Variant report

Variant	rs7964074
Chromosome Location	chr12:57930374-57930375
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	POLR2A	chr12:57929606-57930706	K562	blood:	n/a	n/a
2	POLR2A	chr12:57930202-57930728	K562	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr12:57930321..57931863-chr12:57935932..57937739,2	MCF-7	breast:
2	chr12:57926370..57929353-chr12:57930336..57932506,2	MCF-7	breast:
3	chr12:57929188..57932764-chr12:57939481..57941098,3	MCF-7	breast:
4	chr12:57929794..57931809-chr12:58137772..58140062,2	MCF-7	breast:

Variant related genes	Relation type
DCTN2	TF binding region
ENSG00000175203	Chromatin interaction
ENSG00000135452	Chromatin interaction

Extended variants
information (count: 58 )
Associated
traits (count: 9 )

rSNPs within LD-proxies of this variant (count:48)

rs_ID	r²[population]
rs1148553	0.94[EUR][1000 genomes]
rs1148554	1.00[CEU][hapmap];0.94[EUR][1000 genomes]
rs1148555	1.00[CEU][hapmap];0.83[CHD][hapmap];1.00[GIH][hapmap];1.00[TSI][hapmap];0.93[EUR][1000 genomes]
rs1148557	1.00[CEU][hapmap];0.86[CHB][hapmap];0.83[CHD][hapmap];1.00[GIH][hapmap];0.89[JPT][hapmap];1.00[TSI][hapmap];0.92[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs1284465	0.85[EUR][1000 genomes]
rs1284605	1.00[CEU][hapmap];0.83[CHD][hapmap];1.00[GIH][hapmap];1.00[TSI][hapmap];0.94[EUR][1000 genomes]
rs1299737	0.81[EUR][1000 genomes]
rs1629410	0.86[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs1669294	0.82[EUR][1000 genomes]
rs1669296	1.00[CEU][hapmap];0.83[CHD][hapmap];1.00[GIH][hapmap];1.00[TSI][hapmap];0.97[EUR][1000 genomes]
rs1669297	0.97[EUR][1000 genomes]
rs1678537	0.92[CEU][hapmap];0.95[GIH][hapmap];0.96[TSI][hapmap];0.82[EUR][1000 genomes]
rs1679368	0.89[EUR][1000 genomes]
rs1709871	0.92[CEU][hapmap];0.95[GIH][hapmap];0.96[TSI][hapmap];0.86[EUR][1000 genomes]
rs1709874	0.81[EUR][1000 genomes]
rs2127318	1.00[ASW][hapmap];1.00[CEU][hapmap];0.86[CHB][hapmap];0.81[CHD][hapmap];1.00[GIH][hapmap];0.89[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];0.91[YRI][hapmap];0.97[AFR][1000 genomes];0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2620677	0.81[EUR][1000 genomes]
rs2620679	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]
rs2672571	0.92[CEU][hapmap];0.95[GIH][hapmap];0.89[JPT][hapmap];0.96[TSI][hapmap]
rs2928382	0.81[EUR][1000 genomes]
rs2943696	0.81[EUR][1000 genomes]
rs3782129	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs3825080	0.89[JPT][hapmap]
rs3847699	1.00[CEU][hapmap];0.86[CHB][hapmap];0.89[JPT][hapmap];0.91[YRI][hapmap];0.93[AFR][1000 genomes];0.93[AMR][1000 genomes];0.93[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs474544	0.82[EUR][1000 genomes]
rs4760273	0.82[AMR][1000 genomes]
rs496245	0.92[CEU][hapmap];0.82[EUR][1000 genomes]
rs511752	0.92[CEU][hapmap]
rs542278	0.91[GIH][hapmap];0.96[TSI][hapmap]
rs697221	0.92[CEU][hapmap];0.81[CHD][hapmap];1.00[GIH][hapmap];1.00[TSI][hapmap];0.92[EUR][1000 genomes]
rs703835	1.00[CEU][hapmap];0.86[CHB][hapmap];0.83[CHD][hapmap];1.00[GIH][hapmap];0.89[JPT][hapmap];1.00[TSI][hapmap];0.91[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs703836	0.92[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs703837	1.00[CEU][hapmap];0.86[CHB][hapmap];0.81[CHD][hapmap];1.00[GIH][hapmap];0.89[JPT][hapmap];1.00[TSI][hapmap];0.97[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs703838	0.97[EUR][1000 genomes]
rs703839	0.96[EUR][1000 genomes]
rs7299631	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs747340	0.86[EUR][1000 genomes]
rs775236	0.97[EUR][1000 genomes]
rs775237	0.97[EUR][1000 genomes]
rs775241	1.00[CEU][hapmap];0.86[CHB][hapmap];0.83[CHD][hapmap];0.95[GIH][hapmap];0.89[JPT][hapmap];1.00[TSI][hapmap];0.97[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs775323	0.97[EUR][1000 genomes]
rs775324	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];0.98[ASN][1000 genomes]
rs776038	0.92[CEU][hapmap];0.82[CHB][hapmap];0.95[GIH][hapmap];0.89[JPT][hapmap];0.96[TSI][hapmap];0.81[EUR][1000 genomes]
rs776039	0.81[EUR][1000 genomes]
rs796546	0.82[EUR][1000 genomes]
rs7969683	0.80[AMR][1000 genomes]
rs899653	1.00[ASW][hapmap];0.82[CHB][hapmap];0.83[GIH][hapmap];0.89[JPT][hapmap];0.82[LWK][hapmap];1.00[MEX][hapmap];0.96[TSI][hapmap];0.83[YRI][hapmap]
rs9737891	0.81[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:10 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv899118	chr12:57811414-57946477	Weak transcription Strong transcription Flanking Active TSS Enhancers Flanking Bivalent TSS/Enh Genic enhancers Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	106 gene(s)	inside rSNPs	diseases
2	esv1812398	chr12:57829733-58001868	Flanking Active TSS Active TSS Enhancers Strong transcription Genic enhancers Bivalent/Poised TSS Weak transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	96 gene(s)	inside rSNPs	diseases
3	esv2758310	chr12:57829733-58001868	Active TSS Genic enhancers Enhancers Weak transcription Strong transcription Flanking Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	96 gene(s)	inside rSNPs	diseases
4	esv2759901	chr12:57829733-58001868	Enhancers Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent Enhancer Active TSS Weak transcription Strong transcription Transcr. at gene 5' and 3' Bivalent/Poised TSS Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	96 gene(s)	inside rSNPs	diseases
5	nsv428283	chr12:57829733-58001868	Flanking Active TSS Active TSS Transcr. at gene 5' and 3' Strong transcription Flanking Bivalent TSS/Enh Weak transcription Enhancers Genic enhancers Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	96 gene(s)	inside rSNPs	diseases
6	nsv559033	chr12:57848639-57946477	Flanking Active TSS Transcr. at gene 5' and 3' Weak transcription Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Strong transcription Genic enhancers Bivalent/Poised TSS Enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	92 gene(s)	inside rSNPs	diseases
7	nsv559034	chr12:57859932-58012233	Strong transcription Weak transcription Flanking Active TSS Enhancers Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	89 gene(s)	inside rSNPs	diseases
8	nsv1038741	chr12:57877355-58174506	Weak transcription Enhancers Strong transcription Flanking Active TSS Genic enhancers Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	126 gene(s)	inside rSNPs	diseases
9	nsv541503	chr12:57877355-58174506	Enhancers Strong transcription Flanking Active TSS Bivalent Enhancer Weak transcription Active TSS Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	126 gene(s)	inside rSNPs	diseases
10	nsv1053930	chr12:57921188-57969659	Flanking Active TSS Enhancers Weak transcription Flanking Bivalent TSS/Enh Strong transcription Genic enhancers Bivalent Enhancer Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	21 gene(s)	inside rSNPs	n/a

mRNA abundance (count:9)

SNP	Gene	Cis/trans	Tissue	Source
rs7964074	ATF7	cis	cerebellum	SCAN
rs7964074	RDH5	cis	cerebellum	SCAN
rs7964074	CALCOCO1	cis	cerebellum	SCAN
rs7964074	ITGB7	cis	cerebellum	SCAN
rs7964074	KRT7	cis	cerebellum	SCAN
rs7964074	KRT81	cis	parietal	SCAN
rs7964074	AVIL	cis	cerebellum	SCAN
rs7964074	ACVRL1	cis	cerebellum	SCAN
rs7964074	KRT6B	cis	cerebellum	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:57917600-57939600	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
2	chr12:57918600-57930400	Strong transcription	Lung	lung
3	chr12:57918600-57933600	Strong transcription	Brain Hippocampus Middle	brain
4	chr12:57918600-57934800	Strong transcription	Osteobl	bone
5	chr12:57918600-57936400	Strong transcription	Brain Inferior Temporal Lobe	brain
6	chr12:57918600-57939600	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
7	chr12:57918800-57930600	Strong transcription	Primary T cells from cord blood	blood
8	chr12:57918800-57933800	Strong transcription	NHEK	skin
9	chr12:57919000-57931200	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
10	chr12:57919000-57932000	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
11	chr12:57919000-57935600	Strong transcription	Thymus	Thymus
12	chr12:57919000-57937400	Weak transcription	Right Atrium	heart
13	chr12:57919200-57934800	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
14	chr12:57919200-57939600	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
15	chr12:57919400-57930600	Strong transcription	HMEC	breast
16	chr12:57919400-57933400	Strong transcription	Primary hematopoietic stem cells short term culture	blood
17	chr12:57919400-57933400	Strong transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
18	chr12:57919400-57934400	Strong transcription	Duodenum Smooth Muscle	Duodenum
19	chr12:57919400-57936200	Strong transcription	Primary monocytes fromperipheralblood	blood
20	chr12:57919400-57936200	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
21	chr12:57919400-57936400	Strong transcription	Primary B cells from peripheral blood	blood
22	chr12:57919400-57936800	Strong transcription	Monocytes-CD14+_RO01746	blood
23	chr12:57919400-57937800	Strong transcription	Primary neutrophils fromperipheralblood	blood
24	chr12:57919400-57939400	Strong transcription	Fetal Stomach	stomach
25	chr12:57919600-57934800	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
26	chr12:57919600-57935200	Strong transcription	HepG2	liver
27	chr12:57919600-57936200	Strong transcription	Breast Myoepithelial Primary Cells	Breast
28	chr12:57919800-57935000	Strong transcription	Fetal Intestine Large	intestine
29	chr12:57919800-57937000	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
30	chr12:57919800-57937800	Strong transcription	Fetal Intestine Small	intestine
31	chr12:57920000-57936400	Strong transcription	Cortex derived primary cultured neurospheres	brain
32	chr12:57920000-57937800	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
33	chr12:57920200-57930600	Strong transcription	Skeletal Muscle Female	skeletal muscle
34	chr12:57920200-57933200	Strong transcription	Brain Angular Gyrus	brain
35	chr12:57920200-57934600	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
36	chr12:57920200-57936800	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
37	chr12:57920200-57937400	Strong transcription	Fetal Brain Female	brain
38	chr12:57920400-57933200	Strong transcription	Brain Dorsolateral Prefrontal Cortex	brain
39	chr12:57920400-57936800	Strong transcription	HUES6 Cell Line	embryonic stem cell
40	chr12:57920400-57938600	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
41	chr12:57920600-57933400	Strong transcription	Primary T cells fromperipheralblood	blood
42	chr12:57920600-57938800	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
43	chr12:57920800-57930600	Strong transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
44	chr12:57920800-57934800	Strong transcription	Brain Germinal Matrix	brain
45	chr12:57920800-57935800	Strong transcription	Fetal Thymus	thymus
46	chr12:57920800-57937000	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
47	chr12:57920800-57937200	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
48	chr12:57921000-57933400	Strong transcription	HSMMtube	muscle
49	chr12:57921000-57938800	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
50	chr12:57921200-57930800	Strong transcription	HUVEC	blood vessel

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