

(count:8 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr12:123377544..123379506-chr12:123429321..123431444,2	MCF-7	breast:
2	chr12:123358923..123360581-chr12:123375537..123377864,2	MCF-7	breast:
3	chr12:123376693..123378580-chr12:123401920..123404894,2	MCF-7	breast:
4	chr12:123346271..123349232-chr12:123377793..123379796,2	K562	blood:
5	chr12:123319890..123322592-chr12:123377486..123379203,2	MCF-7	breast:
6	chr12:123355933..123357832-chr12:123377792..123379853,2	K562	blood:
7	chr12:123343167..123345079-chr12:123376349..123378623,2	MCF-7	breast:
8	chr12:123376817..123378822-chr12:123449521..123451963,2	K562	blood:

No data

Variant related genes	Relation type
VPS37B	TF binding region
ENSG00000150967	Chromatin interaction
ENSG00000130787	Chromatin interaction
ENSG00000139722	Chromatin interaction

Extended variants
information (count: 63 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:58)

rs_ID	r²[population]
rs1037593	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]
rs10744394	0.88[EUR][1000 genomes]
rs10744439	0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10773599	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs10847742	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs10847749	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs10847751	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs10847775	1.00[JPT][hapmap]
rs10847910	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10848148	1.00[JPT][hapmap]
rs10848363	1.00[JPT][hapmap]
rs10848365	1.00[JPT][hapmap]
rs11059729	0.86[CEU][hapmap]
rs11060152	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs11060211	0.83[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs11060932	1.00[JPT][hapmap]
rs11060999	1.00[JPT][hapmap]
rs11610441	1.00[MEX][hapmap]
rs12306711	1.00[JPT][hapmap]
rs12311043	1.00[JPT][hapmap]
rs1260121	1.00[JPT][hapmap]
rs1671684	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];0.83[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs1671686	0.83[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs1671687	1.00[JPT][hapmap]
rs1696327	0.83[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs1798563	1.00[JPT][hapmap]
rs1975761	1.00[JPT][hapmap]
rs2061099	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2271048	0.91[AFR][1000 genomes];0.83[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2343107	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2649895	1.00[JPT][hapmap]
rs2649896	1.00[JPT][hapmap]
rs2649903	1.00[JPT][hapmap]
rs2649904	0.83[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs2656812	1.00[JPT][hapmap]
rs3844369	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs4307760	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs4759351	0.96[EUR][1000 genomes]
rs4759352	0.96[EUR][1000 genomes]
rs4759353	1.00[CEU][hapmap];1.00[JPT][hapmap];0.81[AFR][1000 genomes];0.83[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs4759354	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[AFR][1000 genomes];1.00[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs4759384	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[GIH][hapmap];1.00[JPT][hapmap];0.87[LWK][hapmap];1.00[MEX][hapmap];1.00[TSI][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]
rs4759388	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4759438	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[TSI][hapmap]
rs651683	1.00[JPT][hapmap]
rs7138257	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][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]
rs7298176	1.00[CHB][hapmap];0.89[GIH][hapmap];1.00[JPT][hapmap];1.00[TSI][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7306047	0.88[CEU][hapmap];1.00[CHD][hapmap];0.88[GIH][hapmap];0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7306948	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[TSI][hapmap];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs7485652	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7957643	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs7958155	1.00[CEU][hapmap];0.94[GIH][hapmap];1.00[JPT][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs839354	1.00[JPT][hapmap]
rs897384	0.81[AFR][1000 genomes];0.83[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs897388	1.00[CEU][hapmap];1.00[JPT][hapmap];0.81[AFR][1000 genomes];0.83[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs937765	0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs967281	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs9795629	1.00[CHB][hapmap];1.00[JPT][hapmap]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv3388790	chr12:123275902-123655103	Enhancers Strong transcription Weak transcription Flanking Active TSS Genic enhancers Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	55 gene(s)	inside rSNPs	diseases
2	nsv899572	chr12:123292503-123477311	Active TSS Strong transcription Enhancers Flanking Active TSS Genic enhancers Weak transcription Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	43 gene(s)	inside rSNPs	diseases
3	nsv899573	chr12:123312051-123528405	Enhancers Strong transcription Weak transcription Active TSS Flanking Active TSS Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	47 gene(s)	inside rSNPs	diseases
4	nsv517200	chr12:123312051-123654498	Strong transcription Weak transcription Flanking Active TSS Genic enhancers Enhancers Transcr. at gene 5' and 3' Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	55 gene(s)	inside rSNPs	diseases
5	nsv899576	chr12:123335527-123528405	Enhancers Genic enhancers Flanking Active TSS Strong transcription Active TSS Weak transcription Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	45 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:120 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:123366200-123379800	Weak transcription	Ovary	ovary
2	chr12:123370400-123379400	Enhancers	Small Intestine	intestine
3	chr12:123370800-123378000	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
4	chr12:123371600-123380000	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
5	chr12:123371800-123378400	Flanking Active TSS	Primary T helper cells PMA-I stimulated	--
6	chr12:123372200-123378400	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
7	chr12:123373200-123378600	Enhancers	Liver	Liver
8	chr12:123373400-123378800	Enhancers	Fetal Muscle Leg	muscle
9	chr12:123373400-123379000	Enhancers	Primary T killer naive cells fromperipheralblood	blood
10	chr12:123373600-123378800	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
11	chr12:123373800-123378600	Enhancers	Primary T regulatory cells fromperipheralblood	blood
12	chr12:123373800-123378600	Enhancers	Primary T killer memory cells from peripheral blood	blood
13	chr12:123373800-123378600	Enhancers	HUVEC	blood vessel
14	chr12:123373800-123378800	Enhancers	Primary T helper naive cells from peripheral blood	blood
15	chr12:123373800-123378800	Enhancers	Fetal Thymus	thymus
16	chr12:123373800-123379000	Enhancers	Primary T cells fromperipheralblood	blood
17	chr12:123373800-123379000	Enhancers	Primary T helper cells fromperipheralblood	blood
18	chr12:123373800-123379200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
19	chr12:123373800-123379200	Enhancers	Primary T helper naive cells fromperipheralblood	blood
20	chr12:123373800-123379600	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
21	chr12:123374000-123379000	Enhancers	Primary monocytes fromperipheralblood	blood
22	chr12:123374600-123379000	Weak transcription	Gastric	stomach
23	chr12:123375000-123378600	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
24	chr12:123375000-123379200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
25	chr12:123375200-123378800	Enhancers	Fetal Intestine Large	intestine
26	chr12:123375400-123378000	Enhancers	Pancreatic Islets	Pancreatic Islet
27	chr12:123375400-123378600	Enhancers	Brain Cingulate Gyrus	brain
28	chr12:123375400-123378800	Genic enhancers	Primary B cells from peripheral blood	blood
29	chr12:123375400-123379000	Enhancers	HepG2	liver
30	chr12:123375600-123378000	Enhancers	Primary hematopoietic stem cells short term culture	blood
31	chr12:123375600-123378800	Weak transcription	Thymus	Thymus
32	chr12:123375800-123379000	Enhancers	Psoas Muscle	Psoas
33	chr12:123376200-123379000	Enhancers	Placenta	Placenta
34	chr12:123376200-123379200	Enhancers	Colon Smooth Muscle	Colon
35	chr12:123376200-123379400	Enhancers	Spleen	Spleen
36	chr12:123376600-123378000	Enhancers	Right Atrium	heart
37	chr12:123376600-123378000	Enhancers	Stomach Mucosa	stomach
38	chr12:123376600-123378000	Flanking Active TSS	NHEK	skin
39	chr12:123376600-123378600	Enhancers	Fetal Adrenal Gland	Adrenal Gland
40	chr12:123376600-123378600	Weak transcription	Right Ventricle	heart
41	chr12:123376800-123378600	Enhancers	NHLF	lung
42	chr12:123376800-123379400	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
43	chr12:123377000-123378000	Enhancers	Brain Inferior Temporal Lobe	brain
44	chr12:123377000-123378000	Weak transcription	Fetal Kidney	kidney
45	chr12:123377000-123378000	Enhancers	Rectal Mucosa Donor 31	rectum
46	chr12:123377000-123378000	Enhancers	Skeletal Muscle Male	skeletal muscle
47	chr12:123377000-123378000	Transcr. at gene 5' and 3'	GM12878-XiMat	blood
48	chr12:123377000-123378200	Flanking Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
49	chr12:123377000-123378400	Enhancers	Brain Anterior Caudate	brain
50	chr12:123377000-123378600	Enhancers	Brain Angular Gyrus	brain

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