Variant report

Variant	rs17239522
Chromosome Location	chr15:57588129-57588130
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	chr15:57588085-57588282	H1-hESC	embryonic stem cell:	n/a	n/a
2	POLR2A	chr15:57588124-57589126	K562	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr15:57582041..57585604-chr15:57586782..57591985,5	K562	blood:

Variant related genes	Relation type
LINC00926	TF binding region

Extended variants
information (count: 38 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:35)

rs_ID	r²[population]
rs10518910	1.00[CEU][hapmap]
rs1122890	1.00[CEU][hapmap];1.00[AFR][1000 genomes];0.85[AMR][1000 genomes]
rs12438324	1.00[CEU][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs12438331	1.00[AFR][1000 genomes];0.93[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs12438428	1.00[CEU][hapmap];0.85[AMR][1000 genomes]
rs12438782	1.00[CEU][hapmap];1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs12438954	1.00[AFR][1000 genomes]
rs12439017	0.85[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs12439374	1.00[CEU][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs12440036	0.86[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs12440699	1.00[CEU][hapmap]
rs12440729	0.85[AMR][1000 genomes]
rs12440878	1.00[CEU][hapmap];1.00[AFR][1000 genomes];0.88[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs12441107	1.00[AFR][1000 genomes];0.83[EUR][1000 genomes]
rs12441239	0.86[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs12442521	0.85[AMR][1000 genomes]
rs12442879	1.00[CEU][hapmap];0.86[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs12443006	0.86[EUR][1000 genomes]
rs12443076	1.00[CEU][hapmap];1.00[AFR][1000 genomes];0.86[EUR][1000 genomes]
rs12443085	0.86[AMR][1000 genomes]
rs12443097	1.00[AFR][1000 genomes];0.86[EUR][1000 genomes]
rs1462157	1.00[CEU][hapmap];0.85[AMR][1000 genomes]
rs17239313	0.82[AMR][1000 genomes]
rs17239543	1.00[AFR][1000 genomes]
rs17819994	1.00[CEU][hapmap];0.85[AMR][1000 genomes]
rs17820006	0.86[AMR][1000 genomes]
rs17820077	1.00[AFR][1000 genomes];0.86[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs17820119	1.00[CEU][hapmap];1.00[AFR][1000 genomes];0.93[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs17820131	1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2126398	1.00[CEU][hapmap]
rs2414499	1.00[CEU][hapmap];1.00[AFR][1000 genomes];0.85[AMR][1000 genomes]
rs2591050	0.85[AMR][1000 genomes]
rs4514619	1.00[CEU][hapmap]
rs8024992	0.87[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs8031866	1.00[CEU][hapmap]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1045611	chr15:57350965-58070807	Weak transcription Enhancers Strong transcription Genic enhancers Flanking Active TSS Active TSS ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	49 gene(s)	inside rSNPs	diseases
2	nsv833021	chr15:57495413-57751366	Enhancers Weak transcription Flanking Active TSS Strong transcription Genic enhancers Active TSS Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	38 gene(s)	inside rSNPs	diseases
3	nsv526342	chr15:57565859-57597280	Strong transcription Transcr. at gene 5' and 3' Genic enhancers Enhancers Weak transcription ZNF genes & repeats Active TSS Flanking Active TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	18 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:93 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:57537800-57598200	Weak transcription	Colonic Mucosa	Colon
2	chr15:57552200-57588600	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
3	chr15:57557600-57588600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
4	chr15:57566000-57591600	Weak transcription	Esophagus	oesophagus
5	chr15:57568000-57588400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
6	chr15:57568000-57590600	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
7	chr15:57568200-57591600	Weak transcription	Psoas Muscle	Psoas
8	chr15:57573800-57589000	Weak transcription	iPS-15b Cell Line	embryonic stem cell
9	chr15:57575000-57589200	Weak transcription	Skeletal Muscle Male	skeletal muscle
10	chr15:57578200-57589200	Weak transcription	Pancreas	Pancrea
11	chr15:57578600-57591600	Weak transcription	Spleen	Spleen
12	chr15:57578600-57598200	Weak transcription	Right Ventricle	heart
13	chr15:57578800-57588400	Weak transcription	H9 Cell Line	embryonic stem cell
14	chr15:57578800-57592800	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
15	chr15:57579200-57588600	Weak transcription	Brain Cingulate Gyrus	brain
16	chr15:57579200-57589600	Weak transcription	Rectal Smooth Muscle	rectum
17	chr15:57579200-57592800	Weak transcription	Small Intestine	intestine
18	chr15:57579600-57589200	Weak transcription	Brain Substantia Nigra	brain
19	chr15:57579600-57598200	Weak transcription	Skeletal Muscle Female	skeletal muscle
20	chr15:57579800-57588800	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
21	chr15:57579800-57589200	Weak transcription	Brain Anterior Caudate	brain
22	chr15:57579800-57590400	Weak transcription	Brain Angular Gyrus	brain
23	chr15:57579800-57595000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
24	chr15:57580000-57598400	Weak transcription	Primary T helper cells PMA-I stimulated	--
25	chr15:57580000-57598400	Weak transcription	Fetal Brain Male	brain
26	chr15:57580000-57598400	Weak transcription	NHEK	skin
27	chr15:57580200-57588600	Weak transcription	H1 Cell Line	embryonic stem cell
28	chr15:57580200-57588600	Weak transcription	HUES48 Cell Line	embryonic stem cell
29	chr15:57580200-57589000	Weak transcription	Fetal Brain Female	brain
30	chr15:57580200-57589200	Weak transcription	Sigmoid Colon	Sigmoid Colon
31	chr15:57580400-57588800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
32	chr15:57580400-57589200	Weak transcription	HMEC	breast
33	chr15:57580600-57594800	Weak transcription	HepG2	liver
34	chr15:57580800-57589000	Weak transcription	Rectal Mucosa Donor 29	rectum
35	chr15:57581000-57591600	Weak transcription	NHLF	lung
36	chr15:57581200-57591000	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
37	chr15:57581400-57590800	Weak transcription	Monocytes-CD14+_RO01746	blood
38	chr15:57581600-57595000	Weak transcription	iPS-18 Cell Line	embryonic stem cell
39	chr15:57581800-57590600	Weak transcription	NH-A	brain
40	chr15:57582200-57588600	Weak transcription	HUES64 Cell Line	embryonic stem cell
41	chr15:57583200-57591600	Weak transcription	Primary monocytes fromperipheralblood	blood
42	chr15:57583200-57591800	Weak transcription	Placenta	Placenta
43	chr15:57583400-57588600	Weak transcription	iPS-20b Cell Line	embryonic stem cell
44	chr15:57583400-57588600	Weak transcription	Gastric	stomach
45	chr15:57583400-57588800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
46	chr15:57583400-57589400	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
47	chr15:57583400-57590600	Weak transcription	Muscle Satellite Cultured Cells	--
48	chr15:57583400-57595000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
49	chr15:57583400-57598400	Weak transcription	Thymus	Thymus
50	chr15:57583600-57588400	Weak transcription	HUES6 Cell Line	embryonic stem cell

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