Variant report

Variant	rs567895
Chromosome Location	chr12:57823192-57823193
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:7)
CpG islands
(count:0)
Chromatin interactive
region (count:14)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:7 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	MXI1	chr12:57823020-57825888	SK-N-SH	brain:	n/a	chr12:57823711-57823720
2	POLR2A	chr12:57823098-57823509	K562	blood:	n/a	n/a
3	POLR2A	chr12:57823073-57823576	HepG2	liver:	n/a	n/a
4	POLR2A	chr12:57823106-57824642	GM12892	blood:	n/a	n/a
5	POLR2A	chr12:57823119-57824547	PFSK-1	brain:	n/a	n/a
6	POLR2A	chr12:57823155-57823564	ECC-1	luminal epithelium:	n/a	n/a
7	POLR2A	chr12:57821228-57824428	SK-N-MC	brain:	n/a	n/a

No data

(count:14 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr12:57820715..57827591-chr12:57847165..57857509,18	K562	blood:
2	chr12:57808026..57810781-chr12:57822669..57824932,3	MCF-7	breast:
3	chr12:57675498..57678307-chr12:57822743..57825602,2	MCF-7	breast:
4	chr12:57664699..57666780-chr12:57821580..57823850,2	K562	blood:
5	chr12:57822828..57827240-chr12:57828141..57836129,12	MCF-7	breast:
6	chr12:57672368..57674775-chr12:57822497..57825097,2	K562	blood:
7	chr12:57821945..57826454-chr12:57843844..57847049,4	K562	blood:
8	chr12:57685797..57688003-chr12:57821497..57823959,2	K562	blood:
9	chr12:57822673..57825673-chr12:57914537..57916745,4	K562	blood:
10	chr12:57822102..57825804-chr12:57846903..57851131,6	MCF-7	breast:
11	chr12:57822750..57826133-chr12:57852904..57855936,4	K562	blood:
12	chr12:57734038..57735691-chr12:57822012..57824605,2	MCF-7	breast:
13	chr12:57821945..57831494-chr12:57839441..57852842,32	K562	blood:
14	chr12:57654294..57656088-chr12:57822678..57824554,2	MCF-7	breast:

No data

Variant related genes	Relation type
ENSG00000258001	TF binding region
ENSG00000139269	Chromatin interaction
ENSG00000179912	Chromatin interaction
ENSG00000111087	Chromatin interaction
ENSG00000175189	Chromatin interaction
ENSG00000268367	Chromatin interaction
ENSG00000166987	Chromatin interaction
ENSG00000201198	Chromatin interaction

Extended variants
information (count: 30 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:26)

rs_ID	r²[population]
rs10876968	0.92[ASW][hapmap];0.81[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];0.95[GIH][hapmap];0.95[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.90[MKK][hapmap];0.83[TSI][hapmap];1.00[YRI][hapmap]
rs11172142	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];1.00[YRI][hapmap]
rs11172155	0.91[ASW][hapmap];1.00[CEU][hapmap];0.95[CHB][hapmap];0.93[CHD][hapmap];0.98[GIH][hapmap];0.90[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.86[YRI][hapmap]
rs11830804	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];0.98[GIH][hapmap];0.95[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.90[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap]
rs12227309	1.00[ASW][hapmap];0.94[CEU][hapmap];1.00[CHB][hapmap];0.93[CHD][hapmap];0.98[GIH][hapmap];0.95[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.90[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap]
rs12820078	0.86[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2943691	0.98[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2943692	1.00[CEU][hapmap];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2943693	0.91[ASW][hapmap];1.00[CEU][hapmap];0.95[CHB][hapmap];0.92[CHD][hapmap];0.85[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.96[MKK][hapmap];0.96[TSI][hapmap];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs3204635	0.83[ASW][hapmap];0.98[GIH][hapmap];1.00[LWK][hapmap];0.85[MEX][hapmap];0.90[MKK][hapmap];0.83[TSI][hapmap];1.00[YRI][hapmap]
rs473465	1.00[CEU][hapmap];0.80[CHD][hapmap];0.90[JPT][hapmap];0.86[MEX][hapmap];0.92[TSI][hapmap]
rs487722	0.82[AMR][1000 genomes];0.90[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs501055	0.90[AFR][1000 genomes];0.87[AMR][1000 genomes];0.92[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs505479	0.80[AFR][1000 genomes];0.91[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs507562	1.00[CEU][hapmap];0.85[CHB][hapmap];0.90[JPT][hapmap];0.80[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs519452	0.93[AFR][1000 genomes];0.88[AMR][1000 genomes];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs538548	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.98[GIH][hapmap];0.95[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.90[AFR][1000 genomes];0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs568793	0.84[JPT][hapmap]
rs572198	0.85[AMR][1000 genomes];0.92[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs6581138	0.82[ASN][1000 genomes]
rs7297282	1.00[AMR][1000 genomes];0.92[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7302906	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.93[CHD][hapmap];0.98[GIH][hapmap];0.95[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.90[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap]
rs7303542	0.93[AFR][1000 genomes];0.90[AMR][1000 genomes];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs73115907	0.80[AFR][1000 genomes];0.90[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs7976512	1.00[YRI][hapmap]
rs9738646	0.94[AMR][1000 genomes];0.94[EUR][1000 genomes];0.91[ASN][1000 genomes]

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	nsv1046013	chr12:57714676-57895167	Active TSS Enhancers Bivalent Enhancer Genic enhancers Weak transcription Flanking Bivalent TSS/Enh Strong transcription Flanking Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	56 gene(s)	inside rSNPs	diseases
2	nsv541502	chr12:57714676-57895167	Weak transcription Flanking Bivalent TSS/Enh Strong transcription Flanking Active TSS Active TSS Genic enhancers Bivalent Enhancer Enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	56 gene(s)	inside rSNPs	diseases
3	nsv899117	chr12:57811414-57926472	Enhancers Active TSS Flanking Active TSS Weak transcription Strong transcription Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	103 gene(s)	inside rSNPs	diseases
4	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

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs567895	SP7	cis	parietal	SCAN
rs567895	KIAA0748	cis	cerebellum	SCAN
rs567895	DNAJC14	cis	cerebellum	SCAN

Chromatin state (count:118 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:57753200-57823800	Weak transcription	Esophagus	oesophagus
2	chr12:57770800-57824000	Weak transcription	Gastric	stomach
3	chr12:57780800-57823200	Weak transcription	Spleen	Spleen
4	chr12:57783800-57823200	Weak transcription	H9 Cell Line	embryonic stem cell
5	chr12:57788600-57823200	Weak transcription	NHDF-Ad	bronchial
6	chr12:57789400-57823200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
7	chr12:57790000-57823200	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
8	chr12:57795400-57823200	Weak transcription	Adipose Nuclei	Adipose
9	chr12:57795400-57823200	Weak transcription	Stomach Smooth Muscle	stomach
10	chr12:57795400-57823200	Weak transcription	HMEC	breast
11	chr12:57795400-57823600	Weak transcription	Aorta	Aorta
12	chr12:57795800-57823200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
13	chr12:57795800-57823200	Weak transcription	Right Ventricle	heart
14	chr12:57809400-57823200	Weak transcription	HUES64 Cell Line	embryonic stem cell
15	chr12:57809600-57823200	Weak transcription	HUES48 Cell Line	embryonic stem cell
16	chr12:57809600-57823200	Weak transcription	Colon Smooth Muscle	Colon
17	chr12:57809600-57823400	Weak transcription	Fetal Kidney	kidney
18	chr12:57809800-57823200	Weak transcription	iPS-18 Cell Line	embryonic stem cell
19	chr12:57810200-57823400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
20	chr12:57810200-57823400	Weak transcription	HUES6 Cell Line	embryonic stem cell
21	chr12:57812000-57823200	Weak transcription	Placenta Amnion	Placenta Amnion
22	chr12:57812200-57823200	Weak transcription	Brain Anterior Caudate	brain
23	chr12:57812200-57823200	Weak transcription	Brain Inferior Temporal Lobe	brain
24	chr12:57812200-57823200	Weak transcription	Ovary	ovary
25	chr12:57812600-57823200	Weak transcription	Brain Cingulate Gyrus	brain
26	chr12:57812600-57823200	Weak transcription	Pancreas	Pancrea
27	chr12:57812600-57823200	Weak transcription	HSMMtube	muscle
28	chr12:57813000-57823200	Weak transcription	H1 Cell Line	embryonic stem cell
29	chr12:57814000-57823200	Weak transcription	Brain Hippocampus Middle	brain
30	chr12:57814800-57823200	Weak transcription	Rectal Smooth Muscle	rectum
31	chr12:57815000-57823200	Weak transcription	Colonic Mucosa	Colon
32	chr12:57815000-57823200	Weak transcription	Psoas Muscle	Psoas
33	chr12:57815200-57823200	Weak transcription	iPS-20b Cell Line	embryonic stem cell
34	chr12:57815600-57823200	Weak transcription	Primary hematopoietic stem cells	blood
35	chr12:57816600-57823200	Weak transcription	Primary T helper naive cells from peripheral blood	blood
36	chr12:57816600-57823200	Weak transcription	Primary T killer memory cells from peripheral blood	blood
37	chr12:57816600-57823200	Weak transcription	Left Ventricle	heart
38	chr12:57816600-57823200	Weak transcription	Rectal Mucosa Donor 29	rectum
39	chr12:57816600-57823200	Weak transcription	Osteobl	bone
40	chr12:57817000-57823200	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
41	chr12:57817000-57823200	Weak transcription	Primary B cells from cord blood	blood
42	chr12:57817200-57823200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
43	chr12:57818200-57823200	Weak transcription	Lung	lung
44	chr12:57818400-57823200	Weak transcription	HSMM	muscle
45	chr12:57818600-57823200	Weak transcription	Fetal Lung	lung
46	chr12:57819400-57823200	Weak transcription	Sigmoid Colon	Sigmoid Colon
47	chr12:57819800-57823200	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
48	chr12:57819800-57823200	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
49	chr12:57819800-57823200	Weak transcription	Primary neutrophils fromperipheralblood	blood
50	chr12:57819800-57823200	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood

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