Variant report

Variant	rs2345019
Chromosome Location	chr22:28313988-28313989
allele	A/G
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	WRNIP1	chr22:28313849-28314729	GM12878	blood:	n/a	n/a
2	POLR2A	chr22:28313651-28316406	GM12891	blood:	n/a	n/a
3	MXI1	chr22:28313485-28316548	IMR90	lung:	n/a	n/a
4	POLR2A	chr22:28313949-28316312	MCF10A-Er-Src	breast:	n/a	n/a
5	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
6	POLR2A	chr22:28313255-28316499	MCF10A-Er-Src	breast:	n/a	n/a
7	MXI1	chr22:28312696-28316713	SK-N-SH	brain:	n/a	n/a
8	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: 22 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:20)

rs_ID	r²[population]
rs12160891	1.00[CEU][hapmap];0.87[JPT][hapmap];0.85[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs2073028	0.93[JPT][hapmap]
rs2143180	1.00[CEU][hapmap];0.87[JPT][hapmap];0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2267125	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[AFR][1000 genomes];0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28372773	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs5752651	0.95[AFR][1000 genomes];0.95[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs5752670	0.95[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs5762395	0.82[ASN][1000 genomes]
rs5762396	0.82[ASN][1000 genomes]
rs5762398	0.84[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs5762400	0.91[ASN][1000 genomes]
rs5762404	1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs5762410	1.00[CEU][hapmap];0.88[CHB][hapmap];1.00[JPT][hapmap];0.82[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs5762412	0.86[CHB][hapmap];1.00[JPT][hapmap];0.82[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs5762425	0.95[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs5762428	0.95[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs5997318	1.00[AFR][1000 genomes];0.90[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs6005674	0.93[CEU][hapmap];0.88[CHB][hapmap];1.00[JPT][hapmap];0.82[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs714743	1.00[CEU][hapmap];0.87[JPT][hapmap];0.95[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs73166732	0.95[AMR][1000 genomes];0.94[EUR][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

No data

Chromatin state (count:126 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr22:28298400-28314000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
2	chr22:28299200-28314000	Weak transcription	Spleen	Spleen
3	chr22:28306400-28314200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
4	chr22:28306400-28314400	Weak transcription	Esophagus	oesophagus
5	chr22:28308000-28314000	Weak transcription	Fetal Muscle Trunk	muscle
6	chr22:28310800-28314000	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
7	chr22:28311200-28316200	Active TSS	GM12878-XiMat	blood
8	chr22:28311400-28314400	Enhancers	Small Intestine	intestine
9	chr22:28311600-28314000	Enhancers	Primary T helper naive cells from peripheral blood	blood
10	chr22:28311800-28314000	Enhancers	Primary T helper cells fromperipheralblood	blood
11	chr22:28312000-28314000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
12	chr22:28312600-28314400	Enhancers	Sigmoid Colon	Sigmoid Colon
13	chr22:28312800-28314000	Enhancers	Fetal Intestine Small	intestine
14	chr22:28313000-28314000	Enhancers	Primary T regulatory cells fromperipheralblood	blood
15	chr22:28313000-28314200	Flanking Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
16	chr22:28313000-28317200	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
17	chr22:28313200-28314000	Enhancers	Primary T helper naive cells fromperipheralblood	blood
18	chr22:28313200-28314000	Enhancers	Primary T killer memory cells from peripheral blood	blood
19	chr22:28313200-28314000	Transcr. at gene 5' and 3'	A549	lung
20	chr22:28313200-28314000	Enhancers	Monocytes-CD14+_RO01746	blood
21	chr22:28313200-28314200	Enhancers	Primary T cells effector/memory enriched fromperipheralblood	blood
22	chr22:28313200-28314200	Enhancers	Brain Substantia Nigra	brain
23	chr22:28313200-28314200	Flanking Active TSS	Hela-S3	cervix
24	chr22:28313200-28314200	Transcr. at gene 5' and 3'	NHEK	skin
25	chr22:28313200-28314400	Flanking Active TSS	Muscle Satellite Cultured Cells	--
26	chr22:28313200-28314400	Enhancers	Stomach Mucosa	stomach
27	chr22:28313200-28314400	Flanking Active TSS	HUVEC	blood vessel
28	chr22:28313200-28314400	Flanking Active TSS	Osteobl	bone
29	chr22:28313200-28314600	Flanking Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
30	chr22:28313200-28314800	Flanking Active TSS	Primary T helper cells PMA-I stimulated	--
31	chr22:28313200-28316200	Active TSS	Aorta	Aorta
32	chr22:28313400-28314000	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
33	chr22:28313400-28314200	Enhancers	Primary T killer naive cells fromperipheralblood	blood
34	chr22:28313400-28314200	Flanking Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
35	chr22:28313400-28314200	Flanking Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
36	chr22:28313400-28314200	Flanking Active TSS	NH-A	brain
37	chr22:28313400-28314400	Flanking Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
38	chr22:28313400-28314400	Flanking Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
39	chr22:28313600-28314000	Genic enhancers	Primary T cells fromperipheralblood	blood
40	chr22:28313600-28314000	Enhancers	Brain Inferior Temporal Lobe	brain
41	chr22:28313600-28314000	Enhancers	Fetal Kidney	kidney
42	chr22:28313600-28314000	Enhancers	Rectal Mucosa Donor 31	rectum
43	chr22:28313600-28314200	Flanking Active TSS	ES-I3 Cell Line	embryonic stem cell
44	chr22:28313600-28314200	Flanking Active TSS	HUES48 Cell Line	embryonic stem cell
45	chr22:28313600-28314200	Enhancers	Primary neutrophils fromperipheralblood	blood
46	chr22:28313600-28314200	Enhancers	Primary B cells from peripheral blood	blood
47	chr22:28313600-28314200	Flanking Active TSS	Brain Germinal Matrix	brain
48	chr22:28313600-28314200	Flanking Active TSS	HepG2	liver
49	chr22:28313600-28314400	Flanking Active TSS	iPS-20b Cell Line	embryonic stem cell
50	chr22:28313600-28314400	Flanking Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain

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