Variant report

Variant	rs4275659
Chromosome Location	chr12:123447928-123447929
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	GATA1	chr12:123447251-123448359	PBDE	blood:	n/a	n/a
2	RCOR1	chr12:123447897-123448240	K562	blood:	n/a	n/a
3	RCOR1	chr12:123447703-123449527	IMR90	lung:	n/a	n/a
4	CBX3	chr12:123447798-123448228	K562	blood:	n/a	n/a
5	RCOR1	chr12:123447869-123448180	K562	blood:	n/a	n/a
6	TAL1	chr12:123447801-123448086	K562	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr12:123379306..123380972-chr12:123447653..123450288,2	K562	blood:
2	chr12:123443368..123448710-chr12:123448756..123452152,6	MCF-7	breast:

Variant related genes	Relation type
ABCB9	TF binding region
ENSG00000150967	Chromatin interaction
ENSG00000139722	Chromatin interaction

Extended variants
information (count: 42 )
Associated
traits (count: 9 )

rSNPs within LD-proxies of this variant (count:31)

rs_ID	r²[population]
rs1051434	0.96[CEU][hapmap];0.95[MEX][hapmap];0.92[TSI][hapmap];1.00[YRI][hapmap]
rs10773921	1.00[ASW][hapmap];1.00[CEU][hapmap];0.95[CHB][hapmap];0.83[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.93[MKK][hapmap];0.95[TSI][hapmap];1.00[YRI][hapmap];0.89[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs10848428	1.00[ASW][hapmap];1.00[CEU][hapmap];0.95[CHB][hapmap];0.83[GIH][hapmap];0.86[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.91[MKK][hapmap];0.95[TSI][hapmap];1.00[YRI][hapmap]
rs11060853	0.82[CHB][hapmap];0.95[JPT][hapmap];0.89[ASN][1000 genomes]
rs11608811	0.90[ASW][hapmap];1.00[CEU][hapmap];0.95[CHB][hapmap];0.83[GIH][hapmap];0.95[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.91[MKK][hapmap];0.95[TSI][hapmap];1.00[YRI][hapmap];0.89[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs11609798	0.80[ASN][1000 genomes]
rs11613937	0.87[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs12425009	0.90[ASW][hapmap];1.00[CEU][hapmap];0.95[CHB][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.84[LWK][hapmap];1.00[MEX][hapmap];0.95[TSI][hapmap];1.00[YRI][hapmap];0.86[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12425850	1.00[YRI][hapmap];0.86[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1727295	0.91[CEU][hapmap];0.89[CHB][hapmap];1.00[YRI][hapmap]
rs1727307	1.00[CEU][hapmap];0.95[CHB][hapmap];0.83[GIH][hapmap];0.86[JPT][hapmap];0.95[TSI][hapmap]
rs1790094	0.90[ASW][hapmap];1.00[CEU][hapmap];0.95[CHB][hapmap];0.83[GIH][hapmap];0.86[JPT][hapmap];1.00[LWK][hapmap];0.95[MEX][hapmap];0.91[MKK][hapmap];0.95[TSI][hapmap];1.00[YRI][hapmap]
rs1790106	1.00[ASW][hapmap];1.00[CEU][hapmap];0.95[CHB][hapmap];0.83[GIH][hapmap];0.86[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.91[MKK][hapmap];0.95[TSI][hapmap];1.00[YRI][hapmap]
rs1790121	0.90[ASW][hapmap];1.00[CEU][hapmap];0.95[CHB][hapmap];0.83[GIH][hapmap];0.86[JPT][hapmap];0.91[LWK][hapmap];1.00[MEX][hapmap];0.83[MKK][hapmap];0.95[TSI][hapmap];1.00[YRI][hapmap]
rs1984658	0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs28755851	0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs3741530	1.00[CEU][hapmap];0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs3759115	1.00[ASW][hapmap];1.00[CEU][hapmap];0.95[CHB][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.93[MKK][hapmap];0.95[TSI][hapmap];1.00[YRI][hapmap];0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs3897102	0.95[CHB][hapmap];0.95[JPT][hapmap];0.94[ASN][1000 genomes]
rs4148863	0.90[ASW][hapmap];1.00[CEU][hapmap];0.95[CHB][hapmap];0.83[GIH][hapmap];0.86[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.91[MKK][hapmap];0.95[TSI][hapmap];1.00[YRI][hapmap]
rs4148866	0.82[CHB][hapmap];0.90[JPT][hapmap];0.88[ASN][1000 genomes]
rs55742290	0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs61955196	0.94[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs61955214	0.81[AMR][1000 genomes];0.81[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7135296	1.00[ASW][hapmap];1.00[CEU][hapmap];0.95[CHB][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.96[MEX][hapmap];0.93[MKK][hapmap];0.95[TSI][hapmap];1.00[YRI][hapmap];0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7296418	0.91[CEU][hapmap];0.91[CHB][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.97[TSI][hapmap];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7305511	1.00[ASW][hapmap];1.00[CEU][hapmap];0.95[CHB][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.91[MKK][hapmap];0.95[TSI][hapmap];1.00[YRI][hapmap];0.86[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7957096	1.00[CEU][hapmap];0.87[CHB][hapmap];0.95[JPT][hapmap];0.89[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs883562	0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs884956	1.00[ASW][hapmap];0.90[CHB][hapmap];0.90[LWK][hapmap];0.91[MEX][hapmap];0.91[MKK][hapmap];1.00[YRI][hapmap];0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs949143	1.00[ASW][hapmap];1.00[CEU][hapmap];0.95[CHB][hapmap];0.83[GIH][hapmap];0.86[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.91[MKK][hapmap];0.95[TSI][hapmap];1.00[YRI][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	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	nsv899572	chr12:123292503-123477311	Active TSS Strong transcription Enhancers Flanking Active TSS Genic enhancers Weak transcription Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	43 gene(s)	inside rSNPs	diseases
3	nsv899573	chr12:123312051-123528405	Enhancers Strong transcription Weak transcription Active TSS Flanking Active TSS Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	47 gene(s)	inside rSNPs	diseases
4	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
5	nsv899576	chr12:123335527-123528405	Enhancers Genic enhancers Flanking Active TSS Strong transcription Active TSS Weak transcription Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	45 gene(s)	inside rSNPs	diseases
6	nsv832532	chr12:123395927-123573137	Weak transcription Strong transcription Active TSS Flanking Active TSS Enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	37 gene(s)	inside rSNPs	diseases
7	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
8	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
9	nsv455732	chr12:123427573-123574838	Weak transcription Active TSS Strong transcription Enhancers Flanking Active TSS Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	37 gene(s)	inside rSNPs	diseases
10	nsv560492	chr12:123427573-123574838	Weak transcription Enhancers Strong transcription Active TSS Genic enhancers Transcr. at gene 5' and 3' Flanking Active TSS Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	37 gene(s)	inside rSNPs	diseases
11	nsv899577	chr12:123435248-123484474	Weak transcription Enhancers Flanking Active TSS Strong transcription Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	29 gene(s)	inside rSNPs	diseases

mRNA abundance (count:9)

SNP	Gene	Cis/trans	Tissue	Source
rs4275659	ABCB9	cis	Liver	GTEx
rs4275659	C12orf65	cis	cerebellum	SCAN
rs4275659	CDK2AP1	cis	cerebellum	SCAN
rs4275659	TMEM120B	cis	parietal	SCAN
rs4275659	CDK2AP1	cis	Esophagus Mucosa	GTEx
rs4275659	OGFOD2	cis	brain	seeQTL
rs4275659	PITPNM2	cis	cerebellum	SCAN
rs4275659	ARL6IP4	cis	multi-tissue	Pritchard
rs4275659	RP11-282O18.3	cis	Esophagus Mucosa	GTEx

Chromatin state (count:102 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:123412800-123449200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
2	chr12:123413400-123449600	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
3	chr12:123413600-123450000	Weak transcription	Primary T cells from cord blood	blood
4	chr12:123432200-123450000	Weak transcription	Placenta Amnion	Placenta Amnion
5	chr12:123432200-123450200	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
6	chr12:123432400-123448200	Weak transcription	Duodenum Smooth Muscle	Duodenum
7	chr12:123432400-123449600	Weak transcription	Primary T killer memory cells from peripheral blood	blood
8	chr12:123432400-123450000	Weak transcription	Primary T helper cells fromperipheralblood	blood
9	chr12:123432600-123448200	Weak transcription	Skeletal Muscle Female	skeletal muscle
10	chr12:123432600-123450000	Weak transcription	Primary hematopoietic stem cells	blood
11	chr12:123436400-123448000	Weak transcription	HepG2	liver
12	chr12:123436600-123449400	Weak transcription	NHDF-Ad	bronchial
13	chr12:123436800-123448600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
14	chr12:123437200-123449800	Weak transcription	Primary B cells from peripheral blood	blood
15	chr12:123437400-123449800	Weak transcription	Primary T helper cells PMA-I stimulated	--
16	chr12:123439600-123450200	Weak transcription	H9 Cell Line	embryonic stem cell
17	chr12:123440000-123448000	Weak transcription	HSMM	muscle
18	chr12:123440000-123450000	Weak transcription	Primary T helper naive cells from peripheral blood	blood
19	chr12:123441400-123450200	Weak transcription	HUES48 Cell Line	embryonic stem cell
20	chr12:123442600-123448800	Weak transcription	H1 Cell Line	embryonic stem cell
21	chr12:123443200-123448200	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
22	chr12:123443800-123450400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
23	chr12:123444000-123450000	Weak transcription	iPS-15b Cell Line	embryonic stem cell
24	chr12:123444600-123448200	Weak transcription	HMEC	breast
25	chr12:123444600-123448600	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
26	chr12:123444800-123448000	Weak transcription	Adipose Nuclei	Adipose
27	chr12:123444800-123448400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
28	chr12:123444800-123449600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
29	chr12:123444800-123449600	Weak transcription	HUVEC	blood vessel
30	chr12:123444800-123450000	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
31	chr12:123444800-123450000	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
32	chr12:123444800-123450200	Weak transcription	Pancreatic Islets	Pancreatic Islet
33	chr12:123445000-123448000	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
34	chr12:123445000-123448000	Weak transcription	Spleen	Spleen
35	chr12:123445000-123448200	Weak transcription	Brain Anterior Caudate	brain
36	chr12:123445000-123448200	Weak transcription	Brain Hippocampus Middle	brain
37	chr12:123445000-123448200	Weak transcription	Ovary	ovary
38	chr12:123445000-123448400	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
39	chr12:123445000-123448400	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
40	chr12:123445000-123448400	Weak transcription	Esophagus	oesophagus
41	chr12:123445000-123449000	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
42	chr12:123445000-123449000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
43	chr12:123445000-123449200	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
44	chr12:123445000-123449200	Weak transcription	Dnd41	blood
45	chr12:123445000-123449600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
46	chr12:123445000-123450000	Weak transcription	Aorta	Aorta
47	chr12:123445000-123450200	Weak transcription	Thymus	Thymus
48	chr12:123445000-123450400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
49	chr12:123445200-123448000	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
50	chr12:123445200-123448200	Weak transcription	Stomach Smooth Muscle	stomach

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links