Variant report

Variant	rs39506
Chromosome Location	chr8:90792127-90792128
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr8:90788699..90792573-chr8:90996217..90998925,4	MCF-7	breast:
2	chr8:90790967..90797055-chr8:90994383..90998113,5	MCF-7	breast:
3	chr8:90768498..90770140-chr8:90791646..90793949,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000104312	Chromatin interaction
ENSG00000251136	Chromatin interaction
ENSG00000104320	Chromatin interaction

Extended variants
information (count: 86 )
Associated
traits (count: 6 )

rSNPs within LD-proxies of this variant (count:81)

rs_ID	r²[population]
rs1003843	1.00[ASW][hapmap];1.00[CEU][hapmap];0.98[GIH][hapmap];0.91[MEX][hapmap];0.98[TSI][hapmap];0.95[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs10095743	0.97[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs10112852	1.00[CEU][hapmap];0.97[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs13252013	0.85[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs13252917	0.97[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs13259882	0.97[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs13279023	0.85[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs1397308	0.81[CEU][hapmap];0.84[MEX][hapmap]
rs218895	0.80[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs218899	0.96[CEU][hapmap];0.80[GIH][hapmap];1.00[MEX][hapmap];0.83[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs218900	0.96[CEU][hapmap];0.83[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs218901	0.96[CEU][hapmap];0.83[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs218902	1.00[CEU][hapmap];0.84[GIH][hapmap];0.96[MEX][hapmap];0.83[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs218903	0.96[CEU][hapmap];0.84[GIH][hapmap]
rs218905	0.92[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs218907	1.00[CEU][hapmap];0.96[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs218908	1.00[CEU][hapmap];0.96[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs218909	0.96[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs218910	0.82[EUR][1000 genomes]
rs218913	1.00[CEU][hapmap];0.98[GIH][hapmap];0.92[MEX][hapmap];0.98[TSI][hapmap];0.96[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs218914	0.96[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs218925	0.98[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs218929	1.00[CEU][hapmap];0.98[GIH][hapmap];0.92[MEX][hapmap];0.98[TSI][hapmap];0.98[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs218932	0.96[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs218934	0.96[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs218936	0.97[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs218944	0.80[EUR][1000 genomes]
rs218946	0.81[EUR][1000 genomes]
rs218947	0.81[EUR][1000 genomes]
rs2644021	0.97[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs2644033	0.98[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs2735870	0.96[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs2735871	0.96[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs2735873	0.98[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs2735878	0.97[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs2735882	0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs370282	0.88[AMR][1000 genomes]
rs383592	0.89[GIH][hapmap];0.86[MEX][hapmap];0.93[TSI][hapmap];0.84[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs385524	0.98[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs394108	0.82[AMR][1000 genomes]
rs39499	1.00[CEU][hapmap];0.86[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs39500	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs39503	1.00[ASW][hapmap];0.88[CEU][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs39504	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs39505	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs39509	1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[AFR][1000 genomes];0.97[AMR][1000 genomes];0.88[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs39761	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs39767	0.82[AMR][1000 genomes]
rs400411	0.91[AFR][1000 genomes];0.97[AMR][1000 genomes];0.87[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs40246	0.85[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs40247	0.86[CHB][hapmap];1.00[JPT][hapmap];0.85[AFR][1000 genomes];0.96[AMR][1000 genomes];0.87[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs402886	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs40382	0.87[AMR][1000 genomes]
rs40452	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs40453	1.00[ASW][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap];0.93[TSI][hapmap];0.97[AMR][1000 genomes];0.87[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs40459	0.81[CEU][hapmap];0.89[GIH][hapmap]
rs40544	0.96[CEU][hapmap];0.87[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs40545	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs40547	0.85[AMR][1000 genomes]
rs405734	0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs40636	0.89[AMR][1000 genomes]
rs40638	0.84[GIH][hapmap];0.83[MEX][hapmap];0.88[AMR][1000 genomes]
rs410663	0.81[CEU][hapmap]
rs411279	1.00[ASW][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.83[LWK][hapmap];0.96[MEX][hapmap];1.00[MKK][hapmap];0.93[TSI][hapmap];0.91[AFR][1000 genomes];0.96[AMR][1000 genomes];0.87[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs416324	1.00[ASW][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.83[LWK][hapmap];0.96[MEX][hapmap];1.00[MKK][hapmap];0.93[TSI][hapmap];0.94[AFR][1000 genomes];0.97[AMR][1000 genomes];0.86[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs419754	0.98[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs42346	0.84[GIH][hapmap];0.83[MEX][hapmap];0.89[AMR][1000 genomes]
rs42481	0.81[CEU][hapmap];0.89[GIH][hapmap]
rs42490	1.00[CEU][hapmap];0.93[GIH][hapmap];0.96[MEX][hapmap];1.00[TSI][hapmap];0.87[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs431264	0.91[CEU][hapmap];0.86[GIH][hapmap];0.92[TSI][hapmap];0.87[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs43134	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.83[LWK][hapmap];1.00[MEX][hapmap];0.83[MKK][hapmap];1.00[TSI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs43135	0.86[AMR][1000 genomes]
rs43225	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs447618	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.96[MEX][hapmap];1.00[TSI][hapmap];0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs454441	0.85[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs465	0.88[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs51331	0.88[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs6470366	0.97[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs67143546	0.83[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs6992985	0.97[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs6993133	0.97[AMR][1000 genomes];0.94[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv891180	chr8:90697810-90802491	Enhancers Active TSS Flanking Active TSS Weak transcription Strong transcription 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	45 gene(s)	inside rSNPs	diseases
2	nsv933502	chr8:90702392-91049100	Weak transcription Enhancers Active TSS Strong transcription Genic enhancers Flanking Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	62 gene(s)	inside rSNPs	diseases
3	nsv934114	chr8:90720182-90999106	Active TSS Weak transcription Enhancers Flanking Active TSS Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	58 gene(s)	inside rSNPs	diseases
4	nsv891181	chr8:90737258-90819998	Strong transcription Flanking Active TSS Enhancers Active TSS Weak transcription ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	36 gene(s)	inside rSNPs	diseases
5	nsv891182	chr8:90785685-90888786	Flanking Active TSS Genic enhancers Weak transcription Enhancers Strong transcription ZNF genes & repeats Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases

mRNA abundance (count:6)

SNP	Gene	Cis/trans	Tissue	Source
rs39506	RP11-37B2.1	cis	Adipose Subcutaneous	GTEx
rs39506	RP11-37B2.1	cis	Nerve Tibial	GTEx
rs39506	RP11-37B2.1	cis	Artery Tibial	GTEx
rs39506	RP11-37B2.1	cis	Skin Sun Exposed Lower leg	GTEx
rs39506	RIPK2	cis	cerebellum	SCAN
rs39506	RP11-37B2.1	cis	Thyroid	GTEx

Chromatin state (count:116 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr8:90771000-90797000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
2	chr8:90771600-90803800	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
3	chr8:90771800-90805000	Weak transcription	Esophagus	oesophagus
4	chr8:90772000-90796800	Weak transcription	Lung	lung
5	chr8:90772000-90797000	Weak transcription	Ovary	ovary
6	chr8:90772200-90802000	Weak transcription	Colonic Mucosa	Colon
7	chr8:90772200-90802400	Weak transcription	Spleen	Spleen
8	chr8:90772200-90805200	Weak transcription	Fetal Brain Male	brain
9	chr8:90772200-90807200	Weak transcription	Pancreas	Pancrea
10	chr8:90772200-90809400	Weak transcription	Small Intestine	intestine
11	chr8:90772400-90802200	Weak transcription	Colon Smooth Muscle	Colon
12	chr8:90773000-90806800	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
13	chr8:90773000-90812400	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
14	chr8:90773200-90799000	Weak transcription	H1 Cell Line	embryonic stem cell
15	chr8:90774200-90803600	Weak transcription	Fetal Heart	heart
16	chr8:90774400-90793600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
17	chr8:90775800-90807200	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
18	chr8:90776400-90793800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
19	chr8:90776400-90799800	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
20	chr8:90779000-90801200	Weak transcription	Rectal Smooth Muscle	rectum
21	chr8:90779200-90793200	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
22	chr8:90779200-90793400	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
23	chr8:90779200-90793800	Weak transcription	Primary T helper naive cells from peripheral blood	blood
24	chr8:90779600-90802200	Weak transcription	H9 Cell Line	embryonic stem cell
25	chr8:90781400-90806600	Weak transcription	Right Ventricle	heart
26	chr8:90781800-90805600	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
27	chr8:90783400-90794200	Weak transcription	Stomach Mucosa	stomach
28	chr8:90783600-90803600	Weak transcription	Skeletal Muscle Female	skeletal muscle
29	chr8:90783800-90829000	Weak transcription	Aorta	Aorta
30	chr8:90784400-90799400	Weak transcription	Skeletal Muscle Male	skeletal muscle
31	chr8:90785200-90793400	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
32	chr8:90785600-90797000	Weak transcription	Fetal Intestine Small	intestine
33	chr8:90785600-90799200	Weak transcription	Brain Inferior Temporal Lobe	brain
34	chr8:90785600-90813800	Weak transcription	Placenta Amnion	Placenta Amnion
35	chr8:90785800-90807200	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
36	chr8:90785800-90810800	Weak transcription	Fetal Brain Female	brain
37	chr8:90786000-90793600	Weak transcription	GM12878-XiMat	blood
38	chr8:90786000-90793800	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
39	chr8:90786000-90794200	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
40	chr8:90786000-90796000	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
41	chr8:90786000-90799000	Weak transcription	Brain Angular Gyrus	brain
42	chr8:90786000-90799600	Weak transcription	Brain Substantia Nigra	brain
43	chr8:90786000-90813000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
44	chr8:90786200-90794000	Weak transcription	K562	blood
45	chr8:90786400-90794000	Weak transcription	Primary T killer memory cells from peripheral blood	blood
46	chr8:90786400-90794000	Weak transcription	Brain Hippocampus Middle	brain
47	chr8:90786400-90794400	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
48	chr8:90786400-90809800	Weak transcription	HepG2	liver
49	chr8:90786800-90792600	Weak transcription	Fetal Lung	lung
50	chr8:90786800-90797000	Weak transcription	Fetal Adrenal Gland	Adrenal Gland

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