Variant report

Variant	rs3935011
Chromosome Location	chr1:246891269-246891270
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr1:246868796..246870534-chr1:246889935..246891767,2	K562	blood:
2	chr1:246862215..246864763-chr1:246888186..246891481,3	K562	blood:
3	chr1:246884666..246886259-chr1:246889523..246891914,2	MCF-7	breast:
4	chr1:246890586..246893581-chr1:246920009..246921935,2	MCF-7	breast:

Extended variants
information (count: 36 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:27)

rs_ID	r²[population]
rs10754532	0.83[ASW][hapmap];0.86[TSI][hapmap];0.80[EUR][1000 genomes]
rs12049149	0.89[ASN][1000 genomes]
rs12058428	0.83[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs12085823	0.87[ASN][1000 genomes]
rs12129386	0.85[YRI][hapmap]
rs12135184	0.85[CEU][hapmap];0.90[CHB][hapmap];1.00[JPT][hapmap];0.83[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs3795462	0.85[CEU][hapmap];0.95[CHB][hapmap];0.95[CHD][hapmap];0.86[GIH][hapmap];0.95[JPT][hapmap];0.91[MEX][hapmap];0.80[AMR][1000 genomes];0.80[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs3795465	0.95[CHD][hapmap];1.00[JPT][hapmap];0.82[MEX][hapmap];0.87[ASN][1000 genomes]
rs4244628	0.83[AMR][1000 genomes];0.80[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs4926441	0.83[AMR][1000 genomes];0.80[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs4926448	0.95[CHB][hapmap];0.98[CHD][hapmap];0.82[GIH][hapmap];1.00[JPT][hapmap];0.91[ASN][1000 genomes]
rs4926451	0.88[CEU][hapmap];0.90[CHB][hapmap];1.00[JPT][hapmap];0.83[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs4926453	0.85[CEU][hapmap];0.95[CHB][hapmap];0.95[CHD][hapmap];0.86[GIH][hapmap];1.00[JPT][hapmap];0.83[AMR][1000 genomes];0.80[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs6426328	0.90[CHB][hapmap];0.81[JPT][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6426331	0.97[AMR][1000 genomes];0.89[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6426332	0.95[CHB][hapmap];1.00[JPT][hapmap];0.84[AMR][1000 genomes];0.81[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs6426334	0.85[CEU][hapmap];0.91[CHB][hapmap];0.95[JPT][hapmap];0.80[AMR][1000 genomes];0.80[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs6664091	0.93[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[AMR][1000 genomes];0.86[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6686584	0.86[AMR][1000 genomes];0.81[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6689579	0.93[YRI][hapmap];0.86[AFR][1000 genomes]
rs7366187	0.85[LWK][hapmap];0.93[YRI][hapmap]
rs7513496	0.83[LWK][hapmap];0.90[YRI][hapmap]
rs7513803	0.85[CEU][hapmap];0.82[CHB][hapmap];0.88[CHD][hapmap];0.86[GIH][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap];0.80[AMR][1000 genomes];0.80[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7537149	0.82[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs7549965	0.85[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[AMR][1000 genomes];0.81[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7556120	0.84[AMR][1000 genomes];0.81[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs9426267	0.89[AMR][1000 genomes];0.96[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:9 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv949571	chr1:246688635-247240863	Active TSS Weak transcription Flanking Active TSS Strong transcription Enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	61 gene(s)	inside rSNPs	diseases
2	nsv873421	chr1:246818634-247044692	Weak transcription Strong transcription Bivalent/Poised TSS Bivalent Enhancer Enhancers Active TSS Flanking Active TSS ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	19 gene(s)	inside rSNPs	diseases
3	esv2762192	chr1:246823857-247069232	Weak transcription Strong transcription ZNF genes & repeats Enhancers Active TSS Genic enhancers Flanking Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	21 gene(s)	inside rSNPs	diseases
4	nsv1006271	chr1:246832606-247276182	Weak transcription Enhancers Strong transcription Flanking Active TSS Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Active TSS Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	52 gene(s)	inside rSNPs	diseases
5	nsv535416	chr1:246832606-247276182	Strong transcription ZNF genes & repeats Active TSS Enhancers Weak transcription Flanking Active TSS Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	52 gene(s)	inside rSNPs	diseases
6	nsv430413	chr1:246845971-246975015	Enhancers Weak transcription Strong transcription ZNF genes & repeats Flanking Active TSS Genic enhancers Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	16 gene(s)	inside rSNPs	diseases
7	nsv873422	chr1:246854862-247002638	Flanking Active TSS Enhancers Weak transcription ZNF genes & repeats Flanking Bivalent TSS/Enh Strong transcription Bivalent Enhancer Genic enhancers Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	16 gene(s)	inside rSNPs	diseases
8	nsv1011346	chr1:246868799-247133898	Weak transcription Active TSS Enhancers Strong transcription Flanking Active TSS ZNF genes & repeats Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	34 gene(s)	inside rSNPs	diseases
9	nsv870294	chr1:246877043-246927940	Weak transcription Strong transcription Enhancers Flanking Active TSS ZNF genes & repeats Active TSS Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs3935011	SCCPDH	cis	lymphoblastoid	seeQTL
rs3935011	RGS7	cis	cerebellum	SCAN
rs3935011	ZNF669	cis	parietal	SCAN

Chromatin state (count:112 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:246888400-246891600	Weak transcription	Esophagus	oesophagus
2	chr1:246888400-246893400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
3	chr1:246888400-246896000	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
4	chr1:246888400-246900000	Weak transcription	Primary T helper naive cells from peripheral blood	blood
5	chr1:246888400-246902000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
6	chr1:246888400-246903800	Weak transcription	Primary B cells from peripheral blood	blood
7	chr1:246888400-246946400	Weak transcription	Small Intestine	intestine
8	chr1:246888600-246891400	Weak transcription	Right Ventricle	heart
9	chr1:246888600-246893400	Weak transcription	Primary B cells from cord blood	blood
10	chr1:246888600-246901400	Weak transcription	Primary T killer memory cells from peripheral blood	blood
11	chr1:246888600-246945600	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
12	chr1:246888800-246891600	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
13	chr1:246888800-246892400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
14	chr1:246888800-246897400	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
15	chr1:246888800-246904000	Weak transcription	Primary T helper cells fromperipheralblood	blood
16	chr1:246888800-246904800	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
17	chr1:246889000-246893400	Weak transcription	Placenta Amnion	Placenta Amnion
18	chr1:246889000-246893400	Weak transcription	A549	lung
19	chr1:246889000-246929000	Weak transcription	Stomach Mucosa	stomach
20	chr1:246889200-246891600	Weak transcription	iPS-18 Cell Line	embryonic stem cell
21	chr1:246889200-246900600	Weak transcription	iPS-15b Cell Line	embryonic stem cell
22	chr1:246889400-246892200	Genic enhancers	Fetal Adrenal Gland	Adrenal Gland
23	chr1:246889400-246892400	Weak transcription	H9 Cell Line	embryonic stem cell
24	chr1:246889400-246893600	Weak transcription	Fetal Brain Male	brain
25	chr1:246889400-246894000	ZNF genes & repeats	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
26	chr1:246889600-246907000	Strong transcription	Fetal Muscle Trunk	muscle
27	chr1:246889800-246891600	Weak transcription	Primary T cells fromperipheralblood	blood
28	chr1:246889800-246891600	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
29	chr1:246889800-246892400	Strong transcription	HSMM	muscle
30	chr1:246890000-246891800	Strong transcription	Cortex derived primary cultured neurospheres	brain
31	chr1:246890000-246891800	Genic enhancers	HepG2	liver
32	chr1:246890000-246894600	ZNF genes & repeats	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
33	chr1:246890000-246895000	Strong transcription	Fetal Kidney	kidney
34	chr1:246890200-246891400	Genic enhancers	Placenta	Placenta
35	chr1:246890200-246891400	Strong transcription	NH-A	brain
36	chr1:246890200-246891600	Strong transcription	Brain Germinal Matrix	brain
37	chr1:246890200-246892000	Strong transcription	Primary hematopoietic stem cells	blood
38	chr1:246890200-246892200	Strong transcription	Thymus	Thymus
39	chr1:246890200-246892200	ZNF genes & repeats	K562	blood
40	chr1:246890200-246892400	ZNF genes & repeats	Dnd41	blood
41	chr1:246890200-246892400	ZNF genes & repeats	GM12878-XiMat	blood
42	chr1:246890200-246892600	ZNF genes & repeats	H9 Derived Neuron Cultured Cells	ES cell derived
43	chr1:246890200-246892600	ZNF genes & repeats	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
44	chr1:246890200-246894000	ZNF genes & repeats	HUES6 Cell Line	embryonic stem cell
45	chr1:246890200-246895000	Strong transcription	Rectal Mucosa Donor 29	rectum
46	chr1:246890200-246895000	Strong transcription	HUVEC	blood vessel
47	chr1:246890200-246895400	Strong transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
48	chr1:246890200-246896400	Strong transcription	Foreskin Fibroblast Primary Cells skin01	Skin
49	chr1:246890200-246896400	Strong transcription	Rectal Mucosa Donor 31	rectum
50	chr1:246890200-246897800	Strong transcription	Fetal Lung	lung

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