Variant report

Variant	rs2657880
Chromosome Location	chr12:56863770-56863771
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:9)
CpG islands
(count:0)
Chromatin interactive
region (count:19)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:9 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr12:56863634-56863921	H1-hESC	embryonic stem cell:	n/a	n/a
2	POLR2A	chr12:56861856-56866281	SK-N-MC	brain:	n/a	n/a
3	POLR2A	chr12:56862744-56863916	GM12878	blood:	n/a	n/a
4	POLR2A	chr12:56861879-56864649	K562	blood:	n/a	n/a
5	POLR2A	chr12:56863701-56864052	H1-hESC	embryonic stem cell:	n/a	n/a
6	POLR2A	chr12:56863032-56863824	GM12878	blood:	n/a	n/a
7	POLR2A	chr12:56861937-56864331	H1-hESC	embryonic stem cell:	n/a	n/a
8	POLR2A	chr12:56861637-56865382	HepG2	liver:	n/a	n/a
9	POLR2A	chr12:56863347-56864082	K562	blood:	n/a	n/a

No data

(count:19 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr12:56692603..56696463-chr12:56860417..56864951,9	K562	blood:
2	chr12:56727342..56729039-chr12:56862325..56863904,2	K562	blood:
3	chr12:56572264..56574644-chr12:56862894..56865507,2	MCF-7	breast:
4	chr12:56708282..56711640-chr12:56860573..56864710,5	K562	blood:
5	chr12:56860897..56864227-chr12:56865813..56869854,5	MCF-7	breast:
6	chr12:56752523..56755343-chr12:56862151..56864248,2	MCF-7	breast:
7	chr12:56841526..56846188-chr12:56861608..56864760,4	K562	blood:
8	chr12:56650281..56653173-chr12:56862365..56864133,2	K562	blood:
9	chr12:56694327..56696089-chr12:56861619..56863910,2	MCF-7	breast:
10	chr12:56862344..56864045-chr12:56880136..56881879,2	MCF-7	breast:
11	chr12:56862204..56864692-chr12:56870931..56873632,2	MCF-7	breast:
12	chr12:56862988..56864718-chr12:57480349..57483010,2	MCF-7	breast:
13	chr12:56683757..56687058-chr12:56862106..56864198,3	K562	blood:
14	chr12:56861952..56864525-chr12:57027360..57030112,3	MCF-7	breast:
15	chr12:56692603..56696463-chr12:56860417..56864951,8	K562	blood:
16	chr12:56839562..56844740-chr12:56860089..56866019,9	MCF-7	breast:
17	chr12:56708394..56711484-chr12:56860870..56863906,7	MCF-7	breast:
18	chr12:56582327..56583849-chr12:56861847..56864785,2	MCF-7	breast:
19	chr12:56752241..56754348-chr12:56862536..56866569,3	K562	blood:

No data

Variant related genes	Relation type
MIP	TF binding region
ENSG00000257727	Chromatin interaction
ENSG00000076108	Chromatin interaction
ENSG00000139613	Chromatin interaction
ENSG00000257303	Chromatin interaction
ENSG00000135473	Chromatin interaction
ENSG00000144785	Chromatin interaction
ENSG00000170581	Chromatin interaction
ENSG00000139645	Chromatin interaction
ENSG00000111602	Chromatin interaction
ENSG00000166886	Chromatin interaction
ENSG00000166881	Chromatin interaction
ENSG00000135423	Chromatin interaction
ENSG00000062485	Chromatin interaction

Extended variants
information (count: 21 )
Associated
traits (count: 13 )

rSNPs within LD-proxies of this variant (count:18)

rs_ID	r²[population]
rs1043011	1.00[ASW][hapmap];0.83[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.85[GIH][hapmap];1.00[JPT][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1082214	0.82[CHB][hapmap]
rs2638287	0.81[CEU][hapmap];0.82[JPT][hapmap]
rs2638314	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2638315	1.00[ASW][hapmap];0.83[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.85[GIH][hapmap];1.00[JPT][hapmap];0.80[MEX][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2657878	0.91[AFR][1000 genomes];0.82[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs2657879	1.00[ASW][hapmap];0.83[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.85[GIH][hapmap];1.00[JPT][hapmap];0.80[MEX][hapmap];0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2657896	1.00[ASW][hapmap];0.81[CEU][hapmap]
rs2694917	0.82[JPT][hapmap]
rs2933243	0.95[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2939302	0.95[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7298123	0.90[ASN][1000 genomes]
rs7302925	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73114872	0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs774044	1.00[CHB][hapmap]
rs774045	0.82[CHB][hapmap]
rs774211	0.81[CEU][hapmap];0.82[JPT][hapmap]
rs813497	0.81[CEU][hapmap]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1043622	chr12:56571476-56974448	Enhancers Weak transcription Active TSS Strong transcription Flanking Active TSS Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	95 gene(s)	inside rSNPs	diseases
2	nsv541500	chr12:56571476-56974448	Weak transcription Strong transcription Bivalent/Poised TSS Active TSS Enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	95 gene(s)	inside rSNPs	diseases
3	nsv1052713	chr12:56848036-56917602	Weak transcription Enhancers Flanking Bivalent TSS/Enh Active TSS Flanking Active TSS Bivalent Enhancer Genic enhancers Strong transcription Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region miRNA target site	35 gene(s)	inside rSNPs	diseases

Variant related diseases (count:1)

Disease	PMID	Source
Metabolite levels	22916037	GWAS catalog

mRNA abundance (count:12)

SNP	Gene	Cis/trans	Tissue	Source
rs2657880	SPRYD4	cis	lymphoblastoid	seeQTL
rs2657880	SPRYD4	cis	multi-tissue	Pritchard
rs2657880	PAN2	cis	parietal	SCAN
rs2657880	STAC3	cis	parietal	SCAN
rs2657880	RBMS2	cis	multi-tissue	Pritchard
rs2657880	ITGA5	cis	cerebellum	SCAN
rs2657880	LOC283377	cis	multi-tissue	Pritchard
rs2657880	RBMS2	cis	lymphoblastoid	seeQTL
rs2657880	ENSG00000176422	cis	multi-tissue	Pritchard
rs2657880	DCD	cis	parietal	SCAN
rs2657880	OR6C76	cis	parietal	SCAN
rs2657880	DTX3	cis	cerebellum	SCAN

Chromatin state (count:125 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:56862400-56863800	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
2	chr12:56862600-56863800	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
3	chr12:56862600-56863800	Flanking Active TSS	Stomach Smooth Muscle	stomach
4	chr12:56862600-56863800	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
5	chr12:56862800-56863800	Flanking Active TSS	Primary T helper cells PMA-I stimulated	--
6	chr12:56862800-56863800	Flanking Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
7	chr12:56862800-56863800	Flanking Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
8	chr12:56862800-56863800	Flanking Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
9	chr12:56862800-56863800	Flanking Active TSS	Brain Substantia Nigra	brain
10	chr12:56862800-56863800	Flanking Active TSS	Fetal Heart	heart
11	chr12:56862800-56863800	Flanking Active TSS	Rectal Mucosa Donor 29	rectum
12	chr12:56862800-56863800	Flanking Active TSS	Skeletal Muscle Female	skeletal muscle
13	chr12:56862800-56863800	Transcr. at gene 5' and 3'	K562	blood
14	chr12:56862800-56864000	Flanking Active TSS	Liver	Liver
15	chr12:56862800-56864000	Transcr. at gene 5' and 3'	Dnd41	blood
16	chr12:56863000-56863800	Flanking Active TSS	Breast Myoepithelial Primary Cells	Breast
17	chr12:56863000-56863800	Flanking Active TSS	Duodenum Mucosa	Duodenum
18	chr12:56863000-56863800	Flanking Active TSS	GM12878-XiMat	blood
19	chr12:56863000-56864000	Flanking Active TSS	Hela-S3	cervix
20	chr12:56863000-56864200	Transcr. at gene 5' and 3'	Foreskin Fibroblast Primary Cells skin01	Skin
21	chr12:56863000-56865400	Enhancers	Primary neutrophils fromperipheralblood	blood
22	chr12:56863000-56871200	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
23	chr12:56863200-56863800	Transcr. at gene 5' and 3'	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
24	chr12:56863200-56863800	Flanking Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
25	chr12:56863200-56863800	Enhancers	Primary B cells from cord blood	blood
26	chr12:56863200-56863800	Transcr. at gene 5' and 3'	Primary hematopoietic stem cells short term culture	blood
27	chr12:56863200-56863800	Enhancers	Primary T cells effector/memory enriched fromperipheralblood	blood
28	chr12:56863200-56863800	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
29	chr12:56863200-56863800	Flanking Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
30	chr12:56863200-56863800	Enhancers	Sigmoid Colon	Sigmoid Colon
31	chr12:56863200-56864000	Enhancers	Primary T helper naive cells fromperipheralblood	blood
32	chr12:56863200-56864000	Enhancers	Primary T regulatory cells fromperipheralblood	blood
33	chr12:56863200-56864000	Transcr. at gene 5' and 3'	Foreskin Fibroblast Primary Cells skin02	Skin
34	chr12:56863200-56864000	Enhancers	Left Ventricle	heart
35	chr12:56863200-56864000	Enhancers	Small Intestine	intestine
36	chr12:56863200-56864000	Genic enhancers	Thymus	Thymus
37	chr12:56863200-56864000	Enhancers	Spleen	Spleen
38	chr12:56863200-56865000	Enhancers	Primary monocytes fromperipheralblood	blood
39	chr12:56863200-56865200	Weak transcription	Aorta	Aorta
40	chr12:56863200-56881000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
41	chr12:56863200-56881200	Weak transcription	Ovary	ovary
42	chr12:56863400-56863800	Transcr. at gene 5' and 3'	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
43	chr12:56863400-56863800	Transcr. at gene 5' and 3'	iPS-20b Cell Line	embryonic stem cell
44	chr12:56863400-56863800	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
45	chr12:56863400-56863800	Enhancers	Adipose Nuclei	Adipose
46	chr12:56863400-56863800	Enhancers	Brain Anterior Caudate	brain
47	chr12:56863400-56863800	Enhancers	Colonic Mucosa	Colon
48	chr12:56863400-56863800	Enhancers	Colon Smooth Muscle	Colon
49	chr12:56863400-56863800	Genic enhancers	Placenta	Placenta
50	chr12:56863400-56863800	Genic enhancers	Rectal Mucosa Donor 31	rectum

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