Variant report

Variant	rs1109560
Chromosome Location	chr12:123757905-123757906
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:1)
CpG islands
(count:122)
Chromatin interactive
region (count:5)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

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

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr12:123757857-123757974	H1-hESC	embryonic stem cell:	n/a	n/a

(count:122 , 50 per page) page: 1 2 3

No.	Chromosome Location	Cell Line	Cell type	Cell Stage
1	chr12:123757892-123757942	H1-hESC	embryonic stem cell:	embryo
2	chr12:123757892-123757942	GM06990	blood:	n/a
3	chr12:123757860-123757910	AG04450	lung:	fetal
4	chr12:123757892-123757942	Hepatocyte	liver:	n/a
5	chr12:123757892-123757942	SK-N-SH_RA	brain:	n/a
6	chr12:123757892-123757942	MCF-7	breast:	n/a
7	chr12:123757860-123757910	Jurkat	blood:	n/a
8	chr12:123757860-123757910	BE2_C	brain:	n/a
9	chr12:123757892-123757942	HepG2	liver:	n/a
10	chr12:123757892-123757942	NHBE	bronchial:	n/a
11	chr12:123757860-123757910	HRE	kidney:	n/a
12	chr12:123757860-123757910	T-47D	breast:	n/a
13	chr12:123757860-123757910	HRPEpiC	eye:	n/a
14	chr12:123757892-123757942	SAEC	small airway:	n/a
15	chr12:123757860-123757910	NT2-D1	testis:	n/a
16	chr12:123757860-123757910	HEK293	kidney:	embryo
17	chr12:123757860-123757910	LNCaP	prostate:	n/a
18	chr12:123757860-123757910	GM12878	blood:	n/a
19	chr12:123757892-123757942	HNPCEpiC	eye:	n/a
20	chr12:123757860-123757910	NHDF-neo	bronchial:	n/a
21	chr12:123757892-123757942	GM12892	blood:	n/a
22	chr12:123757892-123757942	IMR90	lung:	fetal
23	chr12:123757860-123757910	HNPCEpiC	eye:	n/a
24	chr12:123757892-123757942	AG04449	skin:	fetal
25	chr12:123757892-123757942	HUVEC	blood vessel:	n/a
26	chr12:123757860-123757910	HIPEpiC	eye:	n/a
27	chr12:123757860-123757910	NHBE	bronchial:	n/a
28	chr12:123757860-123757910	HCF	heart:	n/a
29	chr12:123757892-123757942	HRPEpiC	eye:	n/a
30	chr12:123757860-123757910	NH-A	brain:	n/a
31	chr12:123757892-123757942	HMEC	breast:	n/a
32	chr12:123757860-123757910	MCF-7	breast:	n/a
33	chr12:123757892-123757942	HPAEpiC	pulmonary alveolar:	n/a
34	chr12:123757892-123757942	AG10803	skin:	n/a
35	chr12:123757860-123757910	PrEC	prostate:	n/a
36	chr12:123757860-123757910	H1-hESC	embryonic stem cell:	embryo
37	chr12:123757892-123757942	AG09309	skin:	n/a
38	chr12:123757860-123757910	NB4	blood:	n/a
39	chr12:123757860-123757910	HepG2	liver:	n/a
40	chr12:123757860-123757910	HMEC	breast:	n/a
41	chr12:123757892-123757942	ECC-1	luminal epithelium:	n/a
42	chr12:123757892-123757942	HRE	kidney:	n/a
43	chr12:123757860-123757910	HPAEpiC	pulmonary alveolar:	n/a
44	chr12:123757892-123757942	ovcar-3	ovarian:	n/a
45	chr12:123757860-123757910	U87	brain:	n/a
46	chr12:123757860-123757910	SK-N-MC	brain:	n/a
47	chr12:123757892-123757942	NH-A	brain:	n/a
48	chr12:123757892-123757942	SK-N-SH	brain:	n/a
49	chr12:123757892-123757942	HCM	heart:	n/a
50	chr12:123757860-123757910	ovcar-3	ovarian:	n/a

(count:5 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr12:123755164..123758333-chr12:123868507..123873426,5	K562	blood:
2	chr12:123753451..123758032-chr12:123846651..123850459,6	MCF-7	breast:
3	chr12:123756475..123758463-chr12:123849452..123851589,2	K562	blood:
4	chr12:123749757..123758492-chr12:123844437..123851411,15	MCF-7	breast:
5	chr12:123755389..123758333-chr12:123866833..123870129,4	K562	blood:

No data

Variant related genes	Relation type
CDK2AP1	TF binding region
CDK2AP1	CpG island
ENSG00000256092	Chromatin interaction
ENSG00000183955	Chromatin interaction
ENSG00000139697	Chromatin interaction

Extended variants
information (count: 62 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:55)

rs_ID	r²[population]
rs10444439	0.94[JPT][hapmap]
rs10732573	0.84[JPT][hapmap];0.81[ASN][1000 genomes]
rs10734901	0.81[ASN][1000 genomes]
rs10744150	0.82[CHB][hapmap];0.84[JPT][hapmap]
rs10744151	0.82[CHB][hapmap];0.80[JPT][hapmap]
rs10773000	0.91[CHB][hapmap];1.00[JPT][hapmap];0.90[ASN][1000 genomes]
rs10773002	0.82[CHB][hapmap];0.83[JPT][hapmap]
rs10773003	1.00[CEU][hapmap];0.94[JPT][hapmap]
rs10773005	1.00[CEU][hapmap];0.94[JPT][hapmap]
rs10846489	1.00[CHB][hapmap];1.00[JPT][hapmap];0.98[ASN][1000 genomes]
rs11057219	0.97[ASN][1000 genomes]
rs11057223	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[AFR][1000 genomes];0.95[AMR][1000 genomes];0.89[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs11057224	0.98[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11057251	0.94[JPT][hapmap]
rs11057273	1.00[CEU][hapmap];0.84[JPT][hapmap]
rs11057276	0.94[JPT][hapmap]
rs1109559	1.00[CHB][hapmap];1.00[JPT][hapmap];0.99[ASN][1000 genomes]
rs11608305	0.94[JPT][hapmap]
rs12317452	1.00[CEU][hapmap];0.94[JPT][hapmap]
rs12366872	1.00[CEU][hapmap];0.94[JPT][hapmap]
rs1568427	0.83[CHB][hapmap];0.83[JPT][hapmap]
rs1568428	1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[ASN][1000 genomes]
rs1609520	0.83[JPT][hapmap]
rs1727293	0.83[JPT][hapmap]
rs1727301	0.90[CHB][hapmap];0.89[JPT][hapmap]
rs1727331	0.83[JPT][hapmap]
rs1790104	0.91[CHB][hapmap];0.90[JPT][hapmap]
rs1879379	1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[ASN][1000 genomes]
rs1980251	0.81[ASN][1000 genomes]
rs2030401	0.98[ASN][1000 genomes]
rs2271976	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.98[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2280424	0.83[JPT][hapmap]
rs2337630	0.88[ASN][1000 genomes]
rs2337631	0.88[ASN][1000 genomes]
rs2682427	0.91[CHB][hapmap];0.89[JPT][hapmap]
rs28410096	1.00[CEU][hapmap];0.94[JPT][hapmap]
rs28532037	1.00[CEU][hapmap];0.94[JPT][hapmap]
rs28533432	0.94[JPT][hapmap]
rs28660993	1.00[CEU][hapmap];0.94[JPT][hapmap]
rs3088303	1.00[CEU][hapmap];0.94[JPT][hapmap]
rs34841857	0.86[ASN][1000 genomes]
rs3759114	0.83[JPT][hapmap];0.83[ASN][1000 genomes]
rs4553407	0.98[ASN][1000 genomes]
rs4759377	0.92[CEU][hapmap];0.94[JPT][hapmap]
rs4759411	0.84[JPT][hapmap]
rs4759413	0.81[ASN][1000 genomes]
rs4759414	0.84[JPT][hapmap];0.81[ASN][1000 genomes]
rs61953394	0.98[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7139321	1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[ASN][1000 genomes]
rs7304782	0.83[JPT][hapmap]
rs7312955	0.88[ASN][1000 genomes]
rs7315453	1.00[CEU][hapmap];0.94[JPT][hapmap]
rs73231928	0.83[ASN][1000 genomes]
rs7959415	0.82[JPT][hapmap]
rs7972811	1.00[CEU][hapmap];0.94[JPT][hapmap]

Variant overlapped rSNPs/rCNVs (count:7 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv1825473	chr12:123582855-123822503	Weak transcription Strong transcription Flanking Active TSS Genic enhancers Enhancers Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	73 gene(s)	inside rSNPs	diseases
2	esv1803368	chr12:123640853-123822503	Weak transcription Strong transcription Flanking Active TSS Genic enhancers Enhancers Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	70 gene(s)	inside rSNPs	diseases
3	esv1830566	chr12:123640853-123822503	Flanking Active TSS Strong transcription Enhancers Weak transcription Genic enhancers Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	70 gene(s)	inside rSNPs	diseases
4	esv1836043	chr12:123709409-123822503	Weak transcription Flanking Active TSS Strong transcription Enhancers Genic enhancers Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	70 gene(s)	inside rSNPs	diseases
5	esv3371786	chr12:123753799-123757997	Active TSS Enhancers Weak transcription Transcr. at gene 5' and 3' Flanking Active TSS Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region	20 gene(s)	inside rSNPs	diseases
6	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
7	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

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs1109560	RP11-282O18.3	cis	Whole Blood	GTEx
rs1109560	CDK2AP1	cis	Whole Blood	GTEx

Chromatin state (count:34 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:123756800-123758000	Enhancers	Spleen	Spleen
2	chr12:123756800-123758200	Flanking Active TSS	Brain Germinal Matrix	brain
3	chr12:123756800-123758400	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
4	chr12:123757200-123758000	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
5	chr12:123757200-123758000	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
6	chr12:123757200-123758000	Enhancers	Fetal Stomach	stomach
7	chr12:123757200-123759200	Weak transcription	Duodenum Smooth Muscle	Duodenum
8	chr12:123757200-123761800	Weak transcription	Primary monocytes fromperipheralblood	blood
9	chr12:123757200-123762400	Weak transcription	Primary B cells from peripheral blood	blood
10	chr12:123757200-123762600	Weak transcription	GM12878-XiMat	blood
11	chr12:123757200-123773800	Weak transcription	Duodenum Mucosa	Duodenum
12	chr12:123757200-123774000	Weak transcription	K562	blood
13	chr12:123757200-123782600	Weak transcription	Right Atrium	heart
14	chr12:123757400-123758000	Enhancers	ES-I3 Cell Line	embryonic stem cell
15	chr12:123757400-123758000	Enhancers	H1 Cell Line	embryonic stem cell
16	chr12:123757400-123759200	Enhancers	Fetal Brain Male	brain
17	chr12:123757400-123762200	Weak transcription	HUVEC	blood vessel
18	chr12:123757600-123758000	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
19	chr12:123757600-123758000	Enhancers	Cortex derived primary cultured neurospheres	brain
20	chr12:123757600-123758000	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
21	chr12:123757600-123758000	Flanking Active TSS	Fetal Brain Female	brain
22	chr12:123757600-123758200	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
23	chr12:123757600-123758200	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
24	chr12:123757600-123762000	Weak transcription	Primary hematopoietic stem cells	blood
25	chr12:123757600-123762000	Weak transcription	Primary hematopoietic stem cells short term culture	blood
26	chr12:123757600-123762000	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
27	chr12:123757600-123762000	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
28	chr12:123757600-123762800	Weak transcription	NH-A	brain
29	chr12:123757600-123773400	Weak transcription	Fetal Muscle Leg	muscle
30	chr12:123757600-123773400	Weak transcription	Fetal Thymus	thymus
31	chr12:123757600-123773800	Weak transcription	Stomach Smooth Muscle	stomach
32	chr12:123757800-123758000	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
33	chr12:123757800-123758000	Enhancers	Skeletal Muscle Male	skeletal muscle
34	chr12:123757800-123771400	Weak transcription	A549	lung

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