Variant report

Variant	rs1568428
Chromosome Location	chr12:123738876-123738877
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr12:123714199..123721299-chr12:123733822..123739052,7	MCF-7	breast:
2	chr12:123738852..123742382-chr12:123742428..123743998,3	MCF-7	breast:
3	chr12:123737328..123740075-chr12:123754040..123756567,3	MCF-7	breast:
4	chr12:123737049..123739965-chr12:123755070..123757447,2	K562	blood:
5	chr12:123736848..123739836-chr12:123749677..123753155,4	K562	blood:

Variant related genes	Relation type
ENSG00000051825	Chromatin interaction
ENSG00000130921	Chromatin interaction
ENSG00000111328	Chromatin interaction

Extended variants
information (count: 90 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:86)

rs_ID	r²[population]
rs10444439	0.94[JPT][hapmap]
rs1051434	0.88[CEU][hapmap];0.84[GIH][hapmap];0.83[MEX][hapmap];0.82[TSI][hapmap];1.00[YRI][hapmap];0.84[AFR][1000 genomes]
rs10732573	0.84[JPT][hapmap]
rs10744150	0.82[CHB][hapmap];0.84[JPT][hapmap]
rs10744151	0.82[CHB][hapmap];0.80[JPT][hapmap]
rs10772999	0.81[ASN][1000 genomes]
rs10773000	0.91[CHB][hapmap];0.91[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.94[ASN][1000 genomes]
rs10773002	0.83[ASW][hapmap];0.83[CHB][hapmap];0.94[CHD][hapmap];0.84[JPT][hapmap]
rs10773003	0.94[JPT][hapmap]
rs10773005	0.94[JPT][hapmap]
rs10773921	1.00[ASW][hapmap];0.84[CEU][hapmap];1.00[LWK][hapmap];0.91[MEX][hapmap];0.82[MKK][hapmap];0.80[TSI][hapmap];1.00[YRI][hapmap]
rs10846489	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];0.97[TSI][hapmap];1.00[YRI][hapmap];0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs10848428	1.00[ASW][hapmap];0.84[CEU][hapmap];1.00[LWK][hapmap];0.91[MEX][hapmap];0.84[MKK][hapmap];0.80[TSI][hapmap];1.00[YRI][hapmap]
rs11057205	0.81[ASN][1000 genomes]
rs11057207	0.81[ASN][1000 genomes]
rs11057209	0.82[ASN][1000 genomes]
rs11057219	0.92[AFR][1000 genomes];0.98[AMR][1000 genomes];0.94[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs11057223	1.00[CHB][hapmap];0.94[CHD][hapmap];1.00[JPT][hapmap];0.85[ASN][1000 genomes]
rs11057224	0.90[ASN][1000 genomes]
rs11057251	0.90[ASW][hapmap];0.88[CEU][hapmap];0.95[GIH][hapmap];0.94[JPT][hapmap];0.90[LWK][hapmap];0.96[MEX][hapmap];1.00[MKK][hapmap];0.88[TSI][hapmap];1.00[YRI][hapmap]
rs11057273	0.85[JPT][hapmap]
rs11057276	1.00[ASW][hapmap];0.92[CEU][hapmap];0.95[GIH][hapmap];0.94[JPT][hapmap];0.92[MEX][hapmap];0.83[MKK][hapmap];0.90[TSI][hapmap]
rs1109559	1.00[ASW][hapmap];0.96[CEU][hapmap];1.00[CHB][hapmap];0.94[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];0.92[TSI][hapmap];1.00[YRI][hapmap];0.92[AFR][1000 genomes];0.98[AMR][1000 genomes];0.91[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs1109560	1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[ASN][1000 genomes]
rs11608305	0.92[CEU][hapmap];0.94[JPT][hapmap]
rs12317452	0.94[JPT][hapmap]
rs12366872	0.94[JPT][hapmap]
rs1568427	0.83[ASW][hapmap];0.83[CHB][hapmap];0.94[CHD][hapmap];0.84[JPT][hapmap];0.81[TSI][hapmap];0.84[ASN][1000 genomes]
rs1609520	0.85[CHD][hapmap];0.84[JPT][hapmap]
rs1615350	0.83[ASW][hapmap]
rs1616484	0.80[AFR][1000 genomes]
rs1619283	0.81[AFR][1000 genomes]
rs1626703	0.95[AFR][1000 genomes];0.87[ASN][1000 genomes]
rs1716178	0.95[AFR][1000 genomes];0.82[ASN][1000 genomes]
rs1716184	0.84[AFR][1000 genomes]
rs1727286	0.82[AFR][1000 genomes]
rs1727293	1.00[ASW][hapmap];0.88[CEU][hapmap];0.82[GIH][hapmap];0.84[JPT][hapmap];1.00[LWK][hapmap];0.88[MEX][hapmap];0.86[MKK][hapmap];0.82[TSI][hapmap];1.00[YRI][hapmap];0.84[AFR][1000 genomes]
rs1727295	0.87[CEU][hapmap];1.00[YRI][hapmap]
rs1727301	0.91[CHB][hapmap];0.90[JPT][hapmap]
rs1727305	0.84[AFR][1000 genomes]
rs1727307	0.84[CEU][hapmap];0.80[TSI][hapmap]
rs1727331	0.84[JPT][hapmap]
rs1790088	0.82[AFR][1000 genomes]
rs1790094	0.90[ASW][hapmap];0.84[CEU][hapmap];1.00[LWK][hapmap];0.91[MEX][hapmap];0.84[MKK][hapmap];0.80[TSI][hapmap];1.00[YRI][hapmap]
rs1790096	0.95[AFR][1000 genomes];0.80[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs1790104	0.91[CHB][hapmap];0.90[JPT][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];0.81[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs1790106	1.00[ASW][hapmap];0.84[CEU][hapmap];1.00[LWK][hapmap];0.88[MEX][hapmap];0.84[MKK][hapmap];0.80[TSI][hapmap];1.00[YRI][hapmap]
rs1790121	0.90[ASW][hapmap];0.84[CEU][hapmap];0.91[LWK][hapmap];0.88[MEX][hapmap];0.92[MKK][hapmap];0.80[TSI][hapmap];1.00[YRI][hapmap];0.84[AFR][1000 genomes]
rs1790122	0.84[AFR][1000 genomes]
rs1790129	0.83[ASN][1000 genomes]
rs1790134	0.89[AFR][1000 genomes];0.85[ASN][1000 genomes]
rs1879379	1.00[ASW][hapmap];0.92[CEU][hapmap];1.00[CHB][hapmap];0.94[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.91[LWK][hapmap];0.96[MEX][hapmap];1.00[MKK][hapmap];0.95[TSI][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];0.87[AMR][1000 genomes];0.85[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2030401	0.89[ASN][1000 genomes]
rs2271976	1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[ASN][1000 genomes]
rs2280424	0.94[CHD][hapmap];0.84[JPT][hapmap];0.84[ASN][1000 genomes]
rs2337630	0.97[AFR][1000 genomes];0.89[AMR][1000 genomes];0.86[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2337631	0.97[AFR][1000 genomes];0.90[AMR][1000 genomes];0.86[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2682427	0.91[CHB][hapmap];0.90[JPT][hapmap]
rs28410096	0.94[JPT][hapmap]
rs28532037	0.94[JPT][hapmap]
rs28533432	0.84[CEU][hapmap];0.95[GIH][hapmap];0.94[JPT][hapmap];0.87[TSI][hapmap]
rs28660993	0.94[JPT][hapmap]
rs3088303	0.94[JPT][hapmap]
rs34841857	0.97[AFR][1000 genomes];0.88[AMR][1000 genomes];0.85[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs3759114	0.88[CHD][hapmap];0.84[JPT][hapmap]
rs4148863	0.90[ASW][hapmap];0.84[CEU][hapmap];1.00[LWK][hapmap];0.88[MEX][hapmap];0.84[MKK][hapmap];0.80[TSI][hapmap];1.00[YRI][hapmap]
rs4474478	0.82[ASN][1000 genomes]
rs4474479	0.82[ASN][1000 genomes]
rs4553407	0.92[AFR][1000 genomes];0.98[AMR][1000 genomes];0.94[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4594040	0.82[ASN][1000 genomes]
rs4759377	0.94[JPT][hapmap]
rs4759411	0.84[JPT][hapmap]
rs4759414	0.84[JPT][hapmap]
rs61519741	0.81[ASN][1000 genomes]
rs61953394	0.90[ASN][1000 genomes]
rs6488868	0.87[GIH][hapmap]
rs7137286	0.81[ASN][1000 genomes]
rs7139321	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];0.88[AMR][1000 genomes];0.81[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7304782	0.83[ASW][hapmap];0.88[CHD][hapmap];0.84[JPT][hapmap]
rs7312955	0.85[AFR][1000 genomes];0.94[AMR][1000 genomes];0.89[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs7315453	0.94[JPT][hapmap]
rs73231928	0.90[AFR][1000 genomes];0.88[AMR][1000 genomes];0.84[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7957096	0.84[CEU][hapmap]
rs7959415	0.84[JPT][hapmap]
rs7972811	0.94[JPT][hapmap]
rs949143	1.00[ASW][hapmap];0.84[CEU][hapmap];1.00[LWK][hapmap];0.88[MEX][hapmap];0.84[MKK][hapmap];0.80[TSI][hapmap];1.00[YRI][hapmap]

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	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

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs1568428	TMEM120B	cis	parietal	SCAN
rs1568428	CDK2AP1	cis	Esophagus Mucosa	GTEx
rs1568428	RP11-282O18.3	cis	Esophagus Mucosa	GTEx
rs1568428	PITPNM2	cis	cerebellum	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:123718800-123739600	Weak transcription	Fetal Kidney	kidney
2	chr12:123725800-123746400	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
3	chr12:123727600-123739200	Weak transcription	Duodenum Smooth Muscle	Duodenum
4	chr12:123733400-123745000	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
5	chr12:123734600-123753200	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
6	chr12:123735000-123740400	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
7	chr12:123735200-123739600	Enhancers	Fetal Brain Male	brain
8	chr12:123735200-123751800	Strong transcription	Fetal Stomach	stomach
9	chr12:123735400-123739200	Enhancers	Brain Dorsolateral Prefrontal Cortex	brain
10	chr12:123735400-123745400	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
11	chr12:123735600-123743400	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
12	chr12:123735600-123752400	Strong transcription	Thymus	Thymus
13	chr12:123736000-123739400	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
14	chr12:123736000-123739600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
15	chr12:123736000-123740600	Weak transcription	iPS-15b Cell Line	embryonic stem cell
16	chr12:123736000-123745400	Strong transcription	HUES64 Cell Line	embryonic stem cell
17	chr12:123736000-123747800	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
18	chr12:123736000-123748000	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
19	chr12:123736000-123752200	Strong transcription	Dnd41	blood
20	chr12:123736200-123742400	Strong transcription	Fetal Thymus	thymus
21	chr12:123736200-123744200	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
22	chr12:123736200-123751400	Strong transcription	Primary hematopoietic stem cells short term culture	blood
23	chr12:123736400-123750600	Strong transcription	Fetal Lung	lung
24	chr12:123736400-123752200	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
25	chr12:123736400-123752600	Strong transcription	NHLF	lung
26	chr12:123736600-123740400	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
27	chr12:123737000-123744000	Strong transcription	Primary T helper naive cells fromperipheralblood	blood
28	chr12:123737000-123753000	Strong transcription	Fetal Intestine Small	intestine
29	chr12:123737200-123752000	Strong transcription	A549	lung
30	chr12:123737400-123749000	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
31	chr12:123737600-123740000	Strong transcription	Hela-S3	cervix
32	chr12:123737800-123739800	Genic enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
33	chr12:123737800-123741400	Strong transcription	Colonic Mucosa	Colon
34	chr12:123737800-123742000	Strong transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
35	chr12:123737800-123743800	Strong transcription	GM12878-XiMat	blood
36	chr12:123737800-123745000	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
37	chr12:123737800-123745600	Strong transcription	HUES48 Cell Line	embryonic stem cell
38	chr12:123737800-123746800	Strong transcription	Primary neutrophils fromperipheralblood	blood
39	chr12:123738000-123739000	Genic enhancers	Muscle Satellite Cultured Cells	--
40	chr12:123738000-123739200	Strong transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
41	chr12:123738000-123739200	Genic enhancers	Stomach Mucosa	stomach
42	chr12:123738000-123739800	Strong transcription	Primary T killer naive cells fromperipheralblood	blood
43	chr12:123738000-123739800	Genic enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
44	chr12:123738000-123739800	Genic enhancers	Colon Smooth Muscle	Colon
45	chr12:123738000-123739800	Genic enhancers	NHEK	skin
46	chr12:123738000-123740000	Strong transcription	Primary T helper naive cells from peripheral blood	blood
47	chr12:123738000-123740000	Enhancers	Cortex derived primary cultured neurospheres	brain
48	chr12:123738000-123741000	Strong transcription	Primary B cells from cord blood	blood
49	chr12:123738000-123742600	Strong transcription	HepG2	liver
50	chr12:123738000-123743400	Strong transcription	Primary B cells from peripheral blood	blood

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