Variant report

Variant	rs7956285
Chromosome Location	chr12:118570307-118570308
allele	G/T
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	NFIC	chr12:118569165-118570311	HepG2	liver:	n/a	chr12:118569438-118569455 chr12:118569924-118569940 chr12:118569924-118569941 chr12:118569438-118569454
2	MYBL2	chr12:118569142-118570329	HepG2	liver:	n/a	n/a
3	RXRA	chr12:118569669-118570356	HepG2	liver:	n/a	n/a
4	POLR2A	chr12:118569841-118570367	HepG2	liver:	n/a	n/a
5	KAP1	chr12:118569378-118570321	U2OS	brain:	n/a	n/a
6	POLR2A	chr12:118570275-118570616	HepG2	liver:	n/a	n/a
7	ARID3A	chr12:118569744-118570346	HepG2	liver:	n/a	n/a
8	EP300	chr12:118569634-118570369	HepG2	liver:	n/a	n/a
9	MAX	chr12:118569664-118570331	HepG2	liver:	n/a	chr12:118570073-118570082
10	TCF12	chr12:118569729-118570354	A549	lung:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr12:118567809..118570427-chr12:118572115..118574740,3	MCF-7	breast:
2	chr12:118568705..118570458-chr12:118572215..118574320,2	K562	blood:
3	chr12:118497651..118499895-chr12:118570277..118572267,2	MCF-7	breast:
4	chr12:118558694..118561471-chr12:118568462..118574858,6	MCF-7	breast:

Variant related genes	Relation type
PEBP1	TF binding region
ENSG00000089220	Chromatin interaction
ENSG00000176834	Chromatin interaction
ENSG00000176871	Chromatin interaction

Extended variants
information (count: 16 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:15)

rs_ID	r²[population]
rs1051470	0.82[GIH][hapmap]
rs12423154	0.85[CEU][hapmap];1.00[JPT][hapmap];0.83[AMR][1000 genomes];0.88[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12423959	0.83[AMR][1000 genomes];0.86[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs16948161	0.84[YRI][hapmap]
rs2017414	0.85[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2936840	1.00[CHB][hapmap];0.94[GIH][hapmap];1.00[JPT][hapmap];0.91[MKK][hapmap];0.82[AMR][1000 genomes];0.83[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs3847652	0.87[CEU][hapmap];1.00[CHB][hapmap];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs56070243	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs61943518	0.82[AFR][1000 genomes];0.91[AMR][1000 genomes];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs61943519	0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs61943521	0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73217996	0.90[ASN][1000 genomes]
rs7961197	0.82[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7970036	0.93[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs904662	0.85[GIH][hapmap]

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	nsv1053785	chr12:118490955-118874194	Strong transcription Weak transcription Enhancers Flanking Active TSS Active TSS Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	37 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:70 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:118542600-118572800	Weak transcription	Primary hematopoietic stem cells short term culture	blood
2	chr12:118542600-118573400	Weak transcription	Primary T cells from cord blood	blood
3	chr12:118552800-118572800	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
4	chr12:118552800-118573400	Weak transcription	Aorta	Aorta
5	chr12:118553000-118573000	Weak transcription	Fetal Brain Female	brain
6	chr12:118558800-118572800	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
7	chr12:118559200-118572600	Weak transcription	Duodenum Smooth Muscle	Duodenum
8	chr12:118559200-118572600	Weak transcription	NHEK	skin
9	chr12:118559200-118572800	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
10	chr12:118559200-118573000	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
11	chr12:118559200-118573000	Weak transcription	Fetal Kidney	kidney
12	chr12:118559200-118573400	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
13	chr12:118559200-118573400	Weak transcription	Fetal Intestine Small	intestine
14	chr12:118559400-118572600	Weak transcription	iPS-20b Cell Line	embryonic stem cell
15	chr12:118559400-118572800	Weak transcription	HUES6 Cell Line	embryonic stem cell
16	chr12:118560800-118572800	Weak transcription	H1 Cell Line	embryonic stem cell
17	chr12:118561600-118572800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
18	chr12:118561600-118573000	Weak transcription	Primary hematopoietic stem cells	blood
19	chr12:118563200-118573400	Weak transcription	Lung	lung
20	chr12:118564200-118572800	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
21	chr12:118564400-118573200	Weak transcription	Fetal Stomach	stomach
22	chr12:118565000-118572800	Weak transcription	Gastric	stomach
23	chr12:118565200-118572800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
24	chr12:118566800-118573200	Weak transcription	Right Atrium	heart
25	chr12:118567400-118573200	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
26	chr12:118569200-118570400	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
27	chr12:118569200-118570400	Enhancers	Cortex derived primary cultured neurospheres	brain
28	chr12:118569200-118570600	Enhancers	Fetal Adrenal Gland	Adrenal Gland
29	chr12:118569200-118570600	Flanking Active TSS	HepG2	liver
30	chr12:118569400-118570400	Enhancers	Adipose Nuclei	Adipose
31	chr12:118569400-118570400	Enhancers	Rectal Mucosa Donor 29	rectum
32	chr12:118569400-118570600	Enhancers	Pancreas	Pancrea
33	chr12:118569400-118570800	Enhancers	Dnd41	blood
34	chr12:118569400-118572600	Enhancers	Liver	Liver
35	chr12:118569600-118570400	Enhancers	Skeletal Muscle Male	skeletal muscle
36	chr12:118569600-118570400	Enhancers	Skeletal Muscle Female	skeletal muscle
37	chr12:118569800-118570400	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
38	chr12:118569800-118570400	Enhancers	Brain Anterior Caudate	brain
39	chr12:118569800-118570400	Enhancers	Thymus	Thymus
40	chr12:118569800-118572600	Weak transcription	Brain Cingulate Gyrus	brain
41	chr12:118569800-118572800	Weak transcription	Placenta	Placenta
42	chr12:118569800-118573400	Weak transcription	Sigmoid Colon	Sigmoid Colon
43	chr12:118569800-118573600	Weak transcription	Placenta Amnion	Placenta Amnion
44	chr12:118570000-118570400	Enhancers	Primary T helper cells fromperipheralblood	blood
45	chr12:118570000-118570400	Enhancers	Brain Dorsolateral Prefrontal Cortex	brain
46	chr12:118570000-118572600	Weak transcription	Hela-S3	cervix
47	chr12:118570000-118573000	Weak transcription	Fetal Muscle Trunk	muscle
48	chr12:118570200-118570400	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
49	chr12:118570200-118572200	Weak transcription	Primary T cells fromperipheralblood	blood
50	chr12:118570200-118572200	Weak transcription	GM12878-XiMat	blood

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links