Variant report

Variant	rs3780564
Chromosome Location	chr9:97883932-97883933
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:8)
CpG islands
(count:0)
Chromatin interactive
region (count:5)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:8 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	EP300	chr9:97882955-97884038	SK-N-SH	brain:	n/a	n/a
2	POLR2A	chr9:97883314-97884022	A549	lung:	n/a	n/a
3	CTCF	chr9:97883840-97883990	HPF	lung:	n/a	n/a
4	CTCF	chr9:97883840-97883990	BJ	skin:	n/a	n/a
5	CTCF	chr9:97883800-97883950	AG04449	skin:	n/a	n/a
6	CTCF	chr9:97883820-97883970	HFF	foreskin:	n/a	n/a
7	CTCF	chr9:97883880-97884030	BJ	skin:	n/a	n/a
8	CTCF	chr9:97883840-97883990	AG04450	lung:	n/a	n/a

No data

(count:5 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr9:97881903..97884694-chr9:97887705..97889925,3	MCF-7	breast:
2	chr9:97883295..97885445-chr9:97887654..97889773,2	MCF-7	breast:
3	chr9:97883098..97885141-chr9:97887172..97889883,3	K562	blood:
4	chr9:97854598..97856829-chr9:97883315..97884818,2	MCF-7	breast:
5	chr9:97872344..97876290-chr9:97882000..97885153,3	MCF-7	breast:

No data

Variant related genes	Relation type
ENSG00000223849	TF binding region
ENSG00000229065	Chromatin interaction
ENSG00000158169	Chromatin interaction

Extended variants
information (count: 67 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:63)

rs_ID	r²[population]
rs10115247	0.83[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs1011784	0.91[JPT][hapmap]
rs10739992	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.92[MEX][hapmap];0.95[TSI][hapmap];0.91[AMR][1000 genomes];0.92[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs10739993	0.84[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs10761374	0.86[JPT][hapmap]
rs10761377	0.89[AMR][1000 genomes];0.90[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs10821447	0.91[JPT][hapmap]
rs10821451	0.85[AMR][1000 genomes];0.90[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs10821453	0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs10821454	0.81[AFR][1000 genomes];0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs10821455	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.96[MEX][hapmap];1.00[MKK][hapmap];0.95[TSI][hapmap];0.95[YRI][hapmap];0.96[AMR][1000 genomes];0.92[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs10993490	0.93[AMR][1000 genomes];0.91[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs13295862	0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs17686583	0.92[AMR][1000 genomes];0.91[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1979022	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];0.92[MEX][hapmap];0.95[TSI][hapmap];0.88[AMR][1000 genomes];0.91[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2031599	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];0.93[TSI][hapmap];0.90[YRI][hapmap];0.85[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs2166402	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.96[MEX][hapmap];0.95[TSI][hapmap];0.89[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2282216	0.96[CEU][hapmap];0.88[MEX][hapmap];0.91[TSI][hapmap];0.82[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs2297596	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2297597	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];0.98[TSI][hapmap];0.95[YRI][hapmap];0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2404457	0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs3277	1.00[ASW][hapmap];1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.84[LWK][hapmap];0.91[MEX][hapmap];0.97[MKK][hapmap];0.98[TSI][hapmap];0.84[YRI][hapmap];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs34045846	0.93[AMR][1000 genomes];0.91[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs34532504	0.91[AMR][1000 genomes];0.90[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs3737142	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.96[MEX][hapmap];1.00[MKK][hapmap];0.95[TSI][hapmap];0.95[YRI][hapmap];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs3780561	0.80[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs3780562	0.86[AMR][1000 genomes];0.95[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs3780567	0.96[CEU][hapmap];0.82[CHB][hapmap];0.82[CHD][hapmap];0.81[GIH][hapmap];0.92[MEX][hapmap];0.95[TSI][hapmap];0.88[AMR][1000 genomes];0.98[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs3780568	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.96[MEX][hapmap];0.95[TSI][hapmap];0.92[AMR][1000 genomes];0.92[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs3824486	0.88[CEU][hapmap];0.87[MEX][hapmap];0.91[TSI][hapmap];0.91[EUR][1000 genomes]
rs3844341	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.81[YRI][hapmap];0.89[AMR][1000 genomes];0.89[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs3852402	1.00[ASW][hapmap];1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.96[MEX][hapmap];1.00[MKK][hapmap];0.95[TSI][hapmap];0.81[YRI][hapmap];0.89[AMR][1000 genomes];0.89[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs4647382	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.84[LWK][hapmap];0.96[MEX][hapmap];0.97[MKK][hapmap];0.95[TSI][hapmap];0.85[AMR][1000 genomes];0.82[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs4647443	0.88[AMR][1000 genomes];0.92[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs4647459	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[AMR][1000 genomes];0.92[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs4647462	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.96[MEX][hapmap];1.00[MKK][hapmap];0.95[TSI][hapmap];0.90[YRI][hapmap];0.95[AMR][1000 genomes];0.92[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs4647475	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[YRI][hapmap];0.95[AMR][1000 genomes];0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4647528	0.96[CEU][hapmap];0.95[CHB][hapmap];0.98[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.92[MEX][hapmap];0.93[TSI][hapmap];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4647529	0.88[AMR][1000 genomes];0.97[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs4647534	0.96[CEU][hapmap];0.80[CHD][hapmap];0.81[GIH][hapmap];0.92[MEX][hapmap];0.93[TSI][hapmap];0.85[AMR][1000 genomes];0.96[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs4647554	0.92[CEU][hapmap];0.91[CHB][hapmap];0.86[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];0.93[TSI][hapmap];0.92[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4647558	0.85[ASW][hapmap];0.96[CEU][hapmap];0.91[CHB][hapmap];0.86[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.83[MEX][hapmap];0.97[MKK][hapmap];0.91[TSI][hapmap];0.82[AFR][1000 genomes];0.82[AMR][1000 genomes];0.91[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4657	0.91[JPT][hapmap]
rs4743988	0.91[JPT][hapmap]
rs4744442	0.91[JPT][hapmap]
rs4744446	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[YRI][hapmap];0.95[AMR][1000 genomes];0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4744451	0.96[CEU][hapmap];0.82[CHD][hapmap];0.81[GIH][hapmap];0.92[MEX][hapmap];0.95[TSI][hapmap];0.88[EUR][1000 genomes]
rs6479601	0.91[AMR][1000 genomes];0.92[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7019043	0.82[EUR][1000 genomes]
rs7023007	0.90[AMR][1000 genomes];0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7027204	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.91[MEX][hapmap];0.97[MKK][hapmap];0.91[TSI][hapmap];0.85[YRI][hapmap];0.85[AMR][1000 genomes];0.81[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs7034538	0.82[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[AMR][1000 genomes];0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7042293	0.81[JPT][hapmap]
rs7042320	0.82[JPT][hapmap]
rs7046682	0.91[JPT][hapmap]
rs7850958	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7854570	1.00[ASW][hapmap];1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.96[MEX][hapmap];1.00[MKK][hapmap];0.95[TSI][hapmap];0.95[YRI][hapmap];0.95[AMR][1000 genomes];0.91[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7872648	0.88[AMR][1000 genomes];0.96[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs7874310	0.84[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs7874388	0.90[JPT][hapmap]
rs879492	0.91[AFR][1000 genomes];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs881791	0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs963774	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.96[MEX][hapmap];0.95[TSI][hapmap];0.90[AMR][1000 genomes];0.92[EUR][1000 genomes];0.93[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv933919	chr9:97619512-97919344	Weak transcription Transcr. at gene 5' and 3' Genic enhancers Enhancers Flanking Active TSS Strong transcription Flanking Bivalent TSS/Enh Active TSS Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	293 gene(s)	inside rSNPs	diseases
2	nsv1038523	chr9:97797032-97923774	Strong transcription Enhancers Weak transcription Flanking Active TSS Bivalent Enhancer Active TSS Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	274 gene(s)	inside rSNPs	diseases
3	nsv540175	chr9:97797032-97923774	Weak transcription Flanking Bivalent TSS/Enh Enhancers Strong transcription Bivalent/Poised TSS Genic enhancers Flanking Active TSS Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	274 gene(s)	inside rSNPs	diseases
4	nsv831656	chr9:97831551-97989980	Weak transcription Strong transcription Active TSS Genic enhancers Enhancers Bivalent Enhancer Flanking Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	274 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs3780564	SYK	cis	parietal	SCAN
rs3780564	LOC57653	cis	cerebellum	SCAN

Chromatin state (count:83 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:97844000-97898400	Weak transcription	Primary T helper cells fromperipheralblood	blood
2	chr9:97855400-97884800	Weak transcription	iPS-15b Cell Line	embryonic stem cell
3	chr9:97861200-97889800	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
4	chr9:97866000-97889600	Weak transcription	HUES48 Cell Line	embryonic stem cell
5	chr9:97866200-97889600	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
6	chr9:97866400-97886600	Weak transcription	H1 Cell Line	embryonic stem cell
7	chr9:97868600-97889400	Weak transcription	Fetal Heart	heart
8	chr9:97869800-97886400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
9	chr9:97869800-97889800	Weak transcription	Monocytes-CD14+_RO01746	blood
10	chr9:97870400-97889600	Weak transcription	Fetal Thymus	thymus
11	chr9:97870600-97889800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
12	chr9:97874600-97889400	Weak transcription	Colonic Mucosa	Colon
13	chr9:97875000-97889800	Weak transcription	Hela-S3	cervix
14	chr9:97875200-97889600	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
15	chr9:97875200-97889600	Weak transcription	HSMMtube	muscle
16	chr9:97875400-97889400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
17	chr9:97875400-97889400	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
18	chr9:97875400-97895400	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
19	chr9:97875400-97900400	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
20	chr9:97875600-97884600	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
21	chr9:97875600-97887800	Weak transcription	Placenta	Placenta
22	chr9:97875600-97889400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
23	chr9:97875600-97889600	Weak transcription	Primary hematopoietic stem cells	blood
24	chr9:97875600-97889600	Weak transcription	Adipose Nuclei	Adipose
25	chr9:97875600-97900000	Weak transcription	Spleen	Spleen
26	chr9:97875600-97906000	Weak transcription	Primary hematopoietic stem cells short term culture	blood
27	chr9:97875800-97888800	Weak transcription	Skeletal Muscle Male	skeletal muscle
28	chr9:97875800-97892200	Weak transcription	Rectal Mucosa Donor 29	rectum
29	chr9:97876800-97884800	Weak transcription	Thymus	Thymus
30	chr9:97876800-97889600	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
31	chr9:97877000-97886400	Weak transcription	Primary T cells from cord blood	blood
32	chr9:97877000-97886600	Weak transcription	Duodenum Mucosa	Duodenum
33	chr9:97877000-97889600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
34	chr9:97877000-97889600	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
35	chr9:97877000-97892000	Weak transcription	Gastric	stomach
36	chr9:97877000-97896400	Weak transcription	Sigmoid Colon	Sigmoid Colon
37	chr9:97877200-97884800	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
38	chr9:97877200-97885800	Weak transcription	Fetal Intestine Large	intestine
39	chr9:97877600-97884800	Weak transcription	Fetal Intestine Small	intestine
40	chr9:97879000-97889200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
41	chr9:97879200-97886400	Weak transcription	Lung	lung
42	chr9:97879200-97888800	Weak transcription	Skeletal Muscle Female	skeletal muscle
43	chr9:97879200-97889400	Weak transcription	HSMM	muscle
44	chr9:97879200-97889600	Weak transcription	Right Atrium	heart
45	chr9:97879400-97887000	Weak transcription	A549	lung
46	chr9:97879400-97889400	Weak transcription	Left Ventricle	heart
47	chr9:97879400-97889400	Weak transcription	Pancreas	Pancrea
48	chr9:97879600-97886800	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
49	chr9:97879600-97887000	Weak transcription	NHEK	skin
50	chr9:97879600-97887400	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links