Variant report

Variant	rs1393955
Chromosome Location	chr11:19183924-19183925
allele	A/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	EBF1	chr11:19183770-19183970	GM12878	blood:	n/a	n/a

Variant related genes	Relation type
ZDHHC13	TF binding region

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

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

rs_ID	r²[population]
rs10500841	1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[YRI][hapmap];0.97[ASN][1000 genomes]
rs10500842	0.88[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.88[MEX][hapmap];1.00[TSI][hapmap];0.96[YRI][hapmap];0.81[AFR][1000 genomes];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10741761	1.00[CHB][hapmap];0.91[CHD][hapmap];1.00[JPT][hapmap];0.97[ASN][1000 genomes]
rs10766528	0.97[ASN][1000 genomes]
rs10833064	1.00[CHB][hapmap];0.89[CHD][hapmap];1.00[JPT][hapmap];0.97[ASN][1000 genomes]
rs10833065	0.97[ASN][1000 genomes]
rs11025021	0.94[CHB][hapmap];0.94[CHD][hapmap];1.00[JPT][hapmap];0.93[ASN][1000 genomes]
rs11025025	0.97[ASN][1000 genomes]
rs11025026	1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[JPT][hapmap];0.83[LWK][hapmap];0.97[ASN][1000 genomes]
rs11025037	1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[YRI][hapmap];0.82[AFR][1000 genomes];0.99[ASN][1000 genomes]
rs11607797	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.83[AFR][1000 genomes];0.97[ASN][1000 genomes]
rs12270581	1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[YRI][hapmap];0.99[ASN][1000 genomes]
rs1393954	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[YRI][hapmap];0.98[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1503506	1.00[CHB][hapmap];1.00[JPT][hapmap];0.98[ASN][1000 genomes]
rs1503507	1.00[CHB][hapmap];1.00[JPT][hapmap];0.98[ASN][1000 genomes]
rs1875724	0.81[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2042688	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.98[ASN][1000 genomes]
rs2134622	0.94[CHB][hapmap];0.94[JPT][hapmap];0.89[ASN][1000 genomes]
rs2271001	1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[JPT][hapmap];0.97[ASN][1000 genomes]
rs28891775	0.88[ASN][1000 genomes]
rs3758875	1.00[CEU][hapmap];0.94[CHB][hapmap];0.89[JPT][hapmap];0.92[YRI][hapmap];0.92[AFR][1000 genomes];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs3802796	1.00[CHB][hapmap];1.00[JPT][hapmap];0.98[ASN][1000 genomes]
rs3802797	0.84[AFR][1000 genomes];0.99[ASN][1000 genomes]
rs4326774	0.83[ASN][1000 genomes]
rs4757757	0.94[CHB][hapmap];1.00[JPT][hapmap];0.98[ASN][1000 genomes]
rs4757758	1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[JPT][hapmap];0.82[YRI][hapmap];0.97[ASN][1000 genomes]
rs4757759	0.97[ASN][1000 genomes]
rs4757760	1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[YRI][hapmap];0.83[AFR][1000 genomes];0.97[ASN][1000 genomes]
rs59393175	0.87[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7103110	0.95[ASN][1000 genomes]
rs7111105	1.00[CHB][hapmap];0.88[CHD][hapmap];1.00[JPT][hapmap];0.97[ASN][1000 genomes]
rs7111919	0.82[AMR][1000 genomes]
rs7120462	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.83[AFR][1000 genomes];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7129212	1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[JPT][hapmap];0.97[ASN][1000 genomes]
rs7129326	0.97[ASN][1000 genomes]
rs7934179	0.94[CHB][hapmap];0.94[CHD][hapmap];1.00[JPT][hapmap];0.83[ASN][1000 genomes]
rs7950603	1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[ASN][1000 genomes]
rs7950788	0.97[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
rs1393955	IGSF22	cis	parietal	SCAN

Chromatin state (count:115 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:19140000-19186400	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
2	chr11:19140800-19186800	Weak transcription	Colonic Mucosa	Colon
3	chr11:19143400-19185800	Weak transcription	Muscle Satellite Cultured Cells	--
4	chr11:19143400-19186400	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
5	chr11:19143400-19201600	Weak transcription	Primary T killer memory cells from peripheral blood	blood
6	chr11:19143600-19197400	Weak transcription	Small Intestine	intestine
7	chr11:19153200-19186600	Weak transcription	Aorta	Aorta
8	chr11:19156600-19193200	Weak transcription	Fetal Stomach	stomach
9	chr11:19156800-19193800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
10	chr11:19156800-19194200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
11	chr11:19157200-19186200	Weak transcription	H9 Cell Line	embryonic stem cell
12	chr11:19161600-19194400	Weak transcription	HSMM	muscle
13	chr11:19162800-19203000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
14	chr11:19164000-19200400	Weak transcription	Fetal Brain Male	brain
15	chr11:19166200-19186200	Weak transcription	Brain Anterior Caudate	brain
16	chr11:19166400-19203000	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
17	chr11:19166800-19186400	Weak transcription	Brain Cingulate Gyrus	brain
18	chr11:19167000-19194200	Weak transcription	Fetal Kidney	kidney
19	chr11:19167400-19184800	Strong transcription	Primary neutrophils fromperipheralblood	blood
20	chr11:19167400-19186600	Weak transcription	Brain Inferior Temporal Lobe	brain
21	chr11:19167400-19194200	Weak transcription	Brain Hippocampus Middle	brain
22	chr11:19167600-19184200	Strong transcription	Monocytes-CD14+_RO01746	blood
23	chr11:19167800-19199400	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
24	chr11:19168000-19201600	Weak transcription	Rectal Smooth Muscle	rectum
25	chr11:19168400-19184400	Strong transcription	HUES48 Cell Line	embryonic stem cell
26	chr11:19168800-19185200	Weak transcription	Primary T helper naive cells from peripheral blood	blood
27	chr11:19169000-19186800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
28	chr11:19169000-19189000	Weak transcription	Fetal Intestine Small	intestine
29	chr11:19169000-19194600	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
30	chr11:19169200-19185200	Weak transcription	K562	blood
31	chr11:19169400-19197800	Weak transcription	Colon Smooth Muscle	Colon
32	chr11:19169400-19200400	Weak transcription	Brain Angular Gyrus	brain
33	chr11:19169600-19186200	Weak transcription	HepG2	liver
34	chr11:19170000-19186200	Weak transcription	Skeletal Muscle Female	skeletal muscle
35	chr11:19170000-19200200	Strong transcription	Primary B cells from cord blood	blood
36	chr11:19171000-19190200	Weak transcription	NH-A	brain
37	chr11:19171600-19188000	Weak transcription	HMEC	breast
38	chr11:19171600-19192400	Weak transcription	Placenta Amnion	Placenta Amnion
39	chr11:19172000-19185600	Weak transcription	Fetal Thymus	thymus
40	chr11:19172000-19186800	Weak transcription	Hela-S3	cervix
41	chr11:19172200-19208600	Weak transcription	Brain Substantia Nigra	brain
42	chr11:19172600-19186800	Weak transcription	NHDF-Ad	bronchial
43	chr11:19172800-19194200	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
44	chr11:19172800-19194400	Weak transcription	Brain Germinal Matrix	brain
45	chr11:19173400-19196800	Weak transcription	Pancreatic Islets	Pancreatic Islet
46	chr11:19174000-19186600	Weak transcription	Spleen	Spleen
47	chr11:19174000-19209000	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
48	chr11:19174600-19186200	Weak transcription	Osteobl	bone
49	chr11:19174800-19186200	Weak transcription	Lung	lung
50	chr11:19174800-19189800	Weak transcription	Fetal Muscle Trunk	muscle

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