Variant report

Variant	rs1043011
Chromosome Location	chr12:56865040-56865041
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:18)
CpG islands
(count:0)
Chromatin interactive
region (count:6)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:18 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr12:56864398-56865622	PANC-1	pancreas:	n/a	n/a
2	POLR2A	chr12:56861856-56866281	SK-N-MC	brain:	n/a	n/a
3	POLR2A	chr12:56864653-56866126	H1-hESC	embryonic stem cell:	n/a	n/a
4	POLR2A	chr12:56864859-56865774	K562	blood:	n/a	n/a
5	POLR2A	chr12:56864945-56865673	K562	blood:	n/a	n/a
6	POLR2A	chr12:56864857-56866019	K562	blood:	n/a	n/a
7	POLR2A	chr12:56864879-56865233	GM12878	blood:	n/a	n/a
8	POLR2A	chr12:56864705-56866144	GM12878	blood:	n/a	n/a
9	POLR2A	chr12:56864804-56865272	H1-hESC	embryonic stem cell:	n/a	n/a
10	POLR2A	chr12:56864772-56865078	HepG2	liver:	n/a	n/a
11	POLR2A	chr12:56864292-56865066	PFSK-1	brain:	n/a	n/a
12	POLR2A	chr12:56864742-56866064	K562	blood:	n/a	n/a
13	POLR2A	chr12:56864796-56865142	GM12891	blood:	n/a	n/a
14	POLR2A	chr12:56864799-56865740	ECC-1	luminal epithelium:	n/a	n/a
15	POLR2A	chr12:56864762-56866062	GM12892	blood:	n/a	n/a
16	POLR2A	chr12:56861637-56865382	HepG2	liver:	n/a	n/a
17	POLR2A	chr12:56864735-56865547	GM12891	blood:	n/a	n/a
18	POLR2A	chr12:56864851-56865485	Hela-S3	cervix:	n/a	n/a

No data

(count:6 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr12:56708721..56711382-chr12:56864532..56867166,3	K562	blood:
2	chr12:56509686..56511779-chr12:56864045..56866369,2	MCF-7	breast:
3	chr12:56572264..56574644-chr12:56862894..56865507,2	MCF-7	breast:
4	chr12:56510693..56513436-chr12:56864879..56866666,2	K562	blood:
5	chr12:56839562..56844740-chr12:56860089..56866019,9	MCF-7	breast:
6	chr12:56752241..56754348-chr12:56862536..56866569,3	K562	blood:

No data

Variant related genes	Relation type
MIP	TF binding region
ENSG00000139641	Chromatin interaction
ENSG00000135482	Chromatin interaction
ENSG00000111602	Chromatin interaction
ENSG00000144785	Chromatin interaction
ENSG00000229117	Chromatin interaction
ENSG00000139613	Chromatin interaction
ENSG00000170581	Chromatin interaction
ENSG00000257727	Chromatin interaction

Extended variants
information (count: 21 )
Associated
traits (count: 9 )

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

rs_ID	r²[population]
rs1082214	0.82[CHB][hapmap]
rs2638287	0.94[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];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];0.94[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][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];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];1.00[YRI][hapmap];0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2657880	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]
rs2657896	1.00[ASW][hapmap];0.88[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	0.84[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.85[TSI][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	0.88[CEU][hapmap];0.82[JPT][hapmap]
rs813497	0.88[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

mRNA abundance (count:9)

SNP	Gene	Cis/trans	Tissue	Source
rs1043011	DCD	cis	parietal	SCAN
rs1043011	LOC283377	cis	multi-tissue	Pritchard
rs1043011	ZNF529	trans	parietal	SCAN
rs1043011	SPRYD4	cis	multi-tissue	Pritchard
rs1043011	SPRYD4	cis	lymphoblastoid	seeQTL
rs1043011	RBMS2	cis	multi-tissue	Pritchard
rs1043011	ITGA5	cis	cerebellum	SCAN
rs1043011	STAC3	cis	parietal	SCAN
rs1043011	ORMDL2	cis	parietal	SCAN

Chromatin state (count:122 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:56863000-56865400	Enhancers	Primary neutrophils fromperipheralblood	blood
2	chr12:56863000-56871200	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
3	chr12:56863200-56865200	Weak transcription	Aorta	Aorta
4	chr12:56863200-56881000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
5	chr12:56863200-56881200	Weak transcription	Ovary	ovary
6	chr12:56863400-56865600	Strong transcription	NHLF	lung
7	chr12:56863400-56869400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
8	chr12:56863400-56873600	Weak transcription	H9 Cell Line	embryonic stem cell
9	chr12:56863400-56881000	Weak transcription	Rectal Smooth Muscle	rectum
10	chr12:56863400-56881200	Weak transcription	Right Atrium	heart
11	chr12:56863400-56881400	Weak transcription	HSMMtube	muscle
12	chr12:56863600-56865200	Weak transcription	Brain Cingulate Gyrus	brain
13	chr12:56863600-56865200	Enhancers	Pancreas	Pancrea
14	chr12:56863600-56865600	Weak transcription	Brain Angular Gyrus	brain
15	chr12:56863600-56866600	Weak transcription	Fetal Kidney	kidney
16	chr12:56863600-56867800	Strong transcription	HUES64 Cell Line	embryonic stem cell
17	chr12:56863600-56868000	Weak transcription	Placenta Amnion	Placenta Amnion
18	chr12:56863600-56868000	Weak transcription	Psoas Muscle	Psoas
19	chr12:56863600-56868400	Weak transcription	Right Ventricle	heart
20	chr12:56863600-56868600	Strong transcription	HUES48 Cell Line	embryonic stem cell
21	chr12:56863600-56869000	Strong transcription	Fetal Muscle Trunk	muscle
22	chr12:56863600-56869200	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
23	chr12:56863600-56869600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
24	chr12:56863600-56870200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
25	chr12:56863600-56870800	Weak transcription	Duodenum Smooth Muscle	Duodenum
26	chr12:56863600-56871000	Weak transcription	iPS-15b Cell Line	embryonic stem cell
27	chr12:56863600-56874200	Weak transcription	Primary T killer memory cells from peripheral blood	blood
28	chr12:56863600-56880800	Weak transcription	Pancreatic Islets	Pancreatic Islet
29	chr12:56863800-56865200	Transcr. at gene 5' and 3'	GM12878-XiMat	blood
30	chr12:56863800-56866400	Weak transcription	Primary B cells from cord blood	blood
31	chr12:56863800-56866400	Strong transcription	Cortex derived primary cultured neurospheres	brain
32	chr12:56863800-56867000	Weak transcription	Brain Hippocampus Middle	brain
33	chr12:56863800-56867200	Weak transcription	Muscle Satellite Cultured Cells	--
34	chr12:56863800-56867400	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
35	chr12:56863800-56867600	Weak transcription	Fetal Brain Male	brain
36	chr12:56863800-56867600	Strong transcription	A549	lung
37	chr12:56863800-56867600	Weak transcription	HUVEC	blood vessel
38	chr12:56863800-56867800	Strong transcription	HSMM	muscle
39	chr12:56863800-56868800	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
40	chr12:56863800-56869000	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
41	chr12:56863800-56869400	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
42	chr12:56863800-56869400	Weak transcription	NHDF-Ad	bronchial
43	chr12:56863800-56869600	Weak transcription	Osteobl	bone
44	chr12:56863800-56870000	Weak transcription	Placenta	Placenta
45	chr12:56863800-56870800	Weak transcription	Adipose Nuclei	Adipose
46	chr12:56863800-56871400	Weak transcription	Brain Substantia Nigra	brain
47	chr12:56863800-56873400	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
48	chr12:56863800-56879000	Weak transcription	Primary hematopoietic stem cells	blood
49	chr12:56863800-56880800	Weak transcription	Brain Germinal Matrix	brain
50	chr12:56863800-56880800	Weak transcription	Gastric	stomach

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