Variant report

Variant	rs3758218
Chromosome Location	chr9:26948332-26948333
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	MAX	chr9:26945575-26948341	NB4	blood:	n/a	n/a
2	ZNF384	chr9:26948329-26948920	K562	blood:	n/a	n/a
3	POLR2A	chr9:26945741-26948332	H1-hESC	embryonic stem cell:	n/a	n/a
4	POLR2A	chr9:26946666-26948367	GM19099	blood:	n/a	n/a
5	GATA1	chr9:26945386-26948919	PBDE	blood:	n/a	chr9:26948836-26948857 chr9:26948839-26948850
6	MAFK	chr9:26947078-26948373	K562	blood:	n/a	chr9:26948146-26948160 chr9:26948148-26948159 chr9:26948147-26948158 chr9:26948148-26948159 chr9:26948147-26948163
7	MAFK	chr9:26948305-26948338	H1-hESC	embryonic stem cell:	n/a	n/a
8	POLR2A	chr9:26945574-26948342	GM12891	blood:	n/a	n/a
9	CHD1	chr9:26945731-26948413	H1-hESC	embryonic stem cell:	n/a	n/a
10	POLR2A	chr9:26946558-26948456	NB4	blood:	n/a	n/a
11	MXI1	chr9:26945295-26948354	SK-N-SH	brain:	n/a	n/a
12	STAT3	chr9:26948148-26948348	MCF10A-Er-Src	breast:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr9:26891080..26894676-chr9:26945695..26949113,9	K562	blood:
2	chr9:26891080..26895841-chr9:26945501..26948974,8	K562	blood:
3	chr9:26890485..26893190-chr9:26945159..26948755,7	MCF-7	breast:
4	chr9:26943098..26949574-chr9:26949927..26957421,13	K562	blood:
5	chr9:26890972..26893985-chr9:26945405..26948624,3	MCF-7	breast:
6	chr9:26945881..26949167-chr9:26974909..26976838,3	MCF-7	breast:
7	chr9:26947507..26949074-chr9:26950532..26952059,2	MCF-7	breast:
8	chr9:26891961..26892542-chr9:26947832..26948665,2	K562	blood:

Variant related genes	Relation type
PLAA	TF binding region
ENSG00000240306	Chromatin interaction
ENSG00000120159	Chromatin interaction
ENSG00000234676	Chromatin interaction
ENSG00000096872	Chromatin interaction

Extended variants
information (count: 88 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:86)

rs_ID	r²[population]
rs10738762	0.83[ASW][hapmap];0.95[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];0.84[GIH][hapmap];0.94[JPT][hapmap];0.94[MEX][hapmap];0.86[TSI][hapmap];0.86[AMR][1000 genomes];0.87[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs10757634	0.85[ASN][1000 genomes]
rs10757635	0.95[CEU][hapmap];0.94[CHB][hapmap];0.97[CHD][hapmap];0.86[GIH][hapmap];0.94[JPT][hapmap];0.94[MEX][hapmap];0.86[TSI][hapmap];0.86[AMR][1000 genomes];0.87[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs10757636	0.90[AMR][1000 genomes];0.89[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10812488	1.00[CEU][hapmap];0.88[CHB][hapmap];0.83[JPT][hapmap];0.82[EUR][1000 genomes]
rs10812502	0.84[ASN][1000 genomes]
rs10812503	1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.94[MEX][hapmap];0.97[TSI][hapmap];0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10812504	0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10812506	0.81[ASN][1000 genomes]
rs10812507	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[AMR][1000 genomes];0.95[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs10812508	0.83[AMR][1000 genomes];0.91[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs10812510	0.80[JPT][hapmap]
rs10812515	0.84[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs10812517	0.80[JPT][hapmap]
rs10812518	0.83[ASW][hapmap];0.88[CHB][hapmap];0.93[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.94[MEX][hapmap];0.90[MKK][hapmap];0.88[TSI][hapmap];0.84[EUR][1000 genomes]
rs10967586	0.84[JPT][hapmap]
rs10967621	0.83[ASN][1000 genomes]
rs10967622	0.83[ASN][1000 genomes]
rs10967623	0.83[ASN][1000 genomes]
rs10967627	0.80[JPT][hapmap];0.83[ASN][1000 genomes]
rs10967629	0.96[ASN][1000 genomes]
rs10967630	0.80[JPT][hapmap];0.83[ASN][1000 genomes]
rs10967632	0.96[ASN][1000 genomes]
rs10967633	0.80[JPT][hapmap];0.83[ASN][1000 genomes]
rs10967635	0.86[CHD][hapmap];0.80[JPT][hapmap];0.81[ASN][1000 genomes]
rs10967636	0.81[ASN][1000 genomes]
rs10967645	0.94[CHB][hapmap]
rs10967648	0.84[ASN][1000 genomes]
rs10967649	0.88[CHD][hapmap];0.84[JPT][hapmap]
rs10967652	1.00[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];0.87[AMR][1000 genomes];0.93[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs10967661	0.83[CHD][hapmap]
rs10967670	0.85[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs10967679	0.88[CHB][hapmap];1.00[JPT][hapmap]
rs11534184	0.83[ASN][1000 genomes]
rs11555693	0.81[ASN][1000 genomes]
rs11562224	0.81[ASN][1000 genomes]
rs12235490	0.81[ASN][1000 genomes]
rs12236850	0.86[CHD][hapmap]
rs12237867	0.84[ASN][1000 genomes]
rs12337896	0.94[ASW][hapmap];0.89[CHB][hapmap];0.97[CHD][hapmap];0.93[GIH][hapmap];0.84[LWK][hapmap];0.94[MEX][hapmap];0.97[MKK][hapmap];0.91[TSI][hapmap];0.87[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs1541144	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[AFR][1000 genomes];0.87[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1819539	0.89[CHB][hapmap];0.84[JPT][hapmap];0.85[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs2184438	0.94[ASN][1000 genomes]
rs2184439	0.92[ASN][1000 genomes]
rs2225720	0.89[CHB][hapmap];0.84[JPT][hapmap];0.85[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs3739544	0.80[JPT][hapmap];0.83[ASN][1000 genomes]
rs3739547	0.88[CHD][hapmap]
rs4413873	1.00[CEU][hapmap];0.94[CHB][hapmap];0.94[JPT][hapmap];0.81[AFR][1000 genomes];0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs4621911	0.88[CHB][hapmap];1.00[JPT][hapmap]
rs55827505	0.83[ASN][1000 genomes]
rs55870543	0.80[ASN][1000 genomes]
rs57450012	0.83[ASN][1000 genomes]
rs59159685	0.82[ASN][1000 genomes]
rs60841248	0.81[ASN][1000 genomes]
rs6475945	0.85[CEU][hapmap];0.94[JPT][hapmap]
rs6475947	0.85[CEU][hapmap]
rs6475954	0.88[CHB][hapmap];1.00[JPT][hapmap]
rs7018585	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[AMR][1000 genomes];0.93[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs7020010	1.00[CHB][hapmap];0.90[JPT][hapmap];0.96[ASN][1000 genomes]
rs7032756	0.83[TSI][hapmap]
rs7034115	0.96[ASN][1000 genomes]
rs7034478	0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7034888	0.81[ASN][1000 genomes]
rs7034899	0.81[ASN][1000 genomes]
rs7035447	0.86[CHD][hapmap];0.80[JPT][hapmap];0.81[ASN][1000 genomes]
rs7038218	0.89[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];0.82[ASN][1000 genomes]
rs7040505	0.83[CHB][hapmap];0.84[JPT][hapmap];0.87[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs7042133	0.83[ASN][1000 genomes]
rs7042447	0.85[CEU][hapmap];0.94[CHB][hapmap];0.94[JPT][hapmap];0.83[ASN][1000 genomes]
rs7849248	1.00[CHB][hapmap];0.95[CHD][hapmap];0.90[JPT][hapmap];0.91[ASN][1000 genomes]
rs7854191	0.85[EUR][1000 genomes]
rs7856462	0.85[CEU][hapmap];0.83[CHB][hapmap];0.94[JPT][hapmap]
rs7857447	0.80[JPT][hapmap]
rs7857669	0.88[CHB][hapmap];0.97[CHD][hapmap];0.91[GIH][hapmap];1.00[JPT][hapmap];0.88[MEX][hapmap]
rs7860542	0.81[CEU][hapmap];0.94[CHB][hapmap];0.94[JPT][hapmap];0.86[ASN][1000 genomes]
rs7863476	0.90[CEU][hapmap];0.85[CHD][hapmap];0.84[GIH][hapmap];0.94[JPT][hapmap];0.82[LWK][hapmap];0.94[MEX][hapmap];0.85[MKK][hapmap];0.80[TSI][hapmap];0.80[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs7865952	0.82[ASN][1000 genomes]
rs7868158	0.85[CEU][hapmap];0.94[JPT][hapmap];0.94[MEX][hapmap];0.80[TSI][hapmap]
rs7870787	0.94[CHB][hapmap];0.90[JPT][hapmap];0.94[ASN][1000 genomes]
rs7871668	0.88[CHB][hapmap];1.00[JPT][hapmap]
rs7872496	0.84[JPT][hapmap]
rs7873073	0.88[CHD][hapmap]
rs7874940	0.80[JPT][hapmap];0.83[ASN][1000 genomes]
rs7875068	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7875171	0.80[JPT][hapmap];0.83[ASN][1000 genomes]
rs9644870	0.88[CHD][hapmap]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv528614	chr9:26893662-27074233	Flanking Active TSS Strong transcription Weak transcription Enhancers Active TSS ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	17 gene(s)	inside rSNPs	diseases
2	nsv517269	chr9:26945976-27137242	Weak transcription Strong transcription Enhancers Active TSS Flanking Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	19 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs3758218	IFT74	Cis_1M	lymphoblastoid	RTeQTL
rs3758218	IFT74	cis	lymphoblastoid	seeQTL
rs3758218	IFT74	cis	parietal	SCAN
rs3758218	TEK	cis	parietal	SCAN

Chromatin state (count:65 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:26940000-26948400	Active TSS	GM12878-XiMat	blood
2	chr9:26944600-26948400	Active TSS	HUES6 Cell Line	embryonic stem cell
3	chr9:26945200-26948400	Active TSS	HUES48 Cell Line	embryonic stem cell
4	chr9:26945200-26948400	Active TSS	iPS-18 Cell Line	embryonic stem cell
5	chr9:26945600-26948400	Active TSS	ES-I3 Cell Line	embryonic stem cell
6	chr9:26945600-26948400	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
7	chr9:26945800-26948400	Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
8	chr9:26946000-26948400	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
9	chr9:26946000-26948400	Active TSS	A549	lung
10	chr9:26946200-26948400	Active TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
11	chr9:26946400-26948400	Active TSS	iPS-15b Cell Line	embryonic stem cell
12	chr9:26947200-26948400	Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
13	chr9:26947600-26955200	Weak transcription	Spleen	Spleen
14	chr9:26947800-26948400	Flanking Active TSS	Primary hematopoietic stem cells short term culture	blood
15	chr9:26947800-26948400	Flanking Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
16	chr9:26948000-26948400	Flanking Active TSS	H9 Derived Neuron Cultured Cells	ES cell derived
17	chr9:26948000-26948400	Flanking Active TSS	iPS-20b Cell Line	embryonic stem cell
18	chr9:26948000-26948400	Flanking Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
19	chr9:26948000-26948400	Enhancers	Fetal Intestine Small	intestine
20	chr9:26948000-26948400	Flanking Active TSS	Dnd41	blood
21	chr9:26948000-26948400	Flanking Active TSS	HepG2	liver
22	chr9:26948000-26948400	Flanking Active TSS	NHEK	skin
23	chr9:26948000-26949800	Weak transcription	Placenta	Placenta
24	chr9:26948000-26955200	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
25	chr9:26948200-26948400	Enhancers	Breast Myoepithelial Primary Cells	Breast
26	chr9:26948200-26948400	Enhancers	Primary T cells from cord blood	blood
27	chr9:26948200-26948400	Enhancers	Primary hematopoietic stem cells	blood
28	chr9:26948200-26948400	Enhancers	Primary T helper naive cells fromperipheralblood	blood
29	chr9:26948200-26948400	Enhancers	Primary T helper cells PMA-I stimulated	--
30	chr9:26948200-26948400	Active TSS	Primary T regulatory cells fromperipheralblood	blood
31	chr9:26948200-26948400	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
32	chr9:26948200-26948400	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
33	chr9:26948200-26948400	Enhancers	Muscle Satellite Cultured Cells	--
34	chr9:26948200-26948400	Enhancers	Cortex derived primary cultured neurospheres	brain
35	chr9:26948200-26948400	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
36	chr9:26948200-26948400	Enhancers	Liver	Liver
37	chr9:26948200-26948400	Enhancers	Fetal Adrenal Gland	Adrenal Gland
38	chr9:26948200-26948400	Enhancers	Fetal Brain Male	brain
39	chr9:26948200-26948400	Enhancers	Fetal Heart	heart
40	chr9:26948200-26948400	Enhancers	Fetal Intestine Large	intestine
41	chr9:26948200-26948400	Enhancers	Skeletal Muscle Male	skeletal muscle
42	chr9:26948200-26948400	Active TSS	HMEC	breast
43	chr9:26948200-26948600	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
44	chr9:26948200-26949400	Enhancers	Hela-S3	cervix
45	chr9:26948200-26949400	Weak transcription	K562	blood
46	chr9:26948200-26949400	Weak transcription	NH-A	brain
47	chr9:26948200-26949600	Weak transcription	Small Intestine	intestine
48	chr9:26948200-26953600	Weak transcription	Primary monocytes fromperipheralblood	blood
49	chr9:26948200-26953600	Weak transcription	Monocytes-CD14+_RO01746	blood
50	chr9:26948200-26954000	Weak transcription	Osteobl	bone

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