Variant report

Variant	rs3780567
Chromosome Location	chr9:97898220-97898221
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	RCOR1	chr9:97898161-97898350	K562	blood:	n/a	n/a
2	RCOR1	chr9:97898072-97898408	K562	blood:	n/a	n/a
3	ZNF143	chr9:97898134-97898356	K562	blood:	n/a	n/a

Variant related genes	Relation type
FANCC	TF binding region

Extended variants
information (count: 75 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:71)

rs_ID	r²[population]
rs10115247	0.81[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1045276	0.81[JPT][hapmap]
rs10491560	0.81[JPT][hapmap]
rs10739992	1.00[CEU][hapmap];0.82[CHB][hapmap];0.82[CHD][hapmap];0.81[GIH][hapmap];1.00[MEX][hapmap];0.87[MKK][hapmap];1.00[TSI][hapmap];0.91[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs10739993	0.84[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs10761377	0.89[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs10821451	0.83[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs10821453	0.87[AMR][1000 genomes];0.98[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs10821454	0.85[AMR][1000 genomes];0.96[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs10821455	0.96[CEU][hapmap];0.82[CHB][hapmap];0.82[CHD][hapmap];0.81[GIH][hapmap];0.96[MEX][hapmap];1.00[TSI][hapmap];0.87[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs10993490	0.83[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs13295862	0.85[AMR][1000 genomes];0.98[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs171417	0.90[JPT][hapmap]
rs17686583	0.82[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs184818	0.90[JPT][hapmap]
rs1979022	1.00[CEU][hapmap];0.82[CHB][hapmap];0.82[CHD][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.88[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs2031599	0.96[CEU][hapmap];0.82[CHB][hapmap];0.82[CHD][hapmap];0.81[GIH][hapmap];0.92[MEX][hapmap];0.98[TSI][hapmap];0.81[EUR][1000 genomes]
rs2166402	1.00[CEU][hapmap];0.82[CHB][hapmap];0.82[CHD][hapmap];0.81[GIH][hapmap];0.96[MEX][hapmap];0.85[MKK][hapmap];1.00[TSI][hapmap];0.87[AMR][1000 genomes];0.99[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2282216	0.94[ASW][hapmap];1.00[CEU][hapmap];0.95[CHB][hapmap];0.93[CHD][hapmap];0.96[GIH][hapmap];0.95[JPT][hapmap];0.96[MEX][hapmap];0.85[MKK][hapmap];0.95[TSI][hapmap];0.86[YRI][hapmap];0.82[AFR][1000 genomes];0.90[AMR][1000 genomes];0.92[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2297596	1.00[CEU][hapmap];0.82[CHB][hapmap];0.88[AMR][1000 genomes];0.95[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs2297597	0.96[CEU][hapmap];0.82[CHB][hapmap];0.82[CHD][hapmap];0.81[GIH][hapmap];0.92[MEX][hapmap];0.98[TSI][hapmap];0.85[AMR][1000 genomes];0.95[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs2404457	0.83[AMR][1000 genomes];0.94[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs3277	0.96[CEU][hapmap];0.82[CHD][hapmap];0.81[GIH][hapmap];0.92[MEX][hapmap];1.00[TSI][hapmap];0.86[AMR][1000 genomes];0.99[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs34045846	0.89[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs34532504	0.83[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs356666	0.90[JPT][hapmap]
rs356673	0.90[JPT][hapmap]
rs356675	0.90[JPT][hapmap]
rs356677	0.90[JPT][hapmap]
rs356678	0.90[JPT][hapmap]
rs356680	0.90[JPT][hapmap]
rs356684	0.90[JPT][hapmap]
rs356689	0.90[JPT][hapmap]
rs3737142	0.96[CEU][hapmap];0.82[CHB][hapmap];0.82[CHD][hapmap];0.81[GIH][hapmap];0.96[MEX][hapmap];1.00[TSI][hapmap];0.87[AMR][1000 genomes];0.98[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs3780561	0.80[AFR][1000 genomes];0.90[AMR][1000 genomes];0.93[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs3780562	0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs3780564	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	1.00[CEU][hapmap];0.82[CHB][hapmap];0.82[CHD][hapmap];0.81[GIH][hapmap];0.96[MEX][hapmap];0.85[MKK][hapmap];1.00[TSI][hapmap];0.90[AMR][1000 genomes];0.94[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs3824486	0.94[ASW][hapmap];0.92[CEU][hapmap];0.95[CHB][hapmap];0.95[CHD][hapmap];0.96[GIH][hapmap];0.95[JPT][hapmap];0.96[MEX][hapmap];1.00[MKK][hapmap];0.95[TSI][hapmap];0.86[YRI][hapmap];0.88[AMR][1000 genomes];0.93[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs3844341	0.96[CEU][hapmap];0.81[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs3852402	0.96[CEU][hapmap];0.82[CHD][hapmap];0.81[GIH][hapmap];0.96[MEX][hapmap];1.00[TSI][hapmap];0.81[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs416792	0.90[JPT][hapmap]
rs4647376	0.86[CHB][hapmap];0.90[CHD][hapmap];0.95[JPT][hapmap];1.00[LWK][hapmap];0.81[MKK][hapmap];0.89[YRI][hapmap]
rs4647382	0.96[CEU][hapmap];0.82[CHB][hapmap];0.82[CHD][hapmap];0.81[GIH][hapmap];0.96[MEX][hapmap];1.00[TSI][hapmap];0.84[EUR][1000 genomes]
rs4647443	0.86[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs4647459	1.00[CEU][hapmap];0.82[CHB][hapmap];0.90[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs4647462	0.96[CEU][hapmap];0.82[CHB][hapmap];0.82[CHD][hapmap];0.81[GIH][hapmap];0.96[MEX][hapmap];1.00[TSI][hapmap];0.86[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs4647475	0.96[CEU][hapmap];0.82[CHB][hapmap];0.86[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs4647528	1.00[CEU][hapmap];0.81[GIH][hapmap];1.00[MEX][hapmap];0.83[MKK][hapmap];0.98[TSI][hapmap];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs4647529	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4647534	0.94[ASW][hapmap];1.00[CEU][hapmap];0.95[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.89[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];0.98[TSI][hapmap];0.89[YRI][hapmap];0.88[AFR][1000 genomes];0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4647554	0.96[CEU][hapmap];0.83[GIH][hapmap];0.87[MEX][hapmap];0.93[TSI][hapmap];0.93[EUR][1000 genomes]
rs4647558	0.92[CEU][hapmap];0.83[GIH][hapmap];0.83[MEX][hapmap];0.87[TSI][hapmap];0.92[EUR][1000 genomes]
rs4744446	0.96[CEU][hapmap];0.82[CHB][hapmap];0.86[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs4744451	1.00[ASW][hapmap];1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.95[LWK][hapmap];1.00[MEX][hapmap];0.87[MKK][hapmap];1.00[TSI][hapmap];0.96[YRI][hapmap];0.91[AMR][1000 genomes];0.89[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs540412	0.81[JPT][hapmap]
rs565293	0.90[JPT][hapmap]
rs6479601	0.91[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs7019043	0.85[AMR][1000 genomes];0.84[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs7023007	0.90[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs7027204	0.96[CEU][hapmap];0.82[CHB][hapmap];0.82[CHD][hapmap];0.83[MEX][hapmap];0.95[TSI][hapmap];0.83[EUR][1000 genomes]
rs7033633	0.81[JPT][hapmap]
rs7034538	0.86[CEU][hapmap];0.85[CHB][hapmap];0.90[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs7850958	1.00[CEU][hapmap];0.82[CHB][hapmap];0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs7854570	0.96[CEU][hapmap];0.82[CHD][hapmap];0.81[GIH][hapmap];0.96[MEX][hapmap];1.00[TSI][hapmap];0.86[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs7872648	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7874310	0.84[AFR][1000 genomes];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs879492	0.83[AMR][1000 genomes];0.94[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs881791	0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs944934	0.81[JPT][hapmap]
rs963774	0.96[CEU][hapmap];0.82[CHB][hapmap];0.82[CHD][hapmap];0.81[GIH][hapmap];0.96[MEX][hapmap];1.00[TSI][hapmap];0.88[AMR][1000 genomes];0.93[EUR][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
rs3780567	SYK	cis	parietal	SCAN
rs3780567	LOC57653	cis	cerebellum	SCAN

Chromatin state (count:63 , 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	chr9:97875400-97900400	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
3	chr9:97875600-97900000	Weak transcription	Spleen	Spleen
4	chr9:97875600-97906000	Weak transcription	Primary hematopoietic stem cells short term culture	blood
5	chr9:97887400-97916400	Weak transcription	Thymus	Thymus
6	chr9:97888000-97900000	Weak transcription	Primary T cells from cord blood	blood
7	chr9:97890000-97898600	Weak transcription	Left Ventricle	heart
8	chr9:97890000-97898600	Weak transcription	Right Atrium	heart
9	chr9:97890000-97900000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
10	chr9:97890000-97906600	Weak transcription	Right Ventricle	heart
11	chr9:97890000-97919600	Weak transcription	Hela-S3	cervix
12	chr9:97890000-97928000	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
13	chr9:97890200-97898400	Weak transcription	Primary monocytes fromperipheralblood	blood
14	chr9:97890200-97900400	Weak transcription	Esophagus	oesophagus
15	chr9:97890400-97902800	Weak transcription	Muscle Satellite Cultured Cells	--
16	chr9:97890600-97900000	Weak transcription	Breast Myoepithelial Primary Cells	Breast
17	chr9:97890600-97900000	Weak transcription	Rectal Smooth Muscle	rectum
18	chr9:97892600-97900400	Weak transcription	Brain Germinal Matrix	brain
19	chr9:97893200-97901600	Weak transcription	Pancreatic Islets	Pancreatic Islet
20	chr9:97893800-97904800	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
21	chr9:97893800-97905400	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
22	chr9:97893800-97905800	Weak transcription	Osteobl	bone
23	chr9:97893800-97906400	Weak transcription	Ovary	ovary
24	chr9:97893800-97912600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
25	chr9:97893800-97918800	Weak transcription	Gastric	stomach
26	chr9:97893800-97940400	Weak transcription	Pancreas	Pancrea
27	chr9:97894200-97906200	Weak transcription	Colon Smooth Muscle	Colon
28	chr9:97894200-97909800	Weak transcription	A549	lung
29	chr9:97894200-97925600	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
30	chr9:97894600-97899400	Weak transcription	Stomach Smooth Muscle	stomach
31	chr9:97894600-97905000	Weak transcription	Fetal Lung	lung
32	chr9:97894800-97905400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
33	chr9:97895000-97900200	Weak transcription	HUES48 Cell Line	embryonic stem cell
34	chr9:97895600-97899600	Weak transcription	Skeletal Muscle Male	skeletal muscle
35	chr9:97895600-97901000	Weak transcription	H1 Cell Line	embryonic stem cell
36	chr9:97895800-97899400	Weak transcription	Skeletal Muscle Female	skeletal muscle
37	chr9:97895800-97900600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
38	chr9:97895800-97903000	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
39	chr9:97896000-97900200	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
40	chr9:97896000-97900600	Weak transcription	iPS-18 Cell Line	embryonic stem cell
41	chr9:97896000-97909800	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
42	chr9:97896400-97910200	Weak transcription	Small Intestine	intestine
43	chr9:97896400-97918400	Weak transcription	Duodenum Smooth Muscle	Duodenum
44	chr9:97896400-97920000	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
45	chr9:97896600-97905600	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
46	chr9:97896800-97900600	Weak transcription	HUES6 Cell Line	embryonic stem cell
47	chr9:97897000-97910000	Weak transcription	Cortex derived primary cultured neurospheres	brain
48	chr9:97897200-97899400	Weak transcription	Fetal Intestine Small	intestine
49	chr9:97897200-97900000	Weak transcription	Fetal Stomach	stomach
50	chr9:97897200-97900000	Weak transcription	Lung	lung

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links