Variant report

Variant	rs2432045
Chromosome Location	chr19:36712656-36712657
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr19:36703714..36707271-chr19:36711666..36715110,4	MCF-7	breast:
2	chr19:36711072..36713184-chr19:36713372..36715798,2	K562	blood:
3	chr19:36705207..36708225-chr19:36708519..36712657,6	K562	blood:

Variant related genes	Relation type
ENSG00000167635	Chromatin interaction
ENSG00000196357	Chromatin interaction

Extended variants
information (count: 53 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:51)

rs_ID	r²[population]
rs10409091	1.00[CEU][hapmap];0.86[CHB][hapmap];0.86[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs10411031	0.84[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs10416179	0.86[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs10416237	0.86[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs10417892	0.86[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs10418510	0.86[CHB][hapmap];0.83[CHD][hapmap];0.90[MEX][hapmap];0.80[TSI][hapmap]
rs10420071	0.81[CHB][hapmap]
rs12973781	0.89[EUR][1000 genomes]
rs2070132	0.94[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.91[CHD][hapmap];1.00[GIH][hapmap];0.91[JPT][hapmap];0.86[LWK][hapmap];1.00[MEX][hapmap];0.93[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.92[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2271844	0.81[CHB][hapmap];0.81[CHD][hapmap];0.91[MEX][hapmap];0.80[TSI][hapmap]
rs2287897	0.96[CEU][hapmap];0.86[CHB][hapmap];0.82[CHD][hapmap];0.98[GIH][hapmap];0.91[JPT][hapmap];0.91[MEX][hapmap];1.00[TSI][hapmap];0.91[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2287898	0.96[CEU][hapmap];0.86[CHB][hapmap];0.93[GIH][hapmap];0.83[JPT][hapmap];0.91[MEX][hapmap];1.00[TSI][hapmap];0.82[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs2310856	0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2385801	0.91[MEX][hapmap];0.80[TSI][hapmap]
rs2385803	0.86[CHB][hapmap]
rs2385804	0.90[CHB][hapmap]
rs2432039	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.89[AFR][1000 genomes];0.91[AMR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2432042	0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2432043	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2432049	1.00[CEU][hapmap];1.00[CHB][hapmap];0.91[JPT][hapmap];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2432051	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2432052	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2432054	1.00[CEU][hapmap];1.00[CHB][hapmap];0.87[CHD][hapmap];0.95[GIH][hapmap];0.91[JPT][hapmap];1.00[MEX][hapmap];0.82[MKK][hapmap];1.00[TSI][hapmap];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2438514	1.00[CEU][hapmap];1.00[CHB][hapmap];0.87[CHD][hapmap];0.95[GIH][hapmap];0.91[JPT][hapmap];1.00[MEX][hapmap];0.85[MKK][hapmap];1.00[TSI][hapmap];0.87[AMR][1000 genomes];0.93[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2438517	1.00[CEU][hapmap];1.00[CHB][hapmap];0.87[CHD][hapmap];0.95[GIH][hapmap];0.91[JPT][hapmap];1.00[MEX][hapmap];0.85[MKK][hapmap];1.00[TSI][hapmap];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs28408024	0.84[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs2918375	0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2918378	0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2918379	0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2918380	0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2945945	0.90[CHB][hapmap];0.83[CHD][hapmap];0.91[MEX][hapmap];0.80[TSI][hapmap]
rs2945950	0.90[CHB][hapmap]
rs2945961	0.90[CHB][hapmap];0.83[CHD][hapmap];0.90[MEX][hapmap];0.80[TSI][hapmap]
rs2945972	0.90[CHB][hapmap];0.83[CHD][hapmap];0.91[MEX][hapmap];0.80[TSI][hapmap]
rs2945993	0.90[CHB][hapmap];0.83[CHD][hapmap];0.91[MEX][hapmap];0.80[TSI][hapmap]
rs2967484	0.95[CHB][hapmap];0.82[CHD][hapmap];0.91[MEX][hapmap];0.84[TSI][hapmap]
rs2967504	0.81[CHB][hapmap]
rs2967506	0.95[CHB][hapmap];0.80[CHD][hapmap];0.81[MEX][hapmap]
rs2967517	0.81[CHB][hapmap];0.80[CHD][hapmap]
rs2967518	0.85[CHB][hapmap];0.83[CHD][hapmap];0.85[MEX][hapmap]
rs2967521	0.90[CHB][hapmap];0.80[CHD][hapmap]
rs2967524	0.81[CHB][hapmap];0.81[CHD][hapmap];0.95[MEX][hapmap];0.80[TSI][hapmap]
rs2972321	0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2972537	0.88[AMR][1000 genomes];0.97[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2972539	0.91[AMR][1000 genomes];0.91[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2972542	0.94[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4239585	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4806283	0.83[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs6510527	0.86[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs7251727	0.86[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs8102020	0.96[CEU][hapmap];0.86[CHB][hapmap];0.93[GIH][hapmap];0.83[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.85[AMR][1000 genomes];0.92[EUR][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	esv3526489	chr19:36306483-36741945	Enhancers Weak transcription Strong transcription Flanking Active TSS Bivalent/Poised TSS Active TSS Flanking Bivalent TSS/Enh Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	114 gene(s)	inside rSNPs	diseases
2	esv3526490	chr19:36306483-36741945	Genic enhancers Weak transcription Strong transcription Flanking Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer Enhancers Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	114 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs2432045	ITPKC	cis	cerebellum	SCAN

Chromatin state (count:126 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr19:36706800-36716400	Weak transcription	Aorta	Aorta
2	chr19:36707000-36712800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
3	chr19:36707000-36712800	Weak transcription	Sigmoid Colon	Sigmoid Colon
4	chr19:36707000-36716200	Weak transcription	Rectal Smooth Muscle	rectum
5	chr19:36707000-36726800	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
6	chr19:36707400-36730200	ZNF genes & repeats	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
7	chr19:36707600-36712800	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
8	chr19:36707600-36713000	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
9	chr19:36707600-36731800	ZNF genes & repeats	Primary hematopoietic stem cells G-CSF-mobilized Male	--
10	chr19:36707800-36712800	Strong transcription	Primary hematopoietic stem cells short term culture	blood
11	chr19:36707800-36712800	Weak transcription	Brain Cingulate Gyrus	brain
12	chr19:36707800-36712800	Weak transcription	Stomach Smooth Muscle	stomach
13	chr19:36707800-36713000	Weak transcription	Brain Anterior Caudate	brain
14	chr19:36707800-36716400	Weak transcription	Right Ventricle	heart
15	chr19:36707800-36717000	Weak transcription	HSMMtube	muscle
16	chr19:36708000-36712800	Weak transcription	H9 Cell Line	embryonic stem cell
17	chr19:36708000-36712800	Weak transcription	Ovary	ovary
18	chr19:36708000-36713200	Weak transcription	Gastric	stomach
19	chr19:36708000-36714000	Genic enhancers	Dnd41	blood
20	chr19:36708000-36715000	Weak transcription	NHLF	lung
21	chr19:36708000-36716400	Weak transcription	Psoas Muscle	Psoas
22	chr19:36708000-36716800	Weak transcription	Pancreas	Pancrea
23	chr19:36708000-36719800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
24	chr19:36708200-36715000	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
25	chr19:36708200-36730800	ZNF genes & repeats	Primary hematopoietic stem cells G-CSF-mobilized Female	--
26	chr19:36708400-36713800	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
27	chr19:36708400-36715400	Weak transcription	Fetal Heart	heart
28	chr19:36708400-36716400	Weak transcription	Spleen	Spleen
29	chr19:36708600-36712800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
30	chr19:36708800-36712800	Weak transcription	Right Atrium	heart
31	chr19:36709000-36715400	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
32	chr19:36709000-36723000	Strong transcription	HUES48 Cell Line	embryonic stem cell
33	chr19:36709000-36723800	Strong transcription	HUES64 Cell Line	embryonic stem cell
34	chr19:36709000-36724000	Strong transcription	H1 Cell Line	embryonic stem cell
35	chr19:36709200-36716000	Strong transcription	HUES6 Cell Line	embryonic stem cell
36	chr19:36709200-36716000	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
37	chr19:36709400-36715200	Strong transcription	Fetal Lung	lung
38	chr19:36709400-36723800	Strong transcription	Fetal Muscle Trunk	muscle
39	chr19:36709600-36713200	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
40	chr19:36709600-36713200	Strong transcription	Fetal Brain Female	brain
41	chr19:36709800-36714000	Strong transcription	Placenta	Placenta
42	chr19:36710000-36712800	Strong transcription	Left Ventricle	heart
43	chr19:36710000-36713200	Strong transcription	Duodenum Mucosa	Duodenum
44	chr19:36710000-36714000	ZNF genes & repeats	Primary T regulatory cells fromperipheralblood	blood
45	chr19:36710000-36714000	Strong transcription	Osteobl	bone
46	chr19:36710000-36715000	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
47	chr19:36710000-36715000	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
48	chr19:36710000-36715200	ZNF genes & repeats	H9 Derived Neuron Cultured Cells	ES cell derived
49	chr19:36710000-36716000	Strong transcription	Primary B cells from peripheral blood	blood
50	chr19:36710000-36725000	ZNF genes & repeats	GM12878-XiMat	blood

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