Variant report

Variant	rs17725470
Chromosome Location	chr9:101988731-101988732
allele	C/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	POLR2A	chr9:101988438-101989128	IMR90	lung:	n/a	n/a
2	POLR2A	chr9:101988311-101989176	GM12892	blood:	n/a	n/a
3	POLR2A	chr9:101988449-101989211	GM12891	blood:	n/a	n/a
4	POLR2A	chr9:101988502-101988766	GM12891	blood:	n/a	n/a
5	POLR2A	chr9:101986152-101989214	K562	blood:	n/a	n/a
6	POLR2A	chr9:101988227-101989214	GM12878	blood:	n/a	n/a
7	POLR2A	chr9:101988107-101989262	GM12891	blood:	n/a	n/a
8	POLR2A	chr9:101987285-101988971	MCF10A-Er-Src	breast:	n/a	n/a
9	POLR2A	chr9:101988069-101988915	HepG2	liver:	n/a	n/a
10	POLR2A	chr9:101985979-101989299	HepG2	liver:	n/a	n/a
11	POLR2A	chr9:101987294-101989274	GM12878	blood:	n/a	n/a
12	POLR2A	chr9:101985892-101989278	HepG2	liver:	n/a	n/a
13	POLR2A	chr9:101988405-101989090	K562	blood:	n/a	n/a
14	POLR2A	chr9:101988340-101989008	GM12892	blood:	n/a	n/a
15	POLR2A	chr9:101988434-101989204	GM12892	blood:	n/a	n/a
16	POLR2A	chr9:101987138-101989410	GM12878	blood:	n/a	n/a
17	POLR2A	chr9:101988326-101989243	GM12891	blood:	n/a	n/a
18	POLR2A	chr9:101986192-101988857	MCF10A-Er-Src	breast:	n/a	n/a
19	POLR2A	chr9:101988705-101989220	K562	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr9:101987487..101991719-chr9:101992506..101995890,6	K562	blood:
2	chr9:101939993..101942784-chr9:101986476..101989411,2	K562	blood:

Variant related genes	Relation type
ALG2	TF binding region

Extended variants
information (count: 28 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:27)

rs_ID	r²[population]
rs10819642	0.84[EUR][1000 genomes]
rs11545137	0.92[AMR][1000 genomes];0.92[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs11788822	0.86[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs12002203	1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs12003123	0.87[ASN][1000 genomes]
rs12005715	1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs16918376	1.00[ASN][1000 genomes]
rs17725597	0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17725608	0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17725644	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17725679	1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs17725720	1.00[ASN][1000 genomes]
rs17787503	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17787533	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17787606	0.85[CEU][hapmap];1.00[CHB][hapmap];0.88[AMR][1000 genomes];0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28608552	1.00[ASN][1000 genomes]
rs35626507	0.92[AMR][1000 genomes];0.94[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs3780616	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs41274646	0.92[AMR][1000 genomes];0.94[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs41274648	0.89[AMR][1000 genomes];0.92[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs4265241	1.00[ASN][1000 genomes]
rs4554535	1.00[ASN][1000 genomes]
rs55676416	0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs58644416	1.00[ASN][1000 genomes]
rs73653775	1.00[ASN][1000 genomes]
rs7857426	0.87[ASN][1000 genomes]
rs7863354	1.00[CHB][hapmap];1.00[ASN][1000 genomes]

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

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv831666	chr9:101874985-102018690	Weak transcription Flanking Active TSS Enhancers Genic enhancers Strong transcription Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	20 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	chr9:101985200-101989600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
2	chr9:101985400-101990200	Weak transcription	H9 Cell Line	embryonic stem cell
3	chr9:101985400-101992000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
4	chr9:101985400-101998200	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
5	chr9:101985400-102004400	Weak transcription	Placenta Amnion	Placenta Amnion
6	chr9:101985600-101990200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
7	chr9:101985600-101990200	Weak transcription	Aorta	Aorta
8	chr9:101985600-101990200	Weak transcription	Colonic Mucosa	Colon
9	chr9:101985600-101990400	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
10	chr9:101986000-101988800	Strong transcription	HUES64 Cell Line	embryonic stem cell
11	chr9:101986000-101988800	Strong transcription	iPS-20b Cell Line	embryonic stem cell
12	chr9:101986000-101989000	Transcr. at gene 5' and 3'	GM12878-XiMat	blood
13	chr9:101986000-101993400	Strong transcription	iPS-18 Cell Line	embryonic stem cell
14	chr9:101986000-101995800	Strong transcription	HUES6 Cell Line	embryonic stem cell
15	chr9:101986000-101996400	Strong transcription	HUES48 Cell Line	embryonic stem cell
16	chr9:101986200-101989000	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
17	chr9:101986200-101989200	Enhancers	Skeletal Muscle Male	skeletal muscle
18	chr9:101986200-101989200	Genic enhancers	Skeletal Muscle Female	skeletal muscle
19	chr9:101986200-101990200	Weak transcription	Brain Angular Gyrus	brain
20	chr9:101986200-101994400	Strong transcription	A549	lung
21	chr9:101986200-101995600	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
22	chr9:101986200-101995800	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
23	chr9:101986200-101995800	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
24	chr9:101986200-101996000	Strong transcription	Fetal Muscle Trunk	muscle
25	chr9:101986200-101997200	Strong transcription	Placenta	Placenta
26	chr9:101986200-102003000	Strong transcription	Fetal Muscle Leg	muscle
27	chr9:101986400-101988800	Enhancers	Right Ventricle	heart
28	chr9:101986400-101993400	Strong transcription	Fetal Lung	lung
29	chr9:101986400-101993800	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
30	chr9:101986400-101995800	Strong transcription	Primary hematopoietic stem cells	blood
31	chr9:101986400-101995800	Strong transcription	Primary hematopoietic stem cells short term culture	blood
32	chr9:101986400-101996000	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
33	chr9:101986600-101988800	Strong transcription	H1 Cell Line	embryonic stem cell
34	chr9:101986600-101989000	Genic enhancers	Primary T helper cells PMA-I stimulated	--
35	chr9:101986600-101990200	Weak transcription	Primary T helper naive cells from peripheral blood	blood
36	chr9:101986600-101990200	Weak transcription	Brain Cingulate Gyrus	brain
37	chr9:101986600-101990200	Weak transcription	Hela-S3	cervix
38	chr9:101986600-101993000	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
39	chr9:101986600-101993800	Strong transcription	Cortex derived primary cultured neurospheres	brain
40	chr9:101986600-101995400	Strong transcription	NHEK	skin
41	chr9:101986600-101995800	Strong transcription	Fetal Intestine Large	intestine
42	chr9:101986600-101996000	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
43	chr9:101986600-101996000	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
44	chr9:101986800-101990200	Weak transcription	Rectal Smooth Muscle	rectum
45	chr9:101986800-101990400	Weak transcription	Colon Smooth Muscle	Colon
46	chr9:101986800-101994200	Strong transcription	Fetal Thymus	thymus
47	chr9:101986800-101995000	Strong transcription	NHDF-Ad	bronchial
48	chr9:101986800-101995800	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
49	chr9:101986800-101995800	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
50	chr9:101986800-101995800	Strong transcription	Rectal Mucosa Donor 29	rectum

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