Variant report

Variant	rs28660993
Chromosome Location	chr12:123875394-123875395
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:7)
CpG islands
(count:0)
Chromatin interactive
region (count:12)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:7 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr12:123874909-123875430	HUVEC	blood vessel:	n/a	n/a
2	POLR2A	chr12:123874824-123875875	HUVEC	blood vessel:	n/a	n/a
3	POLR2A	chr12:123874116-123875878	HUVEC	blood vessel:	n/a	n/a
4	POLR2A	chr12:123875389-123875558	HepG2	liver:	n/a	n/a
5	POLR2A	chr12:123874157-123875850	HUVEC	blood vessel:	n/a	n/a
6	CTCF	chr12:123875300-123875450	HFF-Myc	foreskin:	n/a	n/a
7	POLR2A	chr12:123875379-123875450	GM12878	blood:	n/a	n/a

No data

(count:12 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr12:123873719..123876506-chr12:124067448..124069174,2	K562	blood:
2	chr12:123754082..123756520-chr12:123873506..123875645,3	K562	blood:
3	chr12:123872355..123875545-chr12:123919640..123922793,3	MCF-7	breast:
4	chr12:123872223..123875553-chr12:124085591..124088201,3	MCF-7	breast:
5	chr12:123845329..123854937-chr12:123865496..123876607,58	K562	blood:
6	chr12:123871385..123875741-chr12:124017374..124019532,6	MCF-7	breast:
7	chr12:123872778..123876196-chr12:124065295..124071344,6	MCF-7	breast:
8	chr12:123873866..123876385-chr12:123942538..123944226,2	MCF-7	breast:
9	chr12:123847204..123849398-chr12:123874460..123876425,2	K562	blood:
10	chr12:123872416..123876102-chr12:124017252..124019601,4	MCF-7	breast:
11	chr12:123847748..123850760-chr12:123875045..123877875,5	MCF-7	breast:
12	chr12:123874611..123876401-chr12:123967217..123969868,2	K562	blood:

No data

Variant related genes	Relation type
SETD8	TF binding region
ENSG00000150977	Chromatin interaction
ENSG00000184209	Chromatin interaction
ENSG00000111328	Chromatin interaction
ENSG00000111364	Chromatin interaction
ENSG00000139697	Chromatin interaction
ENSG00000256092	Chromatin interaction
ENSG00000086598	Chromatin interaction
ENSG00000247373	Chromatin interaction
ENSG00000188026	Chromatin interaction

Extended variants
information (count: 74 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:63)

rs_ID	r²[population]
rs10444439	0.95[CHB][hapmap];0.94[JPT][hapmap]
rs10744151	0.80[JPT][hapmap]
rs10744152	0.84[JPT][hapmap]
rs10772997	0.84[JPT][hapmap]
rs10773000	0.94[JPT][hapmap]
rs10773003	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.89[LWK][hapmap];1.00[MEX][hapmap];0.93[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap]
rs10773005	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.84[LWK][hapmap];0.93[MEX][hapmap];0.82[MKK][hapmap];1.00[TSI][hapmap];0.85[YRI][hapmap]
rs10773007	0.82[GIH][hapmap];1.00[YRI][hapmap]
rs10773014	1.00[YRI][hapmap]
rs10846489	0.86[CHD][hapmap];0.94[JPT][hapmap]
rs10846509	0.82[GIH][hapmap];1.00[YRI][hapmap]
rs10846510	1.00[YRI][hapmap]
rs10846514	0.82[GIH][hapmap];1.00[YRI][hapmap]
rs10846517	0.82[CHB][hapmap];0.94[CHD][hapmap];0.84[JPT][hapmap]
rs10846518	0.82[GIH][hapmap];1.00[YRI][hapmap]
rs10846519	0.94[CHD][hapmap];0.84[JPT][hapmap]
rs10846523	0.94[CHD][hapmap];0.84[JPT][hapmap]
rs11057223	1.00[CEU][hapmap];0.86[CHD][hapmap];0.94[GIH][hapmap];0.94[JPT][hapmap];0.86[TSI][hapmap];1.00[YRI][hapmap]
rs11057240	1.00[YRI][hapmap]
rs11057250	1.00[YRI][hapmap]
rs11057251	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap]
rs11057266	0.82[GIH][hapmap];1.00[YRI][hapmap]
rs11057273	1.00[CEU][hapmap];0.90[CHB][hapmap];0.92[JPT][hapmap];1.00[YRI][hapmap]
rs11057276	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap]
rs11057287	0.84[JPT][hapmap]
rs1109559	0.86[CHD][hapmap];0.94[JPT][hapmap]
rs1109560	1.00[CEU][hapmap];0.94[JPT][hapmap]
rs11608305	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs12317452	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap]
rs12366872	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap]
rs12371973	1.00[YRI][hapmap]
rs1402275	0.85[YRI][hapmap]
rs1568428	0.94[JPT][hapmap]
rs1790104	0.85[JPT][hapmap]
rs1879379	0.94[JPT][hapmap]
rs2271976	1.00[CEU][hapmap];0.94[JPT][hapmap]
rs28410096	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]
rs28414347	0.94[CHD][hapmap];0.84[JPT][hapmap]
rs28475177	0.82[GIH][hapmap];1.00[YRI][hapmap]
rs28501453	0.94[CHD][hapmap];0.84[JPT][hapmap]
rs28532037	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[MEX][hapmap];0.93[MKK][hapmap];1.00[TSI][hapmap]
rs28533432	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap]
rs28556815	0.86[ASN][1000 genomes]
rs28565984	0.83[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs28574664	0.84[ASN][1000 genomes]
rs28587386	0.94[CHD][hapmap];0.84[JPT][hapmap]
rs28595660	0.94[CHD][hapmap];0.84[JPT][hapmap]
rs28613486	0.94[CHD][hapmap];0.84[JPT][hapmap]
rs28631104	0.83[ASN][1000 genomes]
rs28655516	0.82[GIH][hapmap];1.00[YRI][hapmap]
rs3088303	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.95[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap]
rs34032470	0.87[ASN][1000 genomes]
rs3803001	0.94[CHD][hapmap];0.84[JPT][hapmap]
rs3825141	0.94[CHD][hapmap];0.84[JPT][hapmap]
rs4759375	1.00[YRI][hapmap]
rs4759377	1.00[ASW][hapmap];0.93[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.89[LWK][hapmap];0.93[MEX][hapmap];0.83[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap]
rs6488873	0.82[ASN][1000 genomes]
rs7139321	0.94[JPT][hapmap]
rs7297649	0.94[CHD][hapmap];0.84[JPT][hapmap]
rs7315453	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];0.92[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap]
rs7959415	0.94[CHD][hapmap];0.89[JPT][hapmap]
rs7972811	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.89[LWK][hapmap];1.00[MEX][hapmap];0.93[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap]
rs9795593	0.94[CHD][hapmap];0.83[JPT][hapmap]

Variant overlapped rSNPs/rCNVs (count:11 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1038841	chr12:123757305-124087671	Weak transcription Enhancers Active TSS Flanking Active TSS Genic enhancers Bivalent/Poised TSS Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	63 gene(s)	inside rSNPs	diseases
2	nsv541622	chr12:123757305-124087671	Enhancers Strong transcription Genic enhancers Active TSS Weak transcription Flanking Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	63 gene(s)	inside rSNPs	diseases
3	nsv1035223	chr12:123795559-123991706	Weak transcription Flanking Active TSS Strong transcription Bivalent Enhancer Enhancers Active TSS Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	48 gene(s)	inside rSNPs	diseases
4	nsv899579	chr12:123843017-123901480	Strong transcription Weak transcription Enhancers Genic enhancers Flanking Active TSS Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	43 gene(s)	inside rSNPs	diseases
5	nsv826534	chr12:123859610-123876354	Transcr. at gene 5' and 3' Weak transcription Genic enhancers Active TSS Enhancers Flanking Active TSS Strong transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	20 gene(s)	inside rSNPs	diseases
6	esv7028	chr12:123874023-123879670	Transcr. at gene 5' and 3' Strong transcription Genic enhancers Weak transcription Active TSS Enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region	14 gene(s)	inside rSNPs	diseases
7	nsv976671	chr12:123874923-123875423	Weak transcription Active TSS Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS Flanking Active TSS Strong transcription Enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region Chromatin interactive region	12 gene(s)	inside rSNPs	diseases
8	esv2417445	chr12:123875177-123879748	Transcr. at gene 5' and 3' Weak transcription Strong transcription Flanking Bivalent TSS/Enh Genic enhancers Flanking Active TSS Bivalent Enhancer Enhancers Active TSS Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region	12 gene(s)	inside rSNPs	diseases
9	esv3449892	chr12:123875199-123879684	Strong transcription Genic enhancers Flanking Active TSS Weak transcription Transcr. at gene 5' and 3' Bivalent Enhancer Enhancers Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region	12 gene(s)	inside rSNPs	diseases
10	esv8369	chr12:123875230-123879694	Strong transcription Genic enhancers Weak transcription Flanking Active TSS Transcr. at gene 5' and 3' Active TSS Enhancers Bivalent Enhancer	TF binding region CpG island Chromatin interactive region	12 gene(s)	inside rSNPs	diseases
11	esv3414733	chr12:123875275-123879643	Weak transcription Genic enhancers Transcr. at gene 5' and 3' Strong transcription Flanking Active TSS Active TSS Enhancers Bivalent Enhancer	TF binding region CpG island Chromatin interactive region	10 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs28660993	RP11-282O18.3	cis	Whole Blood	GTEx
rs28660993	CDK2AP1	cis	Whole Blood	GTEx

Chromatin state (count:123 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:123873000-123875400	Active TSS	Esophagus	oesophagus
2	chr12:123873200-123875400	Active TSS	Aorta	Aorta
3	chr12:123874000-123875400	Flanking Active TSS	Primary hematopoietic stem cells	blood
4	chr12:123874200-123875400	Flanking Active TSS	Primary B cells from cord blood	blood
5	chr12:123874200-123875400	Enhancers	Primary T helper naive cells from peripheral blood	blood
6	chr12:123874200-123875600	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
7	chr12:123874200-123875600	Transcr. at gene 5' and 3'	Foreskin Keratinocyte Primary Cells skin03	Skin
8	chr12:123874200-123876000	Flanking Active TSS	Primary neutrophils fromperipheralblood	blood
9	chr12:123874200-123876200	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
10	chr12:123874200-123876800	Transcr. at gene 5' and 3'	Foreskin Fibroblast Primary Cells skin02	Skin
11	chr12:123874400-123875400	Transcr. at gene 5' and 3'	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
12	chr12:123874400-123875400	Flanking Active TSS	Foreskin Melanocyte Primary Cells skin03	Skin
13	chr12:123874400-123875400	Flanking Active TSS	Brain Anterior Caudate	brain
14	chr12:123874400-123875600	Flanking Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
15	chr12:123874400-123875600	Transcr. at gene 5' and 3'	NHEK	skin
16	chr12:123874400-123875800	Flanking Active TSS	Primary T helper 17 cells PMA-I stimulated	--
17	chr12:123874400-123875800	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
18	chr12:123874600-123875400	Flanking Active TSS	Brain Substantia Nigra	brain
19	chr12:123874600-123875400	Flanking Active TSS	Colon Smooth Muscle	Colon
20	chr12:123874600-123875400	Flanking Active TSS	Duodenum Mucosa	Duodenum
21	chr12:123874600-123875400	Flanking Active TSS	Duodenum Smooth Muscle	Duodenum
22	chr12:123874600-123875400	Flanking Active TSS	Rectal Mucosa Donor 31	rectum
23	chr12:123874600-123875400	Flanking Active TSS	Rectal Smooth Muscle	rectum
24	chr12:123874600-123875400	Flanking Active TSS	HUVEC	blood vessel
25	chr12:123874600-123875600	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
26	chr12:123874600-123875600	Flanking Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
27	chr12:123874600-123875600	Flanking Active TSS	Brain Angular Gyrus	brain
28	chr12:123874600-123875600	Transcr. at gene 5' and 3'	Fetal Adrenal Gland	Adrenal Gland
29	chr12:123874600-123875600	Transcr. at gene 5' and 3'	Fetal Stomach	stomach
30	chr12:123874600-123875600	Transcr. at gene 5' and 3'	Skeletal Muscle Male	skeletal muscle
31	chr12:123874600-123875600	Transcr. at gene 5' and 3'	NHLF	lung
32	chr12:123874800-123875400	Enhancers	Primary T helper naive cells fromperipheralblood	blood
33	chr12:123874800-123875400	Enhancers	Spleen	Spleen
34	chr12:123874800-123875400	Flanking Active TSS	NH-A	brain
35	chr12:123874800-123875400	Transcr. at gene 5' and 3'	Osteobl	bone
36	chr12:123874800-123875600	Transcr. at gene 5' and 3'	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
37	chr12:123874800-123875600	Transcr. at gene 5' and 3'	Primary hematopoietic stem cells short term culture	blood
38	chr12:123874800-123875600	Genic enhancers	Fetal Thymus	thymus
39	chr12:123874800-123875600	Transcr. at gene 5' and 3'	GM12878-XiMat	blood
40	chr12:123874800-123875800	Genic enhancers	Sigmoid Colon	Sigmoid Colon
41	chr12:123874800-123876400	Enhancers	Primary monocytes fromperipheralblood	blood
42	chr12:123875000-123875400	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
43	chr12:123875000-123875400	Weak transcription	iPS-15b Cell Line	embryonic stem cell
44	chr12:123875000-123875400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
45	chr12:123875000-123875400	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
46	chr12:123875000-123875400	Enhancers	Colonic Mucosa	Colon
47	chr12:123875000-123875400	Weak transcription	Lung	lung
48	chr12:123875000-123875400	Weak transcription	Placenta Amnion	Placenta Amnion
49	chr12:123875000-123875400	Genic enhancers	Hela-S3	cervix
50	chr12:123875000-123875600	Genic enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links