Variant report

Variant	rs7292046
Chromosome Location	chr22:28314113-28314114
allele	A/C
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	SIN3A	chr22:28314004-28316383	H1-hESC	embryonic stem cell:	n/a	n/a
2	WRNIP1	chr22:28313849-28314729	GM12878	blood:	n/a	n/a
3	POLR2A	chr22:28313651-28316406	GM12891	blood:	n/a	n/a
4	MXI1	chr22:28313485-28316548	IMR90	lung:	n/a	n/a
5	POLR2A	chr22:28313949-28316312	MCF10A-Er-Src	breast:	n/a	n/a
6	MYC	chr22:28313570-28315642	MCF10A-Er-Src	breast:	n/a	chr22:28314497-28314510 chr22:28314497-28314507 chr22:28314501-28314508 chr22:28314497-28314510 chr22:28314495-28314510 chr22:28315026-28315036 chr22:28314497-28314512 chr22:28314905-28314914 chr22:28314498-28314509 chr22:28314498-28314509 chr22:28314498-28314508 chr22:28314497-28314510 chr22:28314499-28314508
7	POLR2A	chr22:28313255-28316499	MCF10A-Er-Src	breast:	n/a	n/a
8	MXI1	chr22:28312696-28316713	SK-N-SH	brain:	n/a	n/a
9	MAZ	chr22:28313823-28316667	IMR90	lung:	n/a	chr22:28314497-28314510 chr22:28314501-28314508 chr22:28314497-28314510 chr22:28314495-28314510 chr22:28315026-28315036 chr22:28314497-28314512 chr22:28314905-28314914 chr22:28314498-28314509 chr22:28314498-28314509 chr22:28314498-28314508 chr22:28314497-28314510 chr22:28314499-28314508

Variant related genes	Relation type
TTC28-AS1	TF binding region

Extended variants
information (count: 12 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:10)

rs_ID	r²[population]
rs1016495	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.90[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];0.82[MKK][hapmap];0.95[TSI][hapmap];0.87[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs16985722	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.98[ASN][1000 genomes]
rs1807581	0.98[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2267127	0.89[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2267128	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs28529300	0.87[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs56156048	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs5762399	0.84[CEU][hapmap]
rs738454	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.90[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.95[TSI][hapmap];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9613545	0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];0.82[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	nsv1062877	chr22:28163507-28866350	Weak transcription Enhancers Genic enhancers Strong transcription Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh Flanking Active TSS Active TSS Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	18 gene(s)	inside rSNPs	diseases
2	nsv588878	chr22:28248840-28314113	Strong transcription Weak transcription Enhancers Flanking Active TSS Active TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	4 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs7292046	AP1B1	cis	cerebellum	SCAN
rs7292046	CYTSA	cis	parietal	SCAN
rs7292046	TTC28AS	cis	cerebellum	SCAN

Chromatin state (count:127 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr22:28306400-28314200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
2	chr22:28306400-28314400	Weak transcription	Esophagus	oesophagus
3	chr22:28311200-28316200	Active TSS	GM12878-XiMat	blood
4	chr22:28311400-28314400	Enhancers	Small Intestine	intestine
5	chr22:28312600-28314400	Enhancers	Sigmoid Colon	Sigmoid Colon
6	chr22:28313000-28314200	Flanking Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
7	chr22:28313000-28317200	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
8	chr22:28313200-28314200	Enhancers	Primary T cells effector/memory enriched fromperipheralblood	blood
9	chr22:28313200-28314200	Enhancers	Brain Substantia Nigra	brain
10	chr22:28313200-28314200	Flanking Active TSS	Hela-S3	cervix
11	chr22:28313200-28314200	Transcr. at gene 5' and 3'	NHEK	skin
12	chr22:28313200-28314400	Flanking Active TSS	Muscle Satellite Cultured Cells	--
13	chr22:28313200-28314400	Enhancers	Stomach Mucosa	stomach
14	chr22:28313200-28314400	Flanking Active TSS	HUVEC	blood vessel
15	chr22:28313200-28314400	Flanking Active TSS	Osteobl	bone
16	chr22:28313200-28314600	Flanking Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
17	chr22:28313200-28314800	Flanking Active TSS	Primary T helper cells PMA-I stimulated	--
18	chr22:28313200-28316200	Active TSS	Aorta	Aorta
19	chr22:28313400-28314200	Enhancers	Primary T killer naive cells fromperipheralblood	blood
20	chr22:28313400-28314200	Flanking Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
21	chr22:28313400-28314200	Flanking Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
22	chr22:28313400-28314200	Flanking Active TSS	NH-A	brain
23	chr22:28313400-28314400	Flanking Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
24	chr22:28313400-28314400	Flanking Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
25	chr22:28313600-28314200	Flanking Active TSS	ES-I3 Cell Line	embryonic stem cell
26	chr22:28313600-28314200	Flanking Active TSS	HUES48 Cell Line	embryonic stem cell
27	chr22:28313600-28314200	Enhancers	Primary neutrophils fromperipheralblood	blood
28	chr22:28313600-28314200	Enhancers	Primary B cells from peripheral blood	blood
29	chr22:28313600-28314200	Flanking Active TSS	Brain Germinal Matrix	brain
30	chr22:28313600-28314200	Flanking Active TSS	HepG2	liver
31	chr22:28313600-28314400	Flanking Active TSS	iPS-20b Cell Line	embryonic stem cell
32	chr22:28313600-28314400	Flanking Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
33	chr22:28313600-28314400	Flanking Active TSS	Stomach Smooth Muscle	stomach
34	chr22:28313600-28314600	Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
35	chr22:28313600-28314600	Transcr. at gene 5' and 3'	Dnd41	blood
36	chr22:28313600-28314800	Flanking Active TSS	H9 Derived Neuron Cultured Cells	ES cell derived
37	chr22:28313600-28314800	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
38	chr22:28313600-28315400	Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
39	chr22:28313600-28316200	Active TSS	Ovary	ovary
40	chr22:28313800-28314200	Flanking Active TSS	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
41	chr22:28313800-28314200	Flanking Active TSS	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
42	chr22:28313800-28314200	Flanking Active TSS	H9 Cell Line	embryonic stem cell
43	chr22:28313800-28314200	Flanking Active TSS	HUES6 Cell Line	embryonic stem cell
44	chr22:28313800-28314200	Flanking Active TSS	IMR90 fetal lung fibroblasts Cell Line	lung
45	chr22:28313800-28314200	Flanking Active TSS	Breast Myoepithelial Primary Cells	Breast
46	chr22:28313800-28314200	Enhancers	Primary monocytes fromperipheralblood	blood
47	chr22:28313800-28314200	Flanking Active TSS	Primary T helper 17 cells PMA-I stimulated	--
48	chr22:28313800-28314200	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
49	chr22:28313800-28314200	Flanking Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
50	chr22:28313800-28314200	Flanking Active TSS	Foreskin Melanocyte Primary Cells skin03	Skin

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