Variant report

Variant	rs11025021
Chromosome Location	chr11:19138127-19138128
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	chr11:19137874-19139543	GM12891	blood:	n/a	n/a
2	POLR2A	chr11:19137842-19139289	GM12892	blood:	n/a	n/a
3	MAZ	chr11:19137866-19139249	GM12878	blood:	n/a	n/a
4	POLR2A	chr11:19137995-19139315	GM19193	blood:	n/a	n/a
5	RUNX3	chr11:19137762-19138286	GM12878	blood:	n/a	n/a
6	POLR2A	chr11:19137766-19138281	GM12878	blood:	n/a	n/a
7	RUNX3	chr11:19137748-19138338	GM12878	blood:	n/a	n/a
8	EBF1	chr11:19137790-19138205	GM12878	blood:	n/a	chr11:19137949-19137959 chr11:19137949-19137958 chr11:19137947-19137958
9	SMARCB1	chr11:19137934-19139316	Hela-S3	cervix:	n/a	n/a
10	NRF1	chr11:19137916-19138326	GM12878	blood:	n/a	n/a
11	CHD2	chr11:19137986-19138167	H1-hESC	embryonic stem cell:	n/a	chr11:19138056-19138066
12	EP300	chr11:19137845-19138404	GM12878	blood:	n/a	chr11:19138118-19138132 chr11:19138087-19138100
13	TBL1XR1	chr11:19137849-19138989	GM12878	blood:	n/a	n/a
14	ZNF143	chr11:19138033-19138310	H1-hESC	embryonic stem cell:	n/a	n/a
15	POLR2A	chr11:19137938-19139372	GM18526	blood:	n/a	n/a
16	POLR2A	chr11:19138038-19139487	GM18505	blood:	n/a	n/a
17	POLR2A	chr11:19137805-19139313	GM12878	blood:	n/a	n/a
18	POLR2A	chr11:19137821-19139730	GM12878	blood:	n/a	n/a
19	POLR2A	chr11:19137851-19139347	GM12892	blood:	n/a	n/a
20	EBF1	chr11:19137686-19139176	GM12878	blood:	n/a	chr11:19137949-19137959 chr11:19137949-19137958 chr11:19137947-19137958
21	ZNF143	chr11:19137798-19139262	GM12878	blood:	n/a	chr11:19139017-19139036 chr11:19138834-19138844
22	RELA	chr11:19137806-19139501	GM12891	blood:	n/a	n/a
23	MTA3	chr11:19137774-19139105	GM12878	blood:	n/a	n/a
24	POLR2A	chr11:19138010-19139225	GM15510	blood:	n/a	n/a
25	BHLHE40	chr11:19137949-19139391	K562	blood:	n/a	n/a
26	POLR2A	chr11:19137941-19139440	GM18951	blood:	n/a	n/a
27	EBF1	chr11:19137799-19138141	GM12878	blood:	n/a	chr11:19137949-19137959 chr11:19137949-19137958 chr11:19137947-19137958
28	POLR2A	chr11:19137969-19138975	GM12878	blood:	n/a	n/a
29	MXI1	chr11:19137953-19138940	GM12878	blood:	n/a	n/a
30	STAT1	chr11:19137838-19138318	GM12878	blood:	n/a	n/a
31	POLR2A	chr11:19137899-19139406	GM12892	blood:	n/a	n/a
32	TBP	chr11:19137884-19138954	GM12878	blood:	n/a	n/a
33	CHD2	chr11:19137911-19139212	GM12878	blood:	n/a	chr11:19138056-19138066
34	EP300	chr11:19137808-19138262	GM12878	blood:	n/a	chr11:19138118-19138132 chr11:19138087-19138100
35	BHLHE40	chr11:19137951-19139296	GM12878	blood:	n/a	n/a
36	POLR2A	chr11:19138009-19139287	GM19099	blood:	n/a	n/a
37	REST	chr11:19137803-19138239	GM12878	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr11:19137492..19139036-chr11:19169967..19172250,2	MCF-7	breast:

Variant related genes	Relation type
ZDHHC13	TF binding region
ENSG00000177054	Chromatin interaction

Extended variants
information (count: 40 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:38)

rs_ID	r²[population]
rs10500841	0.94[CHB][hapmap];1.00[JPT][hapmap];0.97[ASN][1000 genomes]
rs10500842	0.94[CHB][hapmap];0.97[CHD][hapmap];1.00[JPT][hapmap];0.96[ASN][1000 genomes]
rs10741761	0.94[CHB][hapmap];0.91[CHD][hapmap];1.00[JPT][hapmap];0.96[ASN][1000 genomes]
rs10766528	0.96[ASN][1000 genomes]
rs10833064	0.94[CHB][hapmap];0.88[CHD][hapmap];1.00[JPT][hapmap];0.97[ASN][1000 genomes]
rs10833065	0.96[ASN][1000 genomes]
rs11025025	0.97[ASN][1000 genomes]
rs11025026	0.94[CHB][hapmap];0.97[CHD][hapmap];1.00[JPT][hapmap];0.97[ASN][1000 genomes]
rs11025037	0.94[CHB][hapmap];1.00[JPT][hapmap];0.94[ASN][1000 genomes]
rs11607797	0.94[CHB][hapmap];1.00[JPT][hapmap];0.92[ASN][1000 genomes]
rs12270581	0.94[CHB][hapmap];1.00[JPT][hapmap];0.94[ASN][1000 genomes]
rs1393954	0.88[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];0.93[ASN][1000 genomes]
rs1393955	0.94[CHB][hapmap];0.94[CHD][hapmap];1.00[JPT][hapmap];0.93[ASN][1000 genomes]
rs1503506	0.94[CHB][hapmap];1.00[JPT][hapmap];0.95[ASN][1000 genomes]
rs1503507	0.94[CHB][hapmap];1.00[JPT][hapmap];0.95[ASN][1000 genomes]
rs1875724	0.86[ASN][1000 genomes]
rs2042688	0.94[CHB][hapmap];0.94[CHD][hapmap];1.00[JPT][hapmap];0.95[ASN][1000 genomes]
rs2134622	0.87[CHB][hapmap];0.94[JPT][hapmap];0.87[ASN][1000 genomes]
rs2271001	0.94[CHB][hapmap];0.97[CHD][hapmap];1.00[JPT][hapmap];0.96[ASN][1000 genomes]
rs28891775	0.86[ASN][1000 genomes]
rs3758875	0.88[CHB][hapmap];0.89[JPT][hapmap];0.95[ASN][1000 genomes]
rs3802796	0.94[CHB][hapmap];1.00[JPT][hapmap];0.95[ASN][1000 genomes]
rs3802797	0.92[ASN][1000 genomes]
rs4326774	0.81[ASN][1000 genomes]
rs4757757	0.89[CHB][hapmap];1.00[JPT][hapmap];0.95[ASN][1000 genomes]
rs4757758	0.94[CHB][hapmap];0.97[CHD][hapmap];1.00[JPT][hapmap];0.96[ASN][1000 genomes]
rs4757759	0.96[ASN][1000 genomes]
rs4757760	0.94[CHB][hapmap];1.00[JPT][hapmap];0.96[ASN][1000 genomes]
rs59393175	0.96[ASN][1000 genomes]
rs7103110	0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7111105	0.94[CHB][hapmap];0.88[CHD][hapmap];1.00[JPT][hapmap];0.96[ASN][1000 genomes]
rs7120462	0.94[CHB][hapmap];1.00[JPT][hapmap];0.94[ASN][1000 genomes]
rs7129212	0.94[CHB][hapmap];0.97[CHD][hapmap];1.00[JPT][hapmap];0.96[ASN][1000 genomes]
rs7129326	0.96[ASN][1000 genomes]
rs7934179	0.87[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.82[LWK][hapmap];1.00[MEX][hapmap];0.90[MKK][hapmap];1.00[TSI][hapmap];0.96[YRI][hapmap];0.86[AFR][1000 genomes];0.85[AMR][1000 genomes];0.96[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs7945127	0.87[CEU][hapmap];0.87[TSI][hapmap];0.88[YRI][hapmap];0.90[EUR][1000 genomes]
rs7950603	0.94[CHB][hapmap];1.00[JPT][hapmap];0.95[ASN][1000 genomes]
rs7950788	0.96[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1040805	chr11:19037871-19892803	Enhancers Bivalent Enhancer Weak transcription Transcr. at gene 5' and 3' Flanking Active TSS Genic enhancers Flanking Bivalent TSS/Enh Active TSS Bivalent/Poised TSS Strong transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	25 gene(s)	inside rSNPs	diseases
2	nsv540957	chr11:19037871-19892803	Active TSS Weak transcription Flanking Bivalent TSS/Enh Enhancers Bivalent Enhancer Bivalent/Poised TSS Flanking Active TSS Genic enhancers Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	25 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs11025021	IGSF22	cis	parietal	SCAN

Chromatin state (count:91 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:19125000-19138600	Weak transcription	Gastric	stomach
2	chr11:19134200-19138200	Weak transcription	Pancreatic Islets	Pancreatic Islet
3	chr11:19137400-19138200	Enhancers	NHEK	skin
4	chr11:19137800-19138200	Enhancers	Primary monocytes fromperipheralblood	blood
5	chr11:19137800-19138200	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
6	chr11:19137800-19138200	Enhancers	Brain Germinal Matrix	brain
7	chr11:19137800-19138200	Enhancers	Right Atrium	heart
8	chr11:19137800-19138400	Flanking Active TSS	Primary neutrophils fromperipheralblood	blood
9	chr11:19137800-19138400	Flanking Active TSS	Primary T helper 17 cells PMA-I stimulated	--
10	chr11:19137800-19138400	Bivalent Enhancer	Placenta	Placenta
11	chr11:19137800-19138400	Enhancers	Left Ventricle	heart
12	chr11:19137800-19138400	Bivalent Enhancer	Lung	lung
13	chr11:19137800-19138400	Flanking Active TSS	GM12878-XiMat	blood
14	chr11:19137800-19138400	Flanking Bivalent TSS/Enh	HepG2	liver
15	chr11:19138000-19138200	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
16	chr11:19138000-19138200	Enhancers	HUES48 Cell Line	embryonic stem cell
17	chr11:19138000-19138200	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
18	chr11:19138000-19138200	Bivalent Enhancer	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
19	chr11:19138000-19138200	Enhancers	Breast Myoepithelial Primary Cells	Breast
20	chr11:19138000-19138200	Active TSS	Primary hematopoietic stem cells	blood
21	chr11:19138000-19138200	Flanking Active TSS	Primary hematopoietic stem cells short term culture	blood
22	chr11:19138000-19138200	Enhancers	Primary T helper naive cells from peripheral blood	blood
23	chr11:19138000-19138200	Enhancers	Primary T killer naive cells fromperipheralblood	blood
24	chr11:19138000-19138200	Flanking Active TSS	Primary T killer memory cells from peripheral blood	blood
25	chr11:19138000-19138200	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
26	chr11:19138000-19138200	Flanking Bivalent TSS/Enh	Foreskin Fibroblast Primary Cells skin01	Skin
27	chr11:19138000-19138200	Flanking Active TSS	Brain Angular Gyrus	brain
28	chr11:19138000-19138200	Active TSS	Brain Hippocampus Middle	brain
29	chr11:19138000-19138200	Flanking Active TSS	Brain Inferior Temporal Lobe	brain
30	chr11:19138000-19138200	Enhancers	Brain Substantia Nigra	brain
31	chr11:19138000-19138200	Flanking Active TSS	Colonic Mucosa	Colon
32	chr11:19138000-19138200	Flanking Bivalent TSS/Enh	Duodenum Smooth Muscle	Duodenum
33	chr11:19138000-19138200	Enhancers	Fetal Brain Female	brain
34	chr11:19138000-19138200	Bivalent Enhancer	Fetal Intestine Small	intestine
35	chr11:19138000-19138200	Bivalent Enhancer	Fetal Stomach	stomach
36	chr11:19138000-19138200	Enhancers	Fetal Thymus	thymus
37	chr11:19138000-19138200	Enhancers	Ovary	ovary
38	chr11:19138000-19138200	Enhancers	Right Ventricle	heart
39	chr11:19138000-19138200	Enhancers	Thymus	Thymus
40	chr11:19138000-19138200	Flanking Bivalent TSS/Enh	A549	lung
41	chr11:19138000-19138200	Enhancers	HMEC	breast
42	chr11:19138000-19138200	Enhancers	HUVEC	blood vessel
43	chr11:19138000-19138400	Flanking Active TSS	H1 Cell Line	embryonic stem cell
44	chr11:19138000-19138400	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
45	chr11:19138000-19138400	Enhancers	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
46	chr11:19138000-19138400	Flanking Active TSS	HUES6 Cell Line	embryonic stem cell
47	chr11:19138000-19138400	Flanking Active TSS	iPS-18 Cell Line	embryonic stem cell
48	chr11:19138000-19138400	Enhancers	iPS DF 6.9 Cell Line	embryonic stem cell
49	chr11:19138000-19138400	Flanking Active TSS	Primary B cells from peripheral blood	blood
50	chr11:19138000-19138400	Flanking Active TSS	Primary T cells fromperipheralblood	blood

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