Variant report

Variant	rs3780616
Chromosome Location	chr9:101987760-101987761
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	chr9:101986152-101989214	K562	blood:	n/a	n/a
2	POLR2A	chr9:101987285-101988971	MCF10A-Er-Src	breast:	n/a	n/a
3	POLR2A	chr9:101985979-101989299	HepG2	liver:	n/a	n/a
4	POLR2A	chr9:101987171-101987890	GM12892	blood:	n/a	n/a
5	POLR2A	chr9:101987294-101989274	GM12878	blood:	n/a	n/a
6	POLR2A	chr9:101985892-101989278	HepG2	liver:	n/a	n/a
7	POLR2A	chr9:101987506-101987890	GM12891	blood:	n/a	n/a
8	POLR2A	chr9:101987138-101989410	GM12878	blood:	n/a	n/a
9	POLR2A	chr9:101986192-101988857	MCF10A-Er-Src	breast:	n/a	n/a
10	POLR2A	chr9:101987286-101987907	GM12891	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr9:101987487..101991719-chr9:101992506..101995890,6	K562	blood:
2	chr9:101939993..101942784-chr9:101986476..101989411,2	K562	blood:
3	chr9:101939993..101941881-chr9:101986476..101988684,2	K562	blood:

Variant related genes	Relation type
ALG2	TF binding region

Extended variants
information (count: 29 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:28)

rs_ID	r²[population]
rs10819642	0.82[EUR][1000 genomes]
rs11545137	0.96[AMR][1000 genomes];0.94[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs11568762	1.00[ASW][hapmap]
rs11788822	0.89[AMR][1000 genomes];0.80[EUR][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]
rs17725470	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]
rs17725597	1.00[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17725608	1.00[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17725644	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.96[AMR][1000 genomes];0.96[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];0.96[AMR][1000 genomes];0.98[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];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17787606	0.85[CEU][hapmap];1.00[CHB][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];0.84[TSI][hapmap];0.92[AMR][1000 genomes];0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28608552	1.00[ASN][1000 genomes]
rs35626507	0.96[AMR][1000 genomes];0.92[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs41274646	0.96[AMR][1000 genomes];0.92[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs41274648	0.92[AMR][1000 genomes];0.94[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs4265241	1.00[ASN][1000 genomes]
rs4554535	1.00[ASN][1000 genomes]
rs55676416	0.83[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	chr9:101985200-101988400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
2	chr9:101985200-101989600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
3	chr9:101985400-101988000	Enhancers	Primary T helper naive cells fromperipheralblood	blood
4	chr9:101985400-101988400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
5	chr9:101985400-101990200	Weak transcription	H9 Cell Line	embryonic stem cell
6	chr9:101985400-101992000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
7	chr9:101985400-101998200	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
8	chr9:101985400-102004400	Weak transcription	Placenta Amnion	Placenta Amnion
9	chr9:101985600-101987800	Enhancers	Fetal Heart	heart
10	chr9:101985600-101988600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
11	chr9:101985600-101990200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
12	chr9:101985600-101990200	Weak transcription	Aorta	Aorta
13	chr9:101985600-101990200	Weak transcription	Colonic Mucosa	Colon
14	chr9:101985600-101990400	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
15	chr9:101986000-101988400	Strong transcription	ES-I3 Cell Line	embryonic stem cell
16	chr9:101986000-101988600	Genic enhancers	Liver	Liver
17	chr9:101986000-101988800	Strong transcription	HUES64 Cell Line	embryonic stem cell
18	chr9:101986000-101988800	Strong transcription	iPS-20b Cell Line	embryonic stem cell
19	chr9:101986000-101989000	Transcr. at gene 5' and 3'	GM12878-XiMat	blood
20	chr9:101986000-101993400	Strong transcription	iPS-18 Cell Line	embryonic stem cell
21	chr9:101986000-101995800	Strong transcription	HUES6 Cell Line	embryonic stem cell
22	chr9:101986000-101996400	Strong transcription	HUES48 Cell Line	embryonic stem cell
23	chr9:101986200-101987800	Enhancers	Psoas Muscle	Psoas
24	chr9:101986200-101987800	Genic enhancers	HUVEC	blood vessel
25	chr9:101986200-101988400	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
26	chr9:101986200-101989000	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
27	chr9:101986200-101989200	Enhancers	Skeletal Muscle Male	skeletal muscle
28	chr9:101986200-101989200	Genic enhancers	Skeletal Muscle Female	skeletal muscle
29	chr9:101986200-101990200	Weak transcription	Brain Angular Gyrus	brain
30	chr9:101986200-101994400	Strong transcription	A549	lung
31	chr9:101986200-101995600	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
32	chr9:101986200-101995800	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
33	chr9:101986200-101995800	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
34	chr9:101986200-101996000	Strong transcription	Fetal Muscle Trunk	muscle
35	chr9:101986200-101997200	Strong transcription	Placenta	Placenta
36	chr9:101986200-102003000	Strong transcription	Fetal Muscle Leg	muscle
37	chr9:101986400-101987800	Strong transcription	iPS-15b Cell Line	embryonic stem cell
38	chr9:101986400-101987800	Weak transcription	Stomach Mucosa	stomach
39	chr9:101986400-101988200	Weak transcription	Brain Hippocampus Middle	brain
40	chr9:101986400-101988400	Strong transcription	Primary neutrophils fromperipheralblood	blood
41	chr9:101986400-101988400	Weak transcription	Fetal Intestine Small	intestine
42	chr9:101986400-101988600	Genic enhancers	Duodenum Smooth Muscle	Duodenum
43	chr9:101986400-101988800	Enhancers	Right Ventricle	heart
44	chr9:101986400-101993400	Strong transcription	Fetal Lung	lung
45	chr9:101986400-101993800	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
46	chr9:101986400-101995800	Strong transcription	Primary hematopoietic stem cells	blood
47	chr9:101986400-101995800	Strong transcription	Primary hematopoietic stem cells short term culture	blood
48	chr9:101986400-101996000	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
49	chr9:101986600-101987800	Genic enhancers	Osteobl	bone
50	chr9:101986600-101988400	Weak transcription	Primary T killer memory cells from peripheral blood	blood

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