Variant report

Variant	rs11882031
Chromosome Location	chr19:56193662-56193663
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	chr19:56193472-56194097	PANC-1	pancreas:	n/a	n/a
2	POLR2A	chr19:56193441-56193953	GM12878	blood:	n/a	n/a
3	BCL3	chr19:56193642-56193955	GM12878	blood:	n/a	n/a
4	NFATC1	chr19:56193559-56193859	GM12878	blood:	n/a	n/a
5	POLR2A	chr19:56193487-56193905	GM12892	blood:	n/a	n/a
6	POLR2A	chr19:56193427-56193842	GM12892	blood:	n/a	n/a
7	POLR2A	chr19:56193531-56193862	K562	blood:	n/a	n/a

Variant related genes	Relation type
ENSG00000211571	TF binding region

Extended variants
information (count: 39 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:32)

rs_ID	r²[population]
rs10402618	0.89[ASN][1000 genomes]
rs10403866	0.95[ASN][1000 genomes]
rs10408613	0.91[ASN][1000 genomes]
rs10410404	0.95[CHB][hapmap];0.97[CHD][hapmap];0.94[JPT][hapmap];0.81[MKK][hapmap];0.87[ASN][1000 genomes]
rs10410802	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.96[LWK][hapmap];1.00[MEX][hapmap];0.96[MKK][hapmap];1.00[TSI][hapmap];0.93[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10410886	0.85[CHB][hapmap];0.94[CHD][hapmap];1.00[JPT][hapmap];0.86[ASN][1000 genomes]
rs10412050	0.82[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.88[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs10415521	1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];0.91[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.93[TSI][hapmap];0.82[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10417539	0.96[ASN][1000 genomes]
rs10421319	0.95[CHB][hapmap];0.89[CHD][hapmap];0.83[JPT][hapmap];0.86[ASN][1000 genomes]
rs2287791	0.82[CEU][hapmap];0.90[CHB][hapmap];0.94[JPT][hapmap];0.93[TSI][hapmap]
rs28385383	0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28595590	0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28668166	0.88[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs310437	0.91[CEU][hapmap];0.95[CHB][hapmap];1.00[MEX][hapmap];0.93[TSI][hapmap];0.88[AMR][1000 genomes];0.95[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs310441	0.93[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs3745446	0.81[ASN][1000 genomes]
rs4801526	0.81[ASN][1000 genomes]
rs523509	0.85[ASN][1000 genomes]
rs575274	0.88[JPT][hapmap]
rs57544196	0.97[AFR][1000 genomes];0.97[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs584405	0.88[AMR][1000 genomes];0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs60873246	0.92[ASN][1000 genomes]
rs610811	0.81[JPT][hapmap]
rs617073	0.91[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.93[TSI][hapmap];0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs648651	0.85[AMR][1000 genomes];0.95[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs681804	0.89[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7256441	0.88[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs73613281	0.95[ASN][1000 genomes]
rs8100143	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.91[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.87[MKK][hapmap];1.00[TSI][hapmap];0.83[YRI][hapmap];0.88[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs8104242	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.91[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.84[MKK][hapmap];1.00[TSI][hapmap];0.82[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs8109983	0.98[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:7 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv912487	chr19:55977909-56215184	Enhancers Weak transcription Transcr. at gene 5' and 3' Flanking Active TSS Active TSS Strong transcription Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	109 gene(s)	inside rSNPs	diseases
2	nsv912494	chr19:56026072-56215184	Genic enhancers Bivalent Enhancer Flanking Active TSS Active TSS Enhancers Weak transcription Transcr. at gene 5' and 3' Strong transcription ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	97 gene(s)	inside rSNPs	diseases
3	nsv912498	chr19:56041848-56215184	Active TSS Enhancers Weak transcription Strong transcription Flanking Active TSS Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	97 gene(s)	inside rSNPs	diseases
4	nsv912501	chr19:56093365-56215184	Flanking Active TSS Weak transcription Strong transcription Active TSS Transcr. at gene 5' and 3' Enhancers Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	92 gene(s)	inside rSNPs	diseases
5	nsv428026	chr19:56130849-56423514	Flanking Active TSS Enhancers Genic enhancers Transcr. at gene 5' and 3' Active TSS Strong transcription Weak transcription ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	82 gene(s)	inside rSNPs	diseases
6	nsv833882	chr19:56158633-56326564	Enhancers Active TSS Flanking Active TSS Genic enhancers Strong transcription Bivalent Enhancer Weak transcription Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	66 gene(s)	inside rSNPs	diseases
7	nsv1061024	chr19:56167101-56217359	Active TSS Weak transcription Transcr. at gene 5' and 3' Strong transcription Genic enhancers Enhancers ZNF genes & repeats Flanking Active TSS Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	37 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs11882031	VCAM1	trans	brain	seeQTL
rs11882031	ZNF580	cis	lymphoblastoid	seeQTL
rs11882031	IL8	trans	brain	seeQTL

Chromatin state (count:124 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr19:56188200-56218200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
2	chr19:56188400-56193800	Strong transcription	Brain Cingulate Gyrus	brain
3	chr19:56188400-56194000	Genic enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
4	chr19:56188400-56195000	Weak transcription	Pancreatic Islets	Pancreatic Islet
5	chr19:56188400-56211200	Strong transcription	Cortex derived primary cultured neurospheres	brain
6	chr19:56188400-56213600	Strong transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
7	chr19:56188600-56194000	Strong transcription	A549	lung
8	chr19:56188600-56210000	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
9	chr19:56188600-56212400	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
10	chr19:56188600-56215600	Weak transcription	Fetal Brain Male	brain
11	chr19:56188800-56194000	Strong transcription	Placenta Amnion	Placenta Amnion
12	chr19:56188800-56199800	Weak transcription	HSMMtube	muscle
13	chr19:56188800-56212400	Strong transcription	Thymus	Thymus
14	chr19:56189000-56199600	Strong transcription	Fetal Stomach	stomach
15	chr19:56189000-56210000	Strong transcription	Fetal Brain Female	brain
16	chr19:56189200-56195200	Genic enhancers	Fetal Intestine Small	intestine
17	chr19:56189200-56195400	Strong transcription	HUES48 Cell Line	embryonic stem cell
18	chr19:56189200-56199400	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
19	chr19:56189200-56209400	Strong transcription	HUES64 Cell Line	embryonic stem cell
20	chr19:56189200-56212600	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
21	chr19:56189400-56193800	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
22	chr19:56189400-56193800	Strong transcription	iPS-18 Cell Line	embryonic stem cell
23	chr19:56189400-56194000	Strong transcription	H1 Cell Line	embryonic stem cell
24	chr19:56189400-56194000	Genic enhancers	Fetal Adrenal Gland	Adrenal Gland
25	chr19:56189400-56198000	Strong transcription	Brain Inferior Temporal Lobe	brain
26	chr19:56189400-56199600	Strong transcription	Brain Dorsolateral Prefrontal Cortex	brain
27	chr19:56189400-56209400	Strong transcription	Fetal Thymus	thymus
28	chr19:56189400-56209400	Strong transcription	Dnd41	blood
29	chr19:56189400-56212400	Strong transcription	Brain Germinal Matrix	brain
30	chr19:56189600-56194000	Strong transcription	Osteobl	bone
31	chr19:56189600-56194200	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
32	chr19:56189600-56204600	Strong transcription	Brain Anterior Caudate	brain
33	chr19:56189600-56209400	Strong transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
34	chr19:56189600-56209800	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
35	chr19:56189600-56213200	Strong transcription	Primary T cells from cord blood	blood
36	chr19:56189800-56193800	Strong transcription	iPS-15b Cell Line	embryonic stem cell
37	chr19:56189800-56193800	Strong transcription	iPS-20b Cell Line	embryonic stem cell
38	chr19:56189800-56194200	Strong transcription	H9 Cell Line	embryonic stem cell
39	chr19:56189800-56194800	Strong transcription	Fetal Lung	lung
40	chr19:56189800-56194800	Weak transcription	Right Atrium	heart
41	chr19:56190000-56193800	Strong transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
42	chr19:56190000-56194000	Genic enhancers	Liver	Liver
43	chr19:56190000-56194800	Genic enhancers	Duodenum Mucosa	Duodenum
44	chr19:56190000-56196800	Weak transcription	Primary hematopoietic stem cells	blood
45	chr19:56190000-56198400	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
46	chr19:56190000-56212600	Strong transcription	Primary neutrophils fromperipheralblood	blood
47	chr19:56190200-56210200	Strong transcription	Primary hematopoietic stem cells short term culture	blood
48	chr19:56190200-56212400	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
49	chr19:56190400-56197600	Strong transcription	Brain Angular Gyrus	brain
50	chr19:56190400-56198000	Strong transcription	Colon Smooth Muscle	Colon

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