Variant report

Variant	rs7016139
Chromosome Location	chr8:8895470-8895471
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr8:8895456..8895966-chr8:8922957..8923902,2	MCF-7	breast:

Extended variants
information (count: 48 )
Associated
traits (count: 15 )

rSNPs within LD-proxies of this variant (count:42)

rs_ID	r²[population]
rs1045527	0.85[CEU][hapmap]
rs1045529	0.82[ASW][hapmap];0.96[CEU][hapmap];0.89[CHB][hapmap];0.95[CHD][hapmap];0.98[GIH][hapmap];0.94[JPT][hapmap];0.95[LWK][hapmap];0.85[MEX][hapmap];0.91[MKK][hapmap];0.95[TSI][hapmap];0.88[AFR][1000 genomes];0.98[AMR][1000 genomes];0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs11784393	0.89[CEU][hapmap];0.95[CHB][hapmap];0.83[JPT][hapmap];0.88[AFR][1000 genomes];0.97[AMR][1000 genomes];0.90[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs11785819	0.85[CEU][hapmap]
rs13252797	0.85[CEU][hapmap]
rs13271797	0.85[CEU][hapmap]
rs13272451	0.83[AFR][1000 genomes];0.89[AMR][1000 genomes];0.91[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs1562211	0.91[ASW][hapmap];0.89[CEU][hapmap];0.95[CHB][hapmap];0.95[CHD][hapmap];0.98[GIH][hapmap];0.88[JPT][hapmap];0.91[LWK][hapmap];0.85[MEX][hapmap];0.94[MKK][hapmap];0.98[TSI][hapmap];0.88[AFR][1000 genomes];0.97[AMR][1000 genomes];0.90[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2044387	0.84[CHB][hapmap];0.88[AMR][1000 genomes]
rs2044388	0.85[CHB][hapmap]
rs2288671	0.92[CEU][hapmap];0.90[CHD][hapmap];0.89[GIH][hapmap];0.85[MEX][hapmap];0.80[TSI][hapmap];0.85[EUR][1000 genomes]
rs2288673	0.81[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs2915251	0.92[CEU][hapmap];0.85[CHB][hapmap];0.84[EUR][1000 genomes]
rs2915252	0.90[CHD][hapmap]
rs2921378	0.91[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs2921383	0.88[AFR][1000 genomes];0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2953805	0.90[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs2953806	0.95[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs2956242	0.90[CHD][hapmap]
rs2956243	0.90[CHD][hapmap]
rs2956244	0.96[CEU][hapmap];0.94[CHB][hapmap];0.83[AFR][1000 genomes];0.96[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs2979247	1.00[CEU][hapmap];0.88[AFR][1000 genomes];0.81[EUR][1000 genomes]
rs2979253	0.95[AMR][1000 genomes]
rs2979256	0.92[CEU][hapmap];0.85[EUR][1000 genomes]
rs2979265	0.92[CEU][hapmap];0.80[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs3021416	0.92[AMR][1000 genomes]
rs4537305	0.81[AFR][1000 genomes];0.89[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs4841083	0.96[CEU][hapmap];0.85[EUR][1000 genomes]
rs4841084	0.96[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs4841085	0.88[JPT][hapmap]
rs6601280	0.82[CEU][hapmap]
rs6748	0.85[CEU][hapmap]
rs6987558	0.81[ASW][hapmap];0.92[CEU][hapmap];0.85[CHB][hapmap];0.92[CHD][hapmap];0.84[GIH][hapmap];0.85[LWK][hapmap];0.85[MEX][hapmap];0.81[MKK][hapmap];0.82[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs6993244	0.82[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs7005133	0.89[CEU][hapmap];0.94[CHB][hapmap];0.83[JPT][hapmap];0.88[AFR][1000 genomes];0.97[AMR][1000 genomes];0.90[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7017868	0.85[CEU][hapmap]
rs7813388	0.83[JPT][hapmap];0.84[ASN][1000 genomes]
rs7824140	0.84[ASN][1000 genomes]
rs7839585	0.85[CHB][hapmap];0.92[CHD][hapmap]
rs7853	0.91[AFR][1000 genomes];0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs9329175	0.82[CEU][hapmap]
rs9650616	0.85[CEU][hapmap]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv890331	chr8:8093240-8971100	Weak transcription Enhancers Active TSS Strong transcription Flanking Active TSS ZNF genes & repeats Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	43 gene(s)	inside rSNPs	diseases
2	nsv917117	chr8:8621658-9313799	Active TSS Weak transcription Enhancers Flanking Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Strong transcription Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	43 gene(s)	inside rSNPs	diseases
3	nsv831229	chr8:8751523-8926235	Enhancers Weak transcription Active TSS Strong transcription Flanking Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	17 gene(s)	inside rSNPs	diseases
4	nsv1022468	chr8:8857853-9209167	Enhancers Weak transcription Flanking Active TSS Strong transcription Active TSS Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	31 gene(s)	inside rSNPs	diseases
5	nsv539460	chr8:8857853-9209167	Enhancers Active TSS Weak transcription Strong transcription Flanking Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	31 gene(s)	inside rSNPs	diseases
6	nsv817373	chr8:8857854-9361049	Enhancers ZNF genes & repeats Weak transcription Active TSS Strong transcription Flanking Active TSS Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	36 gene(s)	inside rSNPs	diseases

mRNA abundance (count:15)

SNP	Gene	Cis/trans	Tissue	Source
rs7016139	TDH	cis	cerebellum	SCAN
rs7016139	PRSS55	cis	cerebellum	SCAN
rs7016139	FLJ10661	cis	cerebellum	SCAN
rs7016139	SGK223	cis	Thyroid	GTEx
rs7016139	C8orf5	Cis_chr	lymphoblastoid	RTeQTL
rs7016139	MFHAS1	cis	cerebellum	SCAN
rs7016139	RP11-62H7.2	cis	Stomach	GTEx
rs7016139	C8orf13	cis	multi-tissue	Pritchard
rs7016139	CTSB	cis	cerebellum	SCAN
rs7016139	BLK	Cis_chr	lymphoblastoid	RTeQTL
rs7016139	THEX1	Cis_1M	lymphoblastoid	RTeQTL
rs7016139	CLDN23	cis	multi-tissue	Pritchard
rs7016139	PPP1R3B	cis	cerebellum	SCAN
rs7016139	DEFB134	cis	cerebellum	SCAN
rs7016139	RP11-62H7.2	cis	Thyroid	GTEx

Chromatin state (count:64 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr8:8861400-8907000	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
2	chr8:8861800-8897800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
3	chr8:8861800-8915600	Weak transcription	Pancreas	Pancrea
4	chr8:8871200-8900000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
5	chr8:8875200-8897200	Weak transcription	Gastric	stomach
6	chr8:8875400-8897000	Weak transcription	Lung	lung
7	chr8:8875400-8901200	Weak transcription	Thymus	Thymus
8	chr8:8876400-8898000	Weak transcription	H9 Cell Line	embryonic stem cell
9	chr8:8877000-8895600	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
10	chr8:8877000-8903400	Weak transcription	Sigmoid Colon	Sigmoid Colon
11	chr8:8881000-8900400	Weak transcription	NH-A	brain
12	chr8:8882200-8896400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
13	chr8:8883200-8898400	Weak transcription	Fetal Kidney	kidney
14	chr8:8883600-8902400	Weak transcription	Adipose Nuclei	Adipose
15	chr8:8883800-8897800	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
16	chr8:8883800-8906000	Weak transcription	Primary T cells fromperipheralblood	blood
17	chr8:8884000-8900200	Weak transcription	Left Ventricle	heart
18	chr8:8884000-8906200	Weak transcription	Psoas Muscle	Psoas
19	chr8:8885800-8895800	Weak transcription	Fetal Lung	lung
20	chr8:8887000-8897400	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
21	chr8:8887800-8897600	Weak transcription	GM12878-XiMat	blood
22	chr8:8888400-8910800	Weak transcription	Hela-S3	cervix
23	chr8:8890400-8897400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
24	chr8:8890800-8895800	Weak transcription	H1 Cell Line	embryonic stem cell
25	chr8:8890800-8895800	Weak transcription	Skeletal Muscle Female	skeletal muscle
26	chr8:8890800-8897400	Weak transcription	Primary hematopoietic stem cells	blood
27	chr8:8890800-8897600	Weak transcription	Cortex derived primary cultured neurospheres	brain
28	chr8:8891000-8914800	Weak transcription	Fetal Stomach	stomach
29	chr8:8891200-8897000	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
30	chr8:8891200-8897600	Weak transcription	Primary monocytes fromperipheralblood	blood
31	chr8:8891200-8897800	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
32	chr8:8891200-8897800	Weak transcription	Fetal Muscle Leg	muscle
33	chr8:8891400-8897000	Weak transcription	Primary hematopoietic stem cells short term culture	blood
34	chr8:8891400-8897000	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
35	chr8:8891400-8897600	Weak transcription	Placenta	Placenta
36	chr8:8891400-8897600	Weak transcription	Monocytes-CD14+_RO01746	blood
37	chr8:8891400-8915200	Weak transcription	K562	blood
38	chr8:8892000-8901800	Weak transcription	Primary B cells from cord blood	blood
39	chr8:8892800-8897600	Weak transcription	Stomach Mucosa	stomach
40	chr8:8892800-8897800	Weak transcription	Placenta Amnion	Placenta Amnion
41	chr8:8893600-8898000	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
42	chr8:8893800-8913800	Weak transcription	Primary T cells from cord blood	blood
43	chr8:8894000-8897800	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
44	chr8:8894200-8895800	Enhancers	HepG2	liver
45	chr8:8894400-8896200	Enhancers	Fetal Heart	heart
46	chr8:8894600-8896200	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
47	chr8:8894600-8896200	Enhancers	HMEC	breast
48	chr8:8894600-8897600	Enhancers	ES-I3 Cell Line	embryonic stem cell
49	chr8:8894600-8897600	Enhancers	iPS-20b Cell Line	embryonic stem cell
50	chr8:8894600-8898000	Enhancers	HUES64 Cell Line	embryonic stem cell

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