Variant report

Variant	rs1727307
Chromosome Location	chr12:123575742-123575743
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:0)
CpG islands
(count:0)
Chromatin interactive
region (count:15)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:15 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr12:123573881..123576493-chr12:123631498..123633206,2	K562	blood:
2	chr12:123574871..123577625-chr12:123635000..123637260,3	MCF-7	breast:
3	chr12:123539791..123542781-chr12:123573369..123575868,2	MCF-7	breast:
4	chr12:123574271..123575945-chr12:123599295..123601794,2	MCF-7	breast:
5	chr12:123552557..123554332-chr12:123575460..123578722,3	MCF-7	breast:
6	chr12:123574636..123576162-chr12:123864283..123866660,2	K562	blood:
7	chr12:123574363..123577127-chr12:123716217..123719008,2	K562	blood:
8	chr12:123574363..123577127-chr12:123716097..123719008,3	K562	blood:
9	chr12:123561700..123563404-chr12:123573339..123575824,2	MCF-7	breast:
10	chr12:123569324..123574207-chr12:123574392..123579398,5	K562	blood:
11	chr12:123465851..123467372-chr12:123575346..123577603,2	K562	blood:
12	chr12:123573280..123576168-chr12:123580609..123582204,2	K562	blood:
13	chr12:123463514..123465244-chr12:123572916..123575851,2	MCF-7	breast:
14	chr12:123468080..123470439-chr12:123573373..123575937,2	K562	blood:
15	chr12:123557772..123560593-chr12:123574740..123576717,2	K562	blood:

No data

Variant related genes	Relation type
ENSG00000182196	Chromatin interaction
ENSG00000150967	Chromatin interaction
ENSG00000051825	Chromatin interaction
ENSG00000130921	Chromatin interaction

Extended variants
information (count: 54 )
Associated
traits (count: 13 )

rSNPs within LD-proxies of this variant (count:49)

rs_ID	r²[population]
rs1051434	0.96[CEU][hapmap];0.82[CHB][hapmap];0.81[CHD][hapmap];0.90[GIH][hapmap];0.80[JPT][hapmap];0.97[TSI][hapmap];0.87[EUR][1000 genomes]
rs10773003	0.80[JPT][hapmap]
rs10773921	1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];0.86[JPT][hapmap];1.00[TSI][hapmap];0.88[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs10846489	0.84[CEU][hapmap];0.83[TSI][hapmap]
rs10848428	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[TSI][hapmap];0.81[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11060853	0.81[JPT][hapmap]
rs1109559	0.80[CEU][hapmap]
rs11608811	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];1.00[GIH][hapmap];0.90[JPT][hapmap];1.00[TSI][hapmap];0.85[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs11613937	0.81[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs12425009	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];0.86[GIH][hapmap];0.86[JPT][hapmap];1.00[TSI][hapmap];0.82[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs12425850	0.82[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs1568428	0.84[CEU][hapmap];0.80[TSI][hapmap]
rs1611973	0.87[EUR][1000 genomes]
rs1615350	0.83[CHB][hapmap];0.81[CHD][hapmap];0.85[JPT][hapmap];0.82[TSI][hapmap]
rs1617156	0.85[YRI][hapmap]
rs1716184	0.87[EUR][1000 genomes]
rs1727286	0.81[EUR][1000 genomes]
rs1727293	0.96[CEU][hapmap];0.91[CHB][hapmap];0.81[CHD][hapmap];0.90[GIH][hapmap];0.90[JPT][hapmap];0.97[TSI][hapmap];0.86[EUR][1000 genomes]
rs1727295	0.91[CEU][hapmap];0.95[CHB][hapmap];0.83[JPT][hapmap];0.86[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs1727301	0.85[JPT][hapmap]
rs1727302	0.83[CHB][hapmap];0.81[CHD][hapmap];0.85[JPT][hapmap];0.82[TSI][hapmap]
rs1727305	0.87[EUR][1000 genomes]
rs1727312	0.87[EUR][1000 genomes]
rs1790094	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.83[MEX][hapmap];1.00[TSI][hapmap];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1790104	0.85[JPT][hapmap]
rs1790106	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[TSI][hapmap];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1790121	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[TSI][hapmap];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1790122	0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1790129	0.81[EUR][1000 genomes]
rs1984658	0.81[EUR][1000 genomes]
rs2682427	0.85[JPT][hapmap]
rs28755851	0.80[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs3741530	1.00[CEU][hapmap];0.80[EUR][1000 genomes]
rs3759115	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];0.86[GIH][hapmap];0.86[JPT][hapmap];1.00[TSI][hapmap]
rs3897102	1.00[CHB][hapmap];0.81[JPT][hapmap];0.81[ASN][1000 genomes]
rs4148862	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4148863	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[TSI][hapmap];0.81[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4148866	0.81[CHD][hapmap]
rs4275659	1.00[CEU][hapmap];0.95[CHB][hapmap];0.83[GIH][hapmap];0.86[JPT][hapmap];0.95[TSI][hapmap]
rs520088	0.84[YRI][hapmap]
rs585522	0.80[GIH][hapmap];0.86[MEX][hapmap];0.85[YRI][hapmap]
rs61955214	0.80[ASN][1000 genomes]
rs7135296	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];0.82[GIH][hapmap];0.85[JPT][hapmap];1.00[TSI][hapmap];0.81[EUR][1000 genomes]
rs7296418	1.00[ASW][hapmap];0.91[CEU][hapmap];0.95[CHB][hapmap];0.82[GIH][hapmap];0.86[JPT][hapmap];0.91[MEX][hapmap];0.97[TSI][hapmap];0.91[YRI][hapmap]
rs7305511	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];0.86[GIH][hapmap];0.86[JPT][hapmap];1.00[TSI][hapmap];0.81[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs7957096	1.00[CEU][hapmap];0.91[CHB][hapmap];0.90[JPT][hapmap];0.88[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs884956	0.95[CHB][hapmap]
rs940904	0.80[GIH][hapmap]
rs949143	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[TSI][hapmap];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv3388790	chr12:123275902-123655103	Enhancers Strong transcription Weak transcription Flanking Active TSS Genic enhancers Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	55 gene(s)	inside rSNPs	diseases
2	nsv517200	chr12:123312051-123654498	Strong transcription Weak transcription Flanking Active TSS Genic enhancers Enhancers Transcr. at gene 5' and 3' Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	55 gene(s)	inside rSNPs	diseases
3	nsv832533	chr12:123395927-123589290	Enhancers Genic enhancers Flanking Active TSS Weak transcription Active TSS Strong transcription Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	37 gene(s)	inside rSNPs	diseases
4	nsv427924	chr12:123412172-123722059	Enhancers Active TSS Weak transcription Strong transcription Flanking Active TSS Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	78 gene(s)	inside rSNPs	diseases
5	nsv1042550	chr12:123532028-123659500	Flanking Active TSS Weak transcription Enhancers Strong transcription Genic enhancers Active TSS Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	18 gene(s)	inside rSNPs	diseases

Variant related diseases (count:1)

Disease	PMID	Source
Platelet counts	21507922	GWAS catalog

mRNA abundance (count:12)

SNP	Gene	Cis/trans	Tissue	Source
rs1727307	CDK2AP1	cis	Esophagus Mucosa	GTEx
rs1727307	RP11-282O18.3	cis	Esophagus Mucosa	GTEx
rs1727307	PITPNM2	cis	cerebellum	SCAN
rs1727307	MPHOSPH9	Cis_1M	lymphoblastoid	RTeQTL
rs1727307	TMEM120B	cis	parietal	SCAN
rs1727307	ABCB9	cis	Heart Left Ventricle	GTEx
rs1727307	ARL6IP4	cis	multi-tissue	Pritchard
rs1727307	SBNO1	Cis_1M	lymphoblastoid	RTeQTL
rs1727307	CDK2AP1	cis	cerebellum	SCAN
rs1727307	C12orf65	cis	cerebellum	SCAN
rs1727307	ARL6IP4	Cis_1M	lymphoblastoid	RTeQTL
rs1727307	CDK2AP1	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:80 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:123561000-123578800	Weak transcription	Fetal Intestine Large	intestine
2	chr12:123561200-123590000	Weak transcription	Fetal Intestine Small	intestine
3	chr12:123561600-123604000	Genic enhancers	Fetal Thymus	thymus
4	chr12:123562000-123576200	Weak transcription	Primary T cells from cord blood	blood
5	chr12:123562400-123586600	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
6	chr12:123567400-123588000	Enhancers	Left Ventricle	heart
7	chr12:123568600-123578000	Weak transcription	Colonic Mucosa	Colon
8	chr12:123568800-123576600	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
9	chr12:123569200-123578800	Weak transcription	Sigmoid Colon	Sigmoid Colon
10	chr12:123569200-123579400	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
11	chr12:123569800-123576200	Weak transcription	Ovary	ovary
12	chr12:123569800-123578200	Weak transcription	Colon Smooth Muscle	Colon
13	chr12:123569800-123579200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
14	chr12:123570000-123579800	Weak transcription	Primary T cells fromperipheralblood	blood
15	chr12:123570600-123578600	Weak transcription	Aorta	Aorta
16	chr12:123570600-123578600	Weak transcription	Brain Cingulate Gyrus	brain
17	chr12:123570600-123578600	Weak transcription	Brain Hippocampus Middle	brain
18	chr12:123570600-123578800	Weak transcription	HUES6 Cell Line	embryonic stem cell
19	chr12:123570800-123578200	Weak transcription	Stomach Mucosa	stomach
20	chr12:123570800-123578600	Weak transcription	Pancreas	Pancrea
21	chr12:123570800-123580200	Enhancers	HMEC	breast
22	chr12:123570800-123586600	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
23	chr12:123571000-123586600	Weak transcription	Primary T helper cells PMA-I stimulated	--
24	chr12:123571200-123600000	Genic enhancers	Thymus	Thymus
25	chr12:123571400-123578800	Weak transcription	Brain Anterior Caudate	brain
26	chr12:123571400-123580000	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
27	chr12:123571600-123576400	Weak transcription	Lung	lung
28	chr12:123571600-123578000	Weak transcription	Esophagus	oesophagus
29	chr12:123571600-123578200	Weak transcription	Brain Inferior Temporal Lobe	brain
30	chr12:123571600-123578200	Weak transcription	Fetal Muscle Leg	muscle
31	chr12:123571600-123578600	Weak transcription	Brain Angular Gyrus	brain
32	chr12:123571800-123582200	Weak transcription	iPS-15b Cell Line	embryonic stem cell
33	chr12:123572400-123575800	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
34	chr12:123572600-123577400	Enhancers	Primary hematopoietic stem cells short term culture	blood
35	chr12:123572800-123577200	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
36	chr12:123573000-123577200	Enhancers	Primary monocytes fromperipheralblood	blood
37	chr12:123573200-123584200	Enhancers	Liver	Liver
38	chr12:123573400-123576200	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
39	chr12:123573400-123576400	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
40	chr12:123574000-123576400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
41	chr12:123574000-123577400	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
42	chr12:123574000-123578400	Weak transcription	Small Intestine	intestine
43	chr12:123574000-123579000	Enhancers	HepG2	liver
44	chr12:123574400-123575800	Weak transcription	Skeletal Muscle Female	skeletal muscle
45	chr12:123574400-123576000	Weak transcription	Primary hematopoietic stem cells	blood
46	chr12:123574400-123577200	Weak transcription	Psoas Muscle	Psoas
47	chr12:123574400-123577200	Enhancers	Monocytes-CD14+_RO01746	blood
48	chr12:123574400-123579000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
49	chr12:123574400-123579200	Weak transcription	Duodenum Smooth Muscle	Duodenum
50	chr12:123574400-123586800	Weak transcription	Primary T helper cells fromperipheralblood	blood

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