Variant report

Variant	rs60638501
Chromosome Location	chr12:11900514-11900515
allele	A/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	BHLHE40	chr12:11900324-11900739	GM12878	blood:	n/a	n/a
2	POU2F2	chr12:11900131-11900556	GM12891	blood:	n/a	chr12:11900394-11900407 chr12:11900402-11900411 chr12:11900402-11900412 chr12:11900532-11900546 chr12:11900399-11900414 chr12:11900403-11900410 chr12:11900401-11900411 chr12:11900401-11900411 chr12:11900398-11900416 chr12:11900535-11900542
3	EP300	chr12:11900335-11900643	GM12878	blood:	n/a	n/a
4	ATF2	chr12:11900263-11900696	GM12878	blood:	n/a	n/a
5	POLR2A	chr12:11898596-11900716	GM12892	blood:	n/a	n/a
6	ZNF384	chr12:11900503-11900730	GM12878	blood:	n/a	n/a
7	POU2F2	chr12:11900105-11900665	GM12878	blood:	n/a	chr12:11900394-11900407 chr12:11900402-11900411 chr12:11900402-11900412 chr12:11900532-11900546 chr12:11900399-11900414 chr12:11900403-11900410 chr12:11900401-11900411 chr12:11900401-11900411 chr12:11900398-11900416 chr12:11900535-11900542
8	BCLAF1	chr12:11899965-11900724	GM12878	blood:	n/a	n/a
9	POLR2A	chr12:11896327-11900731	GM12878	blood:	n/a	n/a
10	ATF2	chr12:11898695-11900665	GM12878	blood:	n/a	n/a
11	RUNX3	chr12:11900149-11900598	GM12878	blood:	n/a	n/a
12	POU2F2	chr12:11900201-11900581	GM12878	blood:	n/a	chr12:11900394-11900407 chr12:11900402-11900411 chr12:11900402-11900412 chr12:11900532-11900546 chr12:11900399-11900414 chr12:11900403-11900410 chr12:11900401-11900411 chr12:11900401-11900411 chr12:11900398-11900416 chr12:11900535-11900542
13	EP300	chr12:11900258-11900537	GM12878	blood:	n/a	n/a
14	POLR2A	chr12:11898630-11900595	GM12878	blood:	n/a	n/a
15	PML	chr12:11900265-11900620	GM12878	blood:	n/a	n/a
16	NFIC	chr12:11900207-11900852	GM12878	blood:	n/a	n/a
17	POLR2A	chr12:11898061-11904528	GM12891	blood:	n/a	n/a
18	MTA3	chr12:11898607-11900670	GM12878	blood:	n/a	n/a
19	SMC3	chr12:11900257-11900776	GM12878	blood:	n/a	chr12:11900677-11900684
20	MXI1	chr12:11900350-11900624	GM12878	blood:	n/a	n/a
21	POLR2A	chr12:11899742-11900668	GM12891	blood:	n/a	n/a
22	RUNX3	chr12:11900124-11900730	GM12878	blood:	n/a	n/a
23	POLR2A	chr12:11896700-11904611	GM12878	blood:	n/a	n/a
24	POLR2A	chr12:11900209-11900602	GM12891	blood:	n/a	n/a
25	STAT3	chr12:11900316-11901198	GM12878	blood:	n/a	n/a
26	EP300	chr12:11899766-11900637	GM12878	blood:	n/a	n/a
27	POLR2A	chr12:11900153-11900659	GM12892	blood:	n/a	n/a
28	TBP	chr12:11900242-11900756	GM12878	blood:	n/a	n/a
29	EBF1	chr12:11900236-11900618	GM12878	blood:	n/a	n/a
30	NFIC	chr12:11900104-11901025	GM12878	blood:	n/a	n/a
31	POLR2A	chr12:11898061-11904425	GM12878	blood:	n/a	n/a
32	CUX1	chr12:11900313-11900569	GM12878	blood:	n/a	n/a
33	POLR2A	chr12:11898101-11900619	GM12891	blood:	n/a	n/a
34	POLR2A	chr12:11899682-11900658	GM12891	blood:	n/a	n/a
35	CHD2	chr12:11900349-11900541	GM12878	blood:	n/a	n/a
36	CHD1	chr12:11900514-11900572	GM12878	blood:	n/a	n/a
37	POLR2A	chr12:11899671-11900670	GM12892	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr12:11898044..11900698-chr12:11957221..11959288,2	MCF-7	breast:
2	chr12:11880124..11883020-chr12:11899873..11902243,3	MCF-7	breast:

Variant related genes	Relation type
ETV6	TF binding region

Extended variants
information (count: 12 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:10)

rs_ID	r²[population]
rs2724598	1.00[AMR][1000 genomes]
rs2724637	1.00[AMR][1000 genomes]
rs57222202	1.00[AMR][1000 genomes]
rs59302227	1.00[AMR][1000 genomes]
rs7133092	1.00[AMR][1000 genomes]
rs7302827	1.00[AMR][1000 genomes]
rs7307437	1.00[AMR][1000 genomes]
rs73288759	1.00[AMR][1000 genomes]
rs73288792	1.00[AMR][1000 genomes]
rs73288794	0.89[AFR][1000 genomes];1.00[AMR][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	nsv870039	chr12:11800363-11996598	Enhancers Weak transcription Genic enhancers Strong transcription Transcr. at gene 5' and 3' Flanking Active TSS Active TSS ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region	9 gene(s)	inside rSNPs	diseases
2	nsv1053609	chr12:11898099-11933906	Enhancers Flanking Active TSS Weak transcription Genic enhancers Strong transcription Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region	1 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:104 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:11873200-11902400	Weak transcription	Brain Cingulate Gyrus	brain
2	chr12:11873200-11909400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
3	chr12:11882400-11902600	Weak transcription	Fetal Muscle Leg	muscle
4	chr12:11882400-11903200	Weak transcription	Fetal Muscle Trunk	muscle
5	chr12:11883800-11906000	Weak transcription	Liver	Liver
6	chr12:11885200-11906200	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
7	chr12:11885600-11905200	Weak transcription	Fetal Intestine Large	intestine
8	chr12:11885800-11911600	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
9	chr12:11889800-11901800	Enhancers	Breast Myoepithelial Primary Cells	Breast
10	chr12:11890000-11902400	Weak transcription	Brain Hippocampus Middle	brain
11	chr12:11893200-11915000	Weak transcription	Primary T helper naive cells from peripheral blood	blood
12	chr12:11893800-11901200	Enhancers	HMEC	breast
13	chr12:11894600-11905200	Weak transcription	Fetal Intestine Small	intestine
14	chr12:11894600-11905400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
15	chr12:11894600-11905400	Weak transcription	Primary T cells fromperipheralblood	blood
16	chr12:11894600-11906200	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
17	chr12:11894600-11908400	Weak transcription	Psoas Muscle	Psoas
18	chr12:11894800-11906000	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
19	chr12:11894800-11906600	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
20	chr12:11895000-11906000	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
21	chr12:11895000-11906800	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
22	chr12:11895000-11912600	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
23	chr12:11895400-11906000	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
24	chr12:11895400-11914400	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
25	chr12:11895600-11908800	Weak transcription	Pancreatic Islets	Pancreatic Islet
26	chr12:11895800-11901200	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
27	chr12:11896000-11906200	Enhancers	Primary monocytes fromperipheralblood	blood
28	chr12:11896400-11902800	Enhancers	Primary B cells from peripheral blood	blood
29	chr12:11896800-11900600	Enhancers	NHEK	skin
30	chr12:11896800-11901800	Enhancers	Spleen	Spleen
31	chr12:11897000-11901600	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
32	chr12:11897000-11905400	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
33	chr12:11897000-11906400	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
34	chr12:11897000-11906400	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
35	chr12:11897000-11908800	Weak transcription	Brain Anterior Caudate	brain
36	chr12:11897200-11901000	Weak transcription	Fetal Lung	lung
37	chr12:11897200-11901400	Weak transcription	Cortex derived primary cultured neurospheres	brain
38	chr12:11897200-11902600	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
39	chr12:11897200-11905400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
40	chr12:11897400-11901800	Enhancers	HUVEC	blood vessel
41	chr12:11897400-11902600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
42	chr12:11897600-11902600	Weak transcription	Right Ventricle	heart
43	chr12:11897600-11904200	Weak transcription	iPS-15b Cell Line	embryonic stem cell
44	chr12:11897600-11904600	Enhancers	Thymus	Thymus
45	chr12:11897800-11904200	Weak transcription	H9 Cell Line	embryonic stem cell
46	chr12:11897800-11904200	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
47	chr12:11897800-11904200	Weak transcription	iPS-18 Cell Line	embryonic stem cell
48	chr12:11897800-11904600	Weak transcription	HUES64 Cell Line	embryonic stem cell
49	chr12:11897800-11905200	Weak transcription	Esophagus	oesophagus
50	chr12:11897800-11905400	Weak transcription	Aorta	Aorta

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