Variant report

Variant	rs12541317
Chromosome Location	chr8:99781355-99781356
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr8:99778640..99782967-chr8:99784164..99787375,4	MCF-7	breast:

Extended variants
information (count: 63 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:56)

rs_ID	r²[population]
rs10447977	0.90[CHB][hapmap];0.81[JPT][hapmap];0.85[AMR][1000 genomes];0.84[ASN][1000 genomes]
rs10755896	0.88[YRI][hapmap]
rs10955190	0.83[YRI][hapmap];0.83[AMR][1000 genomes]
rs11778767	1.00[CEU][hapmap];0.90[CHB][hapmap];0.97[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs11780500	1.00[CEU][hapmap];0.90[CHB][hapmap];0.97[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs12114834	1.00[CEU][hapmap];0.95[CHB][hapmap];0.81[JPT][hapmap];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs12550783	0.88[YRI][hapmap]
rs12679734	0.90[CHB][hapmap];0.82[JPT][hapmap];0.83[AMR][1000 genomes];0.81[ASN][1000 genomes]
rs13269932	0.83[YRI][hapmap];0.83[AMR][1000 genomes]
rs13275915	0.85[AMR][1000 genomes]
rs13279438	0.85[AMR][1000 genomes]
rs1447245	0.85[CHB][hapmap]
rs1476181	0.95[CHB][hapmap];0.85[AMR][1000 genomes]
rs2442012	0.87[AFR][1000 genomes];0.89[AMR][1000 genomes]
rs2442014	0.87[AFR][1000 genomes];0.89[AMR][1000 genomes];0.81[ASN][1000 genomes]
rs2442015	0.89[YRI][hapmap]
rs2515214	0.95[CHB][hapmap];0.86[AMR][1000 genomes]
rs2515216	1.00[YRI][hapmap]
rs2922066	0.85[CHB][hapmap]
rs2922075	0.84[AMR][1000 genomes]
rs2922076	0.90[CHB][hapmap]
rs2922078	0.95[CHB][hapmap];0.81[YRI][hapmap];0.84[AMR][1000 genomes]
rs2922081	0.84[AMR][1000 genomes]
rs2922082	0.90[CHB][hapmap];0.83[YRI][hapmap];0.81[AMR][1000 genomes]
rs3019293	0.84[AMR][1000 genomes]
rs34281206	0.85[AMR][1000 genomes];0.84[ASN][1000 genomes]
rs34366206	0.90[CHB][hapmap];0.80[JPT][hapmap];0.91[AMR][1000 genomes];0.85[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs34855977	0.84[AMR][1000 genomes]
rs35536167	0.85[AMR][1000 genomes];0.84[ASN][1000 genomes]
rs35798019	0.88[CEU][hapmap];0.90[CHB][hapmap];0.96[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs35804297	0.87[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs35915594	0.89[AMR][1000 genomes];0.84[ASN][1000 genomes]
rs4131873	0.82[AMR][1000 genomes]
rs4255105	0.90[CHB][hapmap];0.83[AMR][1000 genomes];0.80[ASN][1000 genomes]
rs4279561	0.85[AMR][1000 genomes]
rs4304299	0.87[AFR][1000 genomes];0.89[AMR][1000 genomes];0.81[ASN][1000 genomes]
rs4413739	0.95[CHB][hapmap];0.94[YRI][hapmap];0.88[AMR][1000 genomes];0.81[ASN][1000 genomes]
rs4440607	0.85[AMR][1000 genomes]
rs4509292	0.84[YRI][hapmap]
rs4549741	0.85[AMR][1000 genomes]
rs4562286	0.95[CHB][hapmap];1.00[YRI][hapmap];0.87[AFR][1000 genomes];0.88[AMR][1000 genomes];0.81[ASN][1000 genomes]
rs4612309	0.82[AMR][1000 genomes]
rs4734410	0.83[YRI][hapmap]
rs4734414	0.80[AMR][1000 genomes]
rs4735568	0.88[YRI][hapmap]
rs4735569	0.89[YRI][hapmap]
rs4735570	0.86[YRI][hapmap]
rs4735574	0.84[AMR][1000 genomes]
rs58321500	0.98[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs62532565	0.81[AMR][1000 genomes]
rs62532577	0.87[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs62532587	0.90[AMR][1000 genomes];0.85[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs6651182	0.93[YRI][hapmap]
rs6992925	0.83[YRI][hapmap]
rs7838239	1.00[CEU][hapmap];0.90[CHB][hapmap];0.97[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs9656842	0.93[YRI][hapmap]

Variant overlapped rSNPs/rCNVs (count:7 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv891218	chr8:99507313-99906221	Weak transcription Flanking Active TSS Enhancers Strong transcription ZNF genes & repeats Active TSS Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases
2	nsv1027025	chr8:99672977-100115315	Weak transcription Bivalent/Poised TSS Bivalent Enhancer Active TSS Enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Strong transcription Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	23 gene(s)	inside rSNPs	diseases
3	nsv539690	chr8:99672977-100115315	Weak transcription Flanking Active TSS ZNF genes & repeats Enhancers Strong transcription Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Active TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	23 gene(s)	inside rSNPs	diseases
4	nsv891220	chr8:99681858-99867419	Enhancers Weak transcription Flanking Active TSS Genic enhancers Strong transcription ZNF genes & repeats Active TSS Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region	7 gene(s)	inside rSNPs	diseases
5	nsv1025685	chr8:99706280-99826236	Strong transcription ZNF genes & repeats Weak transcription Enhancers Active TSS Flanking Active TSS Genic enhancers	TF binding region CpG island Chromatin interactive region	4 gene(s)	inside rSNPs	diseases
6	nsv539691	chr8:99706280-99826236	Weak transcription Enhancers Strong transcription ZNF genes & repeats Flanking Active TSS Active TSS Genic enhancers	TF binding region CpG island Chromatin interactive region	4 gene(s)	inside rSNPs	diseases
7	nsv1031089	chr8:99715785-100399935	Flanking Active TSS Flanking Bivalent TSS/Enh Weak transcription Active TSS Enhancers Strong transcription Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	30 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:78 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr8:99741600-99794200	Weak transcription	Pancreas	Pancrea
2	chr8:99746600-99789400	Weak transcription	Psoas Muscle	Psoas
3	chr8:99758600-99794200	Weak transcription	Lung	lung
4	chr8:99759200-99781600	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
5	chr8:99759200-99794400	Weak transcription	Sigmoid Colon	Sigmoid Colon
6	chr8:99759400-99784400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
7	chr8:99759800-99793400	Weak transcription	HUES64 Cell Line	embryonic stem cell
8	chr8:99763800-99794200	Weak transcription	NHLF	lung
9	chr8:99766000-99793200	Weak transcription	Primary T cells from cord blood	blood
10	chr8:99766800-99787600	Weak transcription	GM12878-XiMat	blood
11	chr8:99769400-99782400	Weak transcription	HUES48 Cell Line	embryonic stem cell
12	chr8:99769400-99782600	Weak transcription	HUES6 Cell Line	embryonic stem cell
13	chr8:99769400-99787600	Weak transcription	Ovary	ovary
14	chr8:99773000-99793000	Weak transcription	Skeletal Muscle Male	skeletal muscle
15	chr8:99773200-99791400	Weak transcription	A549	lung
16	chr8:99774600-99793000	Weak transcription	Osteobl	bone
17	chr8:99775200-99793000	Weak transcription	Brain Hippocampus Middle	brain
18	chr8:99775400-99792800	Weak transcription	Primary B cells from cord blood	blood
19	chr8:99775600-99788000	Weak transcription	Primary neutrophils fromperipheralblood	blood
20	chr8:99775600-99796200	Weak transcription	Duodenum Mucosa	Duodenum
21	chr8:99776400-99781400	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
22	chr8:99776400-99788400	Weak transcription	Esophagus	oesophagus
23	chr8:99776600-99787600	Weak transcription	Hela-S3	cervix
24	chr8:99776600-99798600	Weak transcription	Fetal Heart	heart
25	chr8:99776800-99797800	Weak transcription	Stomach Smooth Muscle	stomach
26	chr8:99777200-99793000	Weak transcription	HSMMtube	muscle
27	chr8:99777800-99787600	Weak transcription	Thymus	Thymus
28	chr8:99778000-99791800	Weak transcription	Dnd41	blood
29	chr8:99778400-99786600	Weak transcription	NH-A	brain
30	chr8:99778600-99785800	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
31	chr8:99778600-99788400	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
32	chr8:99778600-99796200	Weak transcription	Rectal Mucosa Donor 31	rectum
33	chr8:99778800-99784400	Weak transcription	Rectal Smooth Muscle	rectum
34	chr8:99778800-99793200	Weak transcription	Small Intestine	intestine
35	chr8:99778800-99793400	Weak transcription	HSMM	muscle
36	chr8:99779000-99782000	Weak transcription	Placenta Amnion	Placenta Amnion
37	chr8:99779000-99782200	Weak transcription	Right Ventricle	heart
38	chr8:99779000-99782600	Weak transcription	Muscle Satellite Cultured Cells	--
39	chr8:99779000-99783400	Weak transcription	Fetal Kidney	kidney
40	chr8:99779000-99784600	Weak transcription	Left Ventricle	heart
41	chr8:99779000-99785000	Weak transcription	Cortex derived primary cultured neurospheres	brain
42	chr8:99779000-99785600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
43	chr8:99779000-99791600	Weak transcription	Duodenum Smooth Muscle	Duodenum
44	chr8:99779000-99792600	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
45	chr8:99779000-99792600	Weak transcription	Adipose Nuclei	Adipose
46	chr8:99779000-99792600	Weak transcription	NHDF-Ad	bronchial
47	chr8:99779000-99796400	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
48	chr8:99779000-99796400	Weak transcription	Aorta	Aorta
49	chr8:99779000-99796400	Weak transcription	Fetal Lung	lung
50	chr8:99779200-99782600	Weak transcription	Primary hematopoietic stem cells short term culture	blood

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