Variant report

Variant	rs7959814
Chromosome Location	chr12:51722633-51722634
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:1)
CpG islands
(count:0)
Chromatin interactive
region (count:5)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

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

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr12:51722134-51725151	K562	blood:	n/a	n/a

No data

(count:5 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr12:51712710..51714894-chr12:51720855..51723845,2	K562	blood:
2	chr12:51710356..51713645-chr12:51720668..51723733,3	MCF-7	breast:
3	chr12:51719185..51720763-chr12:51721819..51723856,2	MCF-7	breast:
4	chr12:51712710..51716828-chr12:51719754..51724043,5	K562	blood:
5	chr12:51566806..51568529-chr12:51720798..51723312,2	K562	blood:

No data

Variant related genes	Relation type
BIN2	TF binding region
ENSG00000135457	Chromatin interaction

Extended variants
information (count: 29 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:25)

rs_ID	r²[population]
rs10516	0.96[CEU][hapmap];0.95[EUR][1000 genomes]
rs10876162	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11169795	0.96[CEU][hapmap];0.95[TSI][hapmap]
rs11169805	0.80[ASW][hapmap];1.00[CEU][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.82[LWK][hapmap];0.97[MKK][hapmap];1.00[TSI][hapmap];0.82[YRI][hapmap];0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs11616158	0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs12310910	0.85[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs12582273	1.00[CEU][hapmap];0.82[GIH][hapmap];1.00[MEX][hapmap];0.87[TSI][hapmap];0.89[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs12829179	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12830766	0.86[AMR][1000 genomes];0.84[ASN][1000 genomes]
rs12831721	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17860300	0.82[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs17860301	0.82[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs17860343	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs3858624	1.00[CEU][hapmap];0.97[GIH][hapmap];1.00[MEX][hapmap];0.97[TSI][hapmap];0.85[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs3858627	0.84[CEU][hapmap];1.00[GIH][hapmap];0.89[MEX][hapmap];0.81[MKK][hapmap];0.89[TSI][hapmap];0.83[EUR][1000 genomes]
rs57941347	0.86[AMR][1000 genomes];0.84[ASN][1000 genomes]
rs61022955	0.86[AMR][1000 genomes];0.84[ASN][1000 genomes]
rs68042460	0.86[AMR][1000 genomes];0.84[ASN][1000 genomes]
rs7133606	0.87[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs7138439	1.00[CEU][hapmap];1.00[TSI][hapmap];0.89[EUR][1000 genomes]
rs7299306	1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs7299453	0.90[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs7306746	0.96[AMR][1000 genomes];0.89[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7964134	1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs9651999	0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.84[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	nsv482304	chr12:51653496-51814917	Active TSS Flanking Active TSS Enhancers Weak transcription Genic enhancers Strong transcription Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	21 gene(s)	inside rSNPs	diseases
2	nsv469377	chr12:51690751-51733951	Enhancers Active TSS Flanking Active TSS Weak transcription Genic enhancers Strong transcription Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
3	nsv558877	chr12:51690751-51733951	Weak transcription Enhancers Flanking Active TSS Strong transcription Active TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
4	nsv832408	chr12:51696605-51871339	Weak transcription Enhancers Flanking Active TSS Strong transcription Genic enhancers Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs7959814	SPATS2	cis	parietal	SCAN

Chromatin state (count:55 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:51718000-51724400	Enhancers	Primary B cells from peripheral blood	blood
2	chr12:51718000-51724400	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
3	chr12:51718400-51723000	Enhancers	Primary T killer naive cells fromperipheralblood	blood
4	chr12:51718400-51723200	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
5	chr12:51718400-51723600	Enhancers	Primary T regulatory cells fromperipheralblood	blood
6	chr12:51718400-51724400	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
7	chr12:51718400-51724400	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
8	chr12:51718400-51724400	Enhancers	Placenta	Placenta
9	chr12:51718400-51724400	Enhancers	Fetal Thymus	thymus
10	chr12:51718400-51727800	Weak transcription	Colonic Mucosa	Colon
11	chr12:51718600-51723000	Enhancers	Primary T cells fromperipheralblood	blood
12	chr12:51719400-51723200	Enhancers	Primary mononuclear cells fromperipheralblood	Blood
13	chr12:51719600-51723200	Enhancers	Primary T killer memory cells from peripheral blood	blood
14	chr12:51719600-51723800	Enhancers	Dnd41	blood
15	chr12:51719800-51724200	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
16	chr12:51720000-51723200	Enhancers	Thymus	Thymus
17	chr12:51720000-51723400	Enhancers	Primary T cells effector/memory enriched fromperipheralblood	blood
18	chr12:51720800-51728600	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
19	chr12:51720800-51735000	Weak transcription	Esophagus	oesophagus
20	chr12:51721000-51723200	Weak transcription	Stomach Mucosa	stomach
21	chr12:51721000-51724200	Enhancers	Rectal Mucosa Donor 29	rectum
22	chr12:51721000-51724400	Enhancers	Primary hematopoietic stem cells	blood
23	chr12:51721200-51722800	Enhancers	Primary neutrophils fromperipheralblood	blood
24	chr12:51721200-51722800	Enhancers	Hela-S3	cervix
25	chr12:51721200-51723000	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
26	chr12:51721200-51723200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
27	chr12:51721200-51723200	Enhancers	Primary monocytes fromperipheralblood	blood
28	chr12:51721200-51723400	Weak transcription	Osteobl	bone
29	chr12:51721200-51723600	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
30	chr12:51721200-51723800	Weak transcription	HSMMtube	muscle
31	chr12:51721200-51724200	Enhancers	Primary B cells from cord blood	blood
32	chr12:51721200-51724600	Weak transcription	A549	lung
33	chr12:51721200-51735000	Weak transcription	NHDF-Ad	bronchial
34	chr12:51721400-51723200	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
35	chr12:51721400-51723200	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
36	chr12:51721400-51723400	Enhancers	Primary hematopoietic stem cells short term culture	blood
37	chr12:51721400-51723600	Weak transcription	Muscle Satellite Cultured Cells	--
38	chr12:51721400-51723600	Enhancers	Spleen	Spleen
39	chr12:51721400-51723800	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
40	chr12:51721400-51723800	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
41	chr12:51721400-51724400	Enhancers	GM12878-XiMat	blood
42	chr12:51722000-51724200	Enhancers	K562	blood
43	chr12:51722200-51723400	Weak transcription	Duodenum Smooth Muscle	Duodenum
44	chr12:51722200-51723600	Enhancers	Rectal Mucosa Donor 31	rectum
45	chr12:51722200-51724000	Flanking Active TSS	Primary T cells from cord blood	blood
46	chr12:51722400-51722800	Flanking Active TSS	Primary T helper naive cells from peripheral blood	blood
47	chr12:51722400-51724200	Flanking Active TSS	Primary T helper naive cells fromperipheralblood	blood
48	chr12:51722400-51724200	Flanking Active TSS	Primary T helper cells PMA-I stimulated	--
49	chr12:51722600-51722800	Enhancers	Fetal Muscle Trunk	muscle
50	chr12:51722600-51722800	Enhancers	Right Atrium	heart

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