Variant report

Variant	rs2272135
Chromosome Location	chr12:122356157-122356158
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	PML	chr12:122356075-122356690	MCF-7	breast:	n/a	n/a
2	POLR2A	chr12:122355807-122356649	K562	blood:	n/a	n/a
3	MXI1	chr12:122356108-122356838	GM12878	blood:	n/a	chr12:122356466-122356481
4	RAD21	chr12:122355934-122356856	HCT-116	colon:	n/a	chr12:122356083-122356093
5	RUNX3	chr12:122356125-122356640	GM12878	blood:	n/a	n/a
6	ELF1	chr12:122355817-122356839	GM12878	blood:	n/a	chr12:122356751-122356763 chr12:122356116-122356128 chr12:122356449-122356458
7	POLR2A	chr12:122355922-122356687	GM12892	blood:	n/a	n/a
8	RAD21	chr12:122355970-122356709	ECC-1	luminal epithelium:	n/a	chr12:122356083-122356093
9	EP300	chr12:122356034-122356566	GM12878	blood:	n/a	chr12:122356073-122356080
10	POLR2A	chr12:122356015-122356718	MCF-7	breast:	n/a	n/a
11	SRF	chr12:122355938-122356793	MCF-7	breast:	n/a	n/a
12	CHD2	chr12:122356079-122356619	GM12878	blood:	n/a	n/a
13	RFX5	chr12:122355885-122356812	GM12878	blood:	n/a	chr12:122356465-122356480 chr12:122356465-122356480 chr12:122356463-122356477 chr12:122356466-122356475 chr12:122356462-122356477 chr12:122356465-122356480 chr12:122356464-122356481
14	POLR2A	chr12:122356155-122356789	HUVEC	blood vessel:	n/a	n/a
15	RAD21	chr12:122356115-122356967	H1-hESC	embryonic stem cell:	n/a	n/a
16	SRF	chr12:122356017-122356817	MCF-7	breast:	n/a	n/a
17	RUNX3	chr12:122356105-122356613	GM12878	blood:	n/a	n/a
18	ELF1	chr12:122356030-122356758	MCF-7	breast:	n/a	chr12:122356116-122356128 chr12:122356449-122356458
19	CREB1	chr12:122356127-122356731	GM12878	blood:	n/a	n/a
20	FOXM1	chr12:122355991-122356613	GM12878	blood:	n/a	n/a
21	RFX5	chr12:122355894-122356806	IMR90	lung:	n/a	chr12:122356465-122356480 chr12:122356465-122356480 chr12:122356463-122356477 chr12:122356466-122356475 chr12:122356462-122356477 chr12:122356465-122356480 chr12:122356464-122356481
22	POLR2A	chr12:122356112-122356613	GM12892	blood:	n/a	n/a
23	MTA3	chr12:122355977-122356634	GM12878	blood:	n/a	n/a
24	RAD21	chr12:122355967-122356801	HCT-116	colon:	n/a	chr12:122356083-122356093
25	USF1	chr12:122356027-122356810	HCT-116	colon:	n/a	chr12:122356750-122356766 chr12:122356406-122356419 chr12:122356408-122356417 chr12:122356409-122356418 chr12:122356407-122356416 chr12:122356408-122356417
26	CTCF	chr12:122356060-122356161	GM19239	blood:	n/a	n/a
27	POLR2A	chr12:122355954-122356211	K562	blood:	n/a	n/a
28	MAX	chr12:122355876-122356699	H1-hESC	embryonic stem cell:	n/a	chr12:122356113-122356120 chr12:122356408-122356417 chr12:122356466-122356475 chr12:122356632-122356641
29	CREB1	chr12:122356140-122356744	H1-hESC	embryonic stem cell:	n/a	n/a
30	RAD21	chr12:122356115-122356572	ECC-1	luminal epithelium:	n/a	n/a
31	CTCF	chr12:122356122-122356599	H1-hESC	embryonic stem cell:	n/a	chr12:122356529-122356542 chr12:122356544-122356557 chr12:122356368-122356381
32	SIN3A	chr12:122356118-122356932	H1-hESC	embryonic stem cell:	n/a	n/a
33	CTCF	chr12:122356045-122356187	GM19238	blood:	n/a	chr12:122356055-122356068
34	USF1	chr12:122355932-122356713	ECC-1	luminal epithelium:	n/a	chr12:122356406-122356419 chr12:122356408-122356417 chr12:122356409-122356418 chr12:122356407-122356416 chr12:122356408-122356417
35	RELA	chr12:122355986-122356564	GM18951	blood:	n/a	n/a
36	POLR2A	chr12:122355981-122356831	U87	brain:	n/a	n/a
37	ELF1	chr12:122356131-122356668	GM12878	blood:	n/a	chr12:122356449-122356458
38	POLR2A	chr12:122355835-122356749	HL-60	blood:	n/a	n/a
39	MYC	chr12:122356152-122356497	HUVEC	blood vessel:	n/a	chr12:122356408-122356417 chr12:122356466-122356475
40	POLR2A	chr12:122356110-122356648	HCT-116	colon:	n/a	n/a
41	ATF2	chr12:122356073-122356620	H1-hESC	embryonic stem cell:	n/a	n/a
42	POLR2A	chr12:122356046-122356667	MCF-7	breast:	n/a	n/a
43	ATF3	chr12:122356143-122356638	GM12878	blood:	n/a	chr12:122356408-122356428
44	USF1	chr12:122356116-122356682	H1-hESC	embryonic stem cell:	n/a	chr12:122356406-122356419 chr12:122356408-122356417 chr12:122356409-122356418 chr12:122356407-122356416 chr12:122356408-122356417
45	ATF2	chr12:122356087-122356586	GM12878	blood:	n/a	n/a
46	E2F6	chr12:122355808-122356806	H1-hESC	embryonic stem cell:	n/a	n/a
47	POLR2A	chr12:122356005-122356836	PANC-1	pancreas:	n/a	n/a
48	POU2F2	chr12:122356011-122356538	GM12891	blood:	n/a	n/a
49	USF2	chr12:122356150-122356613	GM12878	blood:	n/a	chr12:122356406-122356419 chr12:122356408-122356417 chr12:122356409-122356418 chr12:122356407-122356416 chr12:122356408-122356417
50	GABPA	chr12:122356074-122356626	H1-hESC	embryonic stem cell:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr12:122352837..122354864-chr12:122355521..122357983,3	MCF-7	breast:
2	chr12:122354300..122356847-chr12:122457161..122460061,2	K562	blood:
3	chr12:122353848..122356586-chr12:122614343..122616936,2	MCF-7	breast:
4	chr12:122325289..122328252-chr12:122355129..122358130,3	MCF-7	breast:
5	chr12:122239660..122241230-chr12:122355073..122357147,2	MCF-7	breast:
6	chr12:122353381..122358597-chr12:122457924..122463718,11	MCF-7	breast:
7	chr12:122343793..122346484-chr12:122354637..122356922,2	MCF-7	breast:
8	chr12:122353628..122357829-chr12:122368964..122373628,4	MCF-7	breast:
9	chr12:122355691..122357856-chr12:122357924..122360707,2	MCF-7	breast:

Variant related genes	Relation type
WDR66	TF binding region
ENSG00000175727	Chromatin interaction
ENSG00000158023	Chromatin interaction
ENSG00000239082	Chromatin interaction
ENSG00000256950	Chromatin interaction
ENSG00000255856	Chromatin interaction
ENSG00000212694	Chromatin interaction
ENSG00000110801	Chromatin interaction
ENSG00000110987	Chromatin interaction
ENSG00000139725	Chromatin interaction

Extended variants
information (count: 52 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:48)

rs_ID	r²[population]
rs1168658	1.00[CEU][hapmap];0.91[GIH][hapmap];0.86[MEX][hapmap];0.95[TSI][hapmap];0.90[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs1168661	0.90[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs1169076	0.87[CHB][hapmap];0.91[CHD][hapmap];0.95[JPT][hapmap]
rs1169081	0.87[ASW][hapmap];0.95[CEU][hapmap];0.91[CHB][hapmap];0.95[CHD][hapmap];0.94[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];0.97[MKK][hapmap];0.92[TSI][hapmap];0.80[EUR][1000 genomes]
rs1169084	0.82[CHB][hapmap];0.91[CHD][hapmap];0.88[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];0.90[TSI][hapmap]
rs1169091	0.87[CHB][hapmap];0.91[CHD][hapmap];0.88[GIH][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap];0.92[TSI][hapmap]
rs1177588	1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[ASN][1000 genomes]
rs1179947	0.87[CHB][hapmap];0.91[CHD][hapmap];1.00[JPT][hapmap]
rs12578258	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.90[LWK][hapmap];0.95[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.81[AMR][1000 genomes];0.85[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs12579389	0.82[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs12579730	0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1375653	1.00[CHB][hapmap];0.95[CHD][hapmap];1.00[JPT][hapmap];0.83[ASN][1000 genomes]
rs1375654	1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[ASN][1000 genomes]
rs1375655	1.00[CHB][hapmap];0.95[CHD][hapmap];1.00[JPT][hapmap];0.83[ASN][1000 genomes]
rs14259	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1630699	1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[ASN][1000 genomes]
rs1667586	0.83[ASN][1000 genomes]
rs1678952	1.00[CHB][hapmap];0.94[JPT][hapmap];0.83[ASN][1000 genomes]
rs1678953	1.00[CHB][hapmap];0.95[CHD][hapmap];1.00[JPT][hapmap];0.83[ASN][1000 genomes]
rs1720030	1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[ASN][1000 genomes]
rs1720066	0.83[AMR][1000 genomes];0.90[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs1720068	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17852561	0.83[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2009257	0.87[CHB][hapmap];1.00[JPT][hapmap]
rs2272133	0.87[CHB][hapmap];0.88[GIH][hapmap];0.95[JPT][hapmap]
rs2309275	0.95[CEU][hapmap];0.81[CHB][hapmap];0.90[JPT][hapmap];0.81[EUR][1000 genomes]
rs2442439	0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2688409	0.88[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34506529	0.87[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs34930953	0.87[AMR][1000 genomes]
rs35252940	0.81[AMR][1000 genomes];0.86[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs3825172	0.95[CEU][hapmap];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs4069666	1.00[CEU][hapmap];0.91[GIH][hapmap];0.86[MEX][hapmap];0.95[TSI][hapmap];0.88[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs4760108	0.80[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs482421	0.90[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs483416	1.00[CEU][hapmap];0.91[GIH][hapmap];0.86[MEX][hapmap];0.95[TSI][hapmap];0.90[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs508395	0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs55826938	0.94[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs56177852	0.96[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs58379261	0.96[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs59517025	0.94[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs59972569	0.82[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs686220	0.83[ASN][1000 genomes]
rs7309105	0.86[ASW][hapmap];1.00[CEU][hapmap];0.94[GIH][hapmap];0.95[MEX][hapmap];0.83[MKK][hapmap];0.92[TSI][hapmap];0.90[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs7313748	0.86[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];0.85[MKK][hapmap];1.00[TSI][hapmap];0.81[AMR][1000 genomes];0.85[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs745327	0.81[CHB][hapmap]
rs830121	0.91[CEU][hapmap];0.87[CHB][hapmap];0.93[CHD][hapmap];0.91[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];0.90[TSI][hapmap]
rs876934	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv529868	chr12:121956483-122944265	Flanking Active TSS Enhancers Weak transcription Active TSS Genic enhancers Strong transcription ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	173 gene(s)	inside rSNPs	diseases
2	nsv916686	chr12:122240149-122714056	Enhancers Strong transcription Weak transcription Flanking Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer Genic enhancers Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	89 gene(s)	inside rSNPs	diseases
3	nsv899568	chr12:122254713-122456524	Active TSS Enhancers Flanking Active TSS Weak transcription Strong transcription Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	19 gene(s)	inside rSNPs	diseases
4	esv34001	chr12:122298737-122521637	Active TSS Weak transcription Flanking Active TSS Strong transcription Enhancers Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	35 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs2272135	WDR66	cis	cerebellum	SCAN
rs2272135	SUDS3	cis	cerebellum	SCAN

Chromatin state (count:127 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:122332000-122356600	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
2	chr12:122341600-122356600	Weak transcription	iPS-15b Cell Line	embryonic stem cell
3	chr12:122344400-122356400	Weak transcription	iPS-18 Cell Line	embryonic stem cell
4	chr12:122350000-122356200	Strong transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
5	chr12:122353200-122356400	Strong transcription	HepG2	liver
6	chr12:122353400-122356200	Genic enhancers	NHDF-Ad	bronchial
7	chr12:122353400-122356400	Strong transcription	Ovary	ovary
8	chr12:122353600-122356600	Genic enhancers	HSMMtube	muscle
9	chr12:122353600-122356800	Strong transcription	A549	lung
10	chr12:122353800-122356200	Genic enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
11	chr12:122354200-122356200	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
12	chr12:122354200-122356400	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
13	chr12:122354200-122363000	Weak transcription	Small Intestine	intestine
14	chr12:122354600-122356400	Strong transcription	HMEC	breast
15	chr12:122354800-122356600	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
16	chr12:122355000-122356200	Genic enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
17	chr12:122355000-122357600	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
18	chr12:122355000-122357600	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
19	chr12:122355200-122357400	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
20	chr12:122355400-122356200	Genic enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
21	chr12:122355600-122356400	Genic enhancers	Muscle Satellite Cultured Cells	--
22	chr12:122355600-122364800	Weak transcription	K562	blood
23	chr12:122355800-122356200	Genic enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
24	chr12:122355800-122356200	Flanking Active TSS	Brain Anterior Caudate	brain
25	chr12:122355800-122356200	Genic enhancers	Fetal Muscle Trunk	muscle
26	chr12:122355800-122356200	Flanking Active TSS	Stomach Mucosa	stomach
27	chr12:122355800-122356200	Transcr. at gene 5' and 3'	Dnd41	blood
28	chr12:122355800-122356200	Genic enhancers	HUVEC	blood vessel
29	chr12:122355800-122356200	Transcr. at gene 5' and 3'	NHEK	skin
30	chr12:122355800-122356400	Genic enhancers	Foreskin Melanocyte Primary Cells skin01	Skin
31	chr12:122355800-122356400	Flanking Active TSS	Brain Inferior Temporal Lobe	brain
32	chr12:122355800-122356400	Enhancers	Lung	lung
33	chr12:122355800-122356400	Flanking Active TSS	Rectal Mucosa Donor 31	rectum
34	chr12:122355800-122356800	Flanking Active TSS	Primary T helper cells PMA-I stimulated	--
35	chr12:122355800-122356800	Flanking Active TSS	Duodenum Mucosa	Duodenum
36	chr12:122355800-122357000	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
37	chr12:122355800-122357000	Active TSS	Rectal Smooth Muscle	rectum
38	chr12:122355800-122357000	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
39	chr12:122356000-122356200	Genic enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
40	chr12:122356000-122356200	Flanking Active TSS	HUES48 Cell Line	embryonic stem cell
41	chr12:122356000-122356200	Enhancers	iPS DF 6.9 Cell Line	embryonic stem cell
42	chr12:122356000-122356200	Flanking Active TSS	Breast Myoepithelial Primary Cells	Breast
43	chr12:122356000-122356200	Flanking Active TSS	Primary T cells from cord blood	blood
44	chr12:122356000-122356200	Transcr. at gene 5' and 3'	Primary hematopoietic stem cells short term culture	blood
45	chr12:122356000-122356200	Flanking Active TSS	Primary T helper memory cells from peripheral blood 2	blood
46	chr12:122356000-122356200	Flanking Active TSS	Primary T helper naive cells from peripheral blood	blood
47	chr12:122356000-122356200	Transcr. at gene 5' and 3'	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
48	chr12:122356000-122356200	Flanking Active TSS	Brain Angular Gyrus	brain
49	chr12:122356000-122356200	Flanking Active TSS	Brain Hippocampus Middle	brain
50	chr12:122356000-122356200	Flanking Active TSS	Brain Dorsolateral Prefrontal Cortex	brain

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