Variant report

Variant	rs3785635
Chromosome Location	chr17:15551871-15551872
allele	A/C
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	NR2F2	chr17:15551604-15552188	MCF-7	breast:	n/a	n/a
2	RCOR1	chr17:15551683-15552136	K562	blood:	n/a	n/a
3	FOS	chr17:15551692-15551908	MCF10A-Er-Src	breast:	n/a	n/a
4	SMC3	chr17:15551719-15552119	Hela-S3	cervix:	n/a	n/a
5	RCOR1	chr17:15551725-15552413	Hela-S3	cervix:	n/a	n/a
6	MYC	chr17:15551852-15552359	MCF10A-Er-Src	breast:	n/a	n/a
7	USF2	chr17:15551800-15551987	Hela-S3	cervix:	n/a	n/a
8	MYC	chr17:15551771-15551971	K562	blood:	n/a	n/a
9	ELK1	chr17:15551823-15552223	Hela-S3	cervix:	n/a	n/a
10	MAX	chr17:15551519-15552578	A549	lung:	n/a	n/a
11	EP300	chr17:15551634-15551892	K562	blood:	n/a	chr17:15551706-15551716
12	MAX	chr17:15551755-15552254	Hela-S3	cervix:	n/a	n/a
13	MAZ	chr17:15551770-15551970	K562	blood:	n/a	n/a
14	GTF2F1	chr17:15551647-15552262	Hela-S3	cervix:	n/a	n/a
15	STAT3	chr17:15551806-15552025	MCF10A-Er-Src	breast:	n/a	n/a
16	FOS	chr17:15551797-15551947	MCF10A-Er-Src	breast:	n/a	n/a

Variant related genes	Relation type
ENSG00000266261	TF binding region

Extended variants
information (count: 31 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:21)

rs_ID	r²[population]
rs10521309	1.00[CEU][hapmap];0.95[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.92[TSI][hapmap];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1476728	0.90[MEX][hapmap]
rs1503130	0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs16964250	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1875692	0.97[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34398696	0.94[AFR][1000 genomes];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs3760302	1.00[ASW][hapmap];0.85[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.95[LWK][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3760304	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3785642	0.81[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.95[GIH][hapmap];0.92[JPT][hapmap];1.00[MEX][hapmap];0.86[MKK][hapmap];0.84[TSI][hapmap]
rs4791634	0.82[AMR][1000 genomes];0.81[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs4792642	0.86[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.94[MEX][hapmap];0.91[TSI][hapmap];0.97[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4792644	0.90[MEX][hapmap]
rs58352721	0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs61402712	0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs62070421	0.80[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs62070424	0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62071661	0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7213245	0.93[YRI][hapmap]
rs7213827	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[MEX][hapmap];0.96[TSI][hapmap];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7223394	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[MEX][hapmap];1.00[TSI][hapmap];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs8066692	0.90[MEX][hapmap]

Variant overlapped rSNPs/rCNVs (count:10 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv492304	chr17:15043353-15611753	Active TSS Enhancers Weak transcription Flanking Active TSS Bivalent/Poised TSS Strong transcription Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	58 gene(s)	inside rSNPs	diseases
2	nsv916652	chr17:15093600-15856310	Strong transcription Weak transcription Enhancers Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	73 gene(s)	inside rSNPs	diseases
3	nsv1055677	chr17:15294011-15561130	Enhancers Flanking Active TSS Weak transcription Genic enhancers Active TSS Strong transcription Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	34 gene(s)	inside rSNPs	diseases
4	nsv1059056	chr17:15294011-15856861	Strong transcription Weak transcription Active TSS Enhancers Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	55 gene(s)	inside rSNPs	diseases
5	nsv1058286	chr17:15315763-15561130	Strong transcription Enhancers Weak transcription Flanking Active TSS Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	33 gene(s)	inside rSNPs	diseases
6	nsv543213	chr17:15315763-15561130	Weak transcription Enhancers Genic enhancers Strong transcription Active TSS Flanking Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	33 gene(s)	inside rSNPs	diseases
7	nsv457695	chr17:15447364-15611495	Active TSS Enhancers Strong transcription Flanking Active TSS Weak transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	26 gene(s)	inside rSNPs	diseases
8	nsv574462	chr17:15447364-15611495	Active TSS Flanking Active TSS Weak transcription Strong transcription Enhancers ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	26 gene(s)	inside rSNPs	diseases
9	nsv1067123	chr17:15482503-15557728	Enhancers Weak transcription Active TSS Strong transcription Flanking Active TSS Transcr. at gene 5' and 3' Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	diseases
10	nsv907704	chr17:15542933-15567196	Flanking Active TSS Weak transcription Active TSS Enhancers Strong transcription Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs3785635	TRIM16L,TRIM16	cis	brain	BrainEAC
rs3785635	SNORD49A	cis	lymphoblastoid	seeQTL

Chromatin state (count:99 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr17:15529600-15553600	Weak transcription	Primary hematopoietic stem cells short term culture	blood
2	chr17:15530200-15552000	Weak transcription	Rectal Mucosa Donor 31	rectum
3	chr17:15530200-15553800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
4	chr17:15530400-15553200	Weak transcription	Spleen	Spleen
5	chr17:15531800-15553600	Weak transcription	Fetal Kidney	kidney
6	chr17:15532400-15554000	Weak transcription	Ovary	ovary
7	chr17:15533400-15553000	Weak transcription	NHLF	lung
8	chr17:15534000-15553200	Weak transcription	Fetal Brain Female	brain
9	chr17:15534000-15553600	Weak transcription	Liver	Liver
10	chr17:15535400-15553000	Weak transcription	Colonic Mucosa	Colon
11	chr17:15544400-15554200	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
12	chr17:15544800-15553200	Weak transcription	Brain Angular Gyrus	brain
13	chr17:15549200-15553400	Weak transcription	Pancreas	Pancrea
14	chr17:15549200-15554000	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
15	chr17:15549400-15553000	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
16	chr17:15549400-15554000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
17	chr17:15549400-15554200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
18	chr17:15549600-15552000	Weak transcription	Brain Substantia Nigra	brain
19	chr17:15549600-15553000	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
20	chr17:15549600-15553200	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
21	chr17:15549600-15553200	Weak transcription	Fetal Lung	lung
22	chr17:15549600-15553200	Weak transcription	Rectal Smooth Muscle	rectum
23	chr17:15549600-15553400	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
24	chr17:15549600-15553400	Weak transcription	Brain Anterior Caudate	brain
25	chr17:15549600-15553400	Weak transcription	Brain Cingulate Gyrus	brain
26	chr17:15549600-15553600	Weak transcription	HUES64 Cell Line	embryonic stem cell
27	chr17:15549600-15554000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
28	chr17:15549600-15554000	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
29	chr17:15549600-15554000	Weak transcription	HUES6 Cell Line	embryonic stem cell
30	chr17:15549600-15554200	Weak transcription	HUES48 Cell Line	embryonic stem cell
31	chr17:15549600-15554200	Weak transcription	iPS-18 Cell Line	embryonic stem cell
32	chr17:15549600-15554400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
33	chr17:15549600-15554400	Weak transcription	H9 Cell Line	embryonic stem cell
34	chr17:15549600-15554400	Weak transcription	iPS-20b Cell Line	embryonic stem cell
35	chr17:15549600-15554800	Weak transcription	GM12878-XiMat	blood
36	chr17:15550000-15554600	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
37	chr17:15550200-15553200	Weak transcription	Breast Myoepithelial Primary Cells	Breast
38	chr17:15550200-15554200	Weak transcription	H1 Cell Line	embryonic stem cell
39	chr17:15551000-15554400	Active TSS	Esophagus	oesophagus
40	chr17:15551200-15553000	Enhancers	Lung	lung
41	chr17:15551600-15552000	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
42	chr17:15551600-15552000	Enhancers	Colon Smooth Muscle	Colon
43	chr17:15551600-15552200	Genic enhancers	Fetal Muscle Trunk	muscle
44	chr17:15551600-15552200	Genic enhancers	HMEC	breast
45	chr17:15551600-15552400	Genic enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
46	chr17:15551600-15552400	Transcr. at gene 5' and 3'	Foreskin Keratinocyte Primary Cells skin02	Skin
47	chr17:15551600-15552400	Flanking Active TSS	Duodenum Mucosa	Duodenum
48	chr17:15551600-15552400	Flanking Active TSS	Fetal Adrenal Gland	Adrenal Gland
49	chr17:15551600-15552400	Enhancers	K562	blood
50	chr17:15551600-15552400	Transcr. at gene 5' and 3'	NHEK	skin

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