Variant report

Variant	rs967872
Chromosome Location	chr12:106492295-106492296
allele	C/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	SPI1	chr12:106492133-106492944	GM12878	blood:	n/a	chr12:106492555-106492568 chr12:106492554-106492567 chr12:106492681-106492694 chr12:106492557-106492566
2	EP300	chr12:106492193-106493174	HepG2	liver:	n/a	chr12:106492690-106492704 chr12:106492858-106492868 chr12:106492683-106492692
3	MYBL2	chr12:106492262-106493183	HepG2	liver:	n/a	n/a
4	NR2F2	chr12:106492270-106493243	HepG2	liver:	n/a	n/a
5	TCF7L2	chr12:106492086-106493005	HepG2	liver:	n/a	chr12:106492580-106492596 chr12:106492584-106492594 chr12:106492580-106492596 chr12:106492553-106492560 chr12:106492581-106492595 chr12:106492583-106492592 chr12:106492309-106492323 chr12:106492584-106492593
6	RCOR1	chr12:106492247-106492960	HepG2	liver:	n/a	n/a
7	TCF7L2	chr12:106492212-106492799	PANC-1	pancreas:	n/a	chr12:106492580-106492596 chr12:106492584-106492594 chr12:106492580-106492596 chr12:106492553-106492560 chr12:106492581-106492595 chr12:106492583-106492592 chr12:106492309-106492323 chr12:106492584-106492593
8	FOXA2	chr12:106492290-106493328	HepG2	liver:	n/a	chr12:106492855-106492867
9	EP300	chr12:106492287-106493003	HepG2	liver:	n/a	chr12:106492690-106492704 chr12:106492858-106492868 chr12:106492683-106492692
10	NFIC	chr12:106492282-106493149	HepG2	liver:	n/a	chr12:106492342-106492370
11	NR2F2	chr12:106492243-106493215	HepG2	liver:	n/a	n/a
12	SP1	chr12:106492291-106493107	HepG2	liver:	n/a	chr12:106492446-106492460
13	FOXA1	chr12:106492271-106493197	HepG2	liver:	n/a	chr12:106492855-106492867 chr12:106492853-106492868

No.	Distal block	Cell Line	Cell type
1	chr12:106486379..106488971-chr12:106490561..106492780,2	MCF-7	breast:
2	chr12:106491668..106493233-chr12:106494081..106496361,2	MCF-7	breast:
3	chr12:106325602..106327976-chr12:106491240..106494183,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000257438	TF binding region

Extended variants
information (count: 23 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:22)

rs_ID	r²[population]
rs10746055	0.89[AMR][1000 genomes];0.84[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs10861555	0.89[AMR][1000 genomes];0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11112867	0.94[CHB][hapmap]
rs11112868	0.90[AMR][1000 genomes];0.94[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11112870	0.81[AMR][1000 genomes];0.98[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs11112872	0.84[CHB][hapmap]
rs12371401	0.80[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs1427785	0.89[CEU][hapmap];1.00[CHB][hapmap];0.93[CHD][hapmap];0.84[GIH][hapmap];0.95[JPT][hapmap];0.97[ASN][1000 genomes]
rs1427786	1.00[CHB][hapmap];0.86[JPT][hapmap];0.85[AMR][1000 genomes];0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1560000	0.96[CEU][hapmap];0.95[CHB][hapmap];0.91[CHD][hapmap];0.87[GIH][hapmap];0.83[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2434082	0.81[AMR][1000 genomes];0.85[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2436597	0.89[CEU][hapmap];1.00[CHB][hapmap];0.91[JPT][hapmap];0.85[AMR][1000 genomes];0.87[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2436598	0.83[ASN][1000 genomes]
rs2468198	0.91[AMR][1000 genomes];0.87[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2468199	0.97[AMR][1000 genomes];0.86[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2569973	0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2956406	0.91[AMR][1000 genomes];0.86[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs7131912	0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7132167	0.85[CEU][hapmap]
rs754724	0.85[AMR][1000 genomes];0.82[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs7964234	0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs958422	0.86[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	nsv832509	chr12:106363888-106516221	Enhancers Weak transcription ZNF genes & repeats Strong transcription Genic enhancers Flanking Active TSS Bivalent Enhancer Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs967872	CKAP4	cis	parietal	SCAN
rs967872	WSCD2	cis	parietal	SCAN
rs967872	PRDM4	cis	cerebellum	SCAN

Chromatin state (count:79 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:106458800-106500200	Weak transcription	Pancreatic Islets	Pancreatic Islet
2	chr12:106461800-106499600	Weak transcription	Fetal Intestine Large	intestine
3	chr12:106469000-106499400	Weak transcription	Fetal Intestine Small	intestine
4	chr12:106478600-106492400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
5	chr12:106481000-106493000	Enhancers	Brain Inferior Temporal Lobe	brain
6	chr12:106485200-106500400	Weak transcription	HMEC	breast
7	chr12:106485400-106500800	Weak transcription	Lung	lung
8	chr12:106485600-106496200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
9	chr12:106485600-106500600	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
10	chr12:106485800-106495000	Strong transcription	HSMMtube	muscle
11	chr12:106486200-106493400	Enhancers	Brain Substantia Nigra	brain
12	chr12:106487200-106492400	Enhancers	HepG2	liver
13	chr12:106487200-106492600	Enhancers	Psoas Muscle	Psoas
14	chr12:106487400-106499400	Weak transcription	Brain Germinal Matrix	brain
15	chr12:106487600-106500200	Weak transcription	NHLF	lung
16	chr12:106488600-106492400	Weak transcription	Cortex derived primary cultured neurospheres	brain
17	chr12:106488600-106492400	Enhancers	Right Ventricle	heart
18	chr12:106488600-106495600	Weak transcription	Breast Myoepithelial Primary Cells	Breast
19	chr12:106488800-106492800	Enhancers	Brain Dorsolateral Prefrontal Cortex	brain
20	chr12:106489400-106492400	Weak transcription	Brain Anterior Caudate	brain
21	chr12:106489600-106494600	Weak transcription	Fetal Muscle Trunk	muscle
22	chr12:106489800-106492400	Enhancers	Liver	Liver
23	chr12:106490000-106496800	Weak transcription	Aorta	Aorta
24	chr12:106490200-106492800	Enhancers	Brain Angular Gyrus	brain
25	chr12:106490200-106493400	Enhancers	HUES6 Cell Line	embryonic stem cell
26	chr12:106490200-106493400	Enhancers	Brain Hippocampus Middle	brain
27	chr12:106490400-106493400	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
28	chr12:106490400-106494200	Genic enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
29	chr12:106490600-106492400	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
30	chr12:106490600-106493200	Enhancers	HUES64 Cell Line	embryonic stem cell
31	chr12:106490600-106493400	Enhancers	HUES48 Cell Line	embryonic stem cell
32	chr12:106490600-106494600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
33	chr12:106490600-106498200	Weak transcription	Pancreas	Pancrea
34	chr12:106490800-106492400	Enhancers	iPS-20b Cell Line	embryonic stem cell
35	chr12:106490800-106493400	Enhancers	iPS-18 Cell Line	embryonic stem cell
36	chr12:106490800-106493400	Enhancers	Brain Cingulate Gyrus	brain
37	chr12:106490800-106494800	Weak transcription	Fetal Stomach	stomach
38	chr12:106490800-106499600	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
39	chr12:106491000-106493400	Enhancers	iPS-15b Cell Line	embryonic stem cell
40	chr12:106491000-106493400	Enhancers	Fetal Heart	heart
41	chr12:106491000-106493600	Strong transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
42	chr12:106491000-106495000	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
43	chr12:106491000-106496600	Weak transcription	Stomach Smooth Muscle	stomach
44	chr12:106491000-106499600	Weak transcription	Fetal Kidney	kidney
45	chr12:106491200-106493600	Enhancers	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
46	chr12:106491200-106494400	Weak transcription	Adipose Nuclei	Adipose
47	chr12:106491200-106494600	Weak transcription	Gastric	stomach
48	chr12:106491200-106499800	Strong transcription	HSMM	muscle
49	chr12:106491200-106500000	Weak transcription	Fetal Lung	lung
50	chr12:106491200-106500800	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links