Variant report

Variant	rs6993178
Chromosome Location	chr8:125736746-125736747
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr8:125734815..125743876-chr8:125864194..125871100,21	MCF-7	breast:
2	chr8:125736316..125742243-chr8:125861977..125870763,24	MCF-7	breast:
3	chr8:125647571..125649356-chr8:125735665..125737482,2	MCF-7	breast:
4	chr8:125605731..125607581-chr8:125735892..125738512,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000255080	Chromatin interaction

Extended variants
information (count: 21 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:18)

rs_ID	r²[population]
rs12547578	0.85[AMR][1000 genomes];0.85[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1430850	0.85[AMR][1000 genomes];0.85[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1430852	0.86[AFR][1000 genomes];0.95[AMR][1000 genomes];0.86[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1430853	0.84[AFR][1000 genomes];0.95[AMR][1000 genomes];0.86[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1978661	1.00[ASW][hapmap];0.80[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.93[MEX][hapmap];0.90[TSI][hapmap];0.96[YRI][hapmap];0.88[AFR][1000 genomes];0.95[AMR][1000 genomes];0.86[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2288665	1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[YRI][hapmap];0.95[AMR][1000 genomes];0.85[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4870919	0.80[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[YRI][hapmap];0.95[AMR][1000 genomes];0.85[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4870920	0.94[CHB][hapmap];1.00[JPT][hapmap];0.88[YRI][hapmap];0.92[AMR][1000 genomes];0.84[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6470261	1.00[ASW][hapmap];0.80[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.93[MEX][hapmap];0.90[TSI][hapmap];0.96[YRI][hapmap];0.88[AFR][1000 genomes];0.95[AMR][1000 genomes];0.86[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6470262	0.80[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.88[AFR][1000 genomes];0.95[AMR][1000 genomes];0.86[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6470263	1.00[ASW][hapmap];0.80[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.93[MEX][hapmap];0.90[TSI][hapmap];0.96[YRI][hapmap];0.88[AFR][1000 genomes];0.95[AMR][1000 genomes];0.86[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs729513	1.00[ASW][hapmap];0.80[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.87[LWK][hapmap];0.93[MEX][hapmap];0.81[MKK][hapmap];0.90[TSI][hapmap];0.86[YRI][hapmap];0.92[AFR][1000 genomes];0.95[AMR][1000 genomes];0.86[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs733759	0.83[GIH][hapmap]
rs7824588	1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.86[AFR][1000 genomes];0.95[AMR][1000 genomes];0.86[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7833290	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.80[YRI][hapmap];0.89[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7842864	0.80[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[AFR][1000 genomes];0.95[AMR][1000 genomes];0.86[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs878684	0.89[AMR][1000 genomes];0.88[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs891541	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.84[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv891434	chr8:125630655-126324432	Strong transcription Enhancers Weak transcription Active TSS Genic enhancers Flanking Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	80 gene(s)	inside rSNPs	diseases
2	nsv1016502	chr8:125657664-125845074	Weak transcription Strong transcription Flanking Bivalent TSS/Enh Flanking Active TSS Enhancers Active TSS Bivalent Enhancer Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA	19 gene(s)	inside rSNPs	diseases
3	nsv612147	chr8:125733120-125751065	Weak transcription Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent/Poised TSS Enhancers Genic enhancers Transcr. at gene 5' and 3' Strong transcription	TF binding region CpG island Chromatin interactive region	7 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:68 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr8:125723200-125737200	Weak transcription	Colon Smooth Muscle	Colon
2	chr8:125723600-125737200	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
3	chr8:125724600-125738200	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
4	chr8:125724800-125737400	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
5	chr8:125730000-125737600	Enhancers	Cortex derived primary cultured neurospheres	brain
6	chr8:125730200-125737000	Enhancers	Skeletal Muscle Female	skeletal muscle
7	chr8:125730200-125737600	Enhancers	Fetal Heart	heart
8	chr8:125731000-125738200	Enhancers	Primary hematopoietic stem cells short term culture	blood
9	chr8:125731400-125738200	Weak transcription	Duodenum Smooth Muscle	Duodenum
10	chr8:125731400-125738400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
11	chr8:125733000-125738800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
12	chr8:125733200-125737000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
13	chr8:125733200-125738400	Weak transcription	K562	blood
14	chr8:125733400-125737000	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
15	chr8:125733800-125736800	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
16	chr8:125733800-125737000	Enhancers	Fetal Brain Male	brain
17	chr8:125733800-125738000	Flanking Active TSS	Liver	Liver
18	chr8:125734000-125737000	Enhancers	Adipose Nuclei	Adipose
19	chr8:125734000-125738000	Enhancers	Brain Anterior Caudate	brain
20	chr8:125734200-125737200	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
21	chr8:125734200-125738000	Weak transcription	Rectal Mucosa Donor 29	rectum
22	chr8:125734200-125738200	Weak transcription	Rectal Mucosa Donor 31	rectum
23	chr8:125734200-125738400	Weak transcription	Esophagus	oesophagus
24	chr8:125734400-125737200	Genic enhancers	Primary B cells from cord blood	blood
25	chr8:125734600-125737000	Flanking Active TSS	Brain Germinal Matrix	brain
26	chr8:125734600-125738000	Weak transcription	Placenta	Placenta
27	chr8:125734800-125738200	Enhancers	Brain Hippocampus Middle	brain
28	chr8:125735000-125738400	Weak transcription	Stomach Mucosa	stomach
29	chr8:125735200-125737000	Enhancers	Pancreatic Islets	Pancreatic Islet
30	chr8:125735200-125737600	Weak transcription	Fetal Lung	lung
31	chr8:125735600-125737000	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
32	chr8:125735600-125737800	Enhancers	Right Atrium	heart
33	chr8:125735800-125737000	Enhancers	Breast Myoepithelial Primary Cells	Breast
34	chr8:125735800-125737200	Enhancers	Brain Cingulate Gyrus	brain
35	chr8:125735800-125737200	Enhancers	Brain Substantia Nigra	brain
36	chr8:125735800-125737200	Enhancers	Fetal Muscle Leg	muscle
37	chr8:125735800-125737400	Enhancers	Psoas Muscle	Psoas
38	chr8:125735800-125737400	Flanking Active TSS	HepG2	liver
39	chr8:125735800-125738200	Enhancers	Skeletal Muscle Male	skeletal muscle
40	chr8:125736000-125737000	Enhancers	Brain Angular Gyrus	brain
41	chr8:125736000-125737000	Enhancers	HMEC	breast
42	chr8:125736000-125737000	Enhancers	HUVEC	blood vessel
43	chr8:125736000-125737200	Enhancers	Brain Inferior Temporal Lobe	brain
44	chr8:125736000-125737400	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
45	chr8:125736000-125737400	Enhancers	Left Ventricle	heart
46	chr8:125736000-125737600	Genic enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
47	chr8:125736000-125737600	Enhancers	Pancreas	Pancrea
48	chr8:125736000-125737800	Enhancers	Right Ventricle	heart
49	chr8:125736000-125738400	Enhancers	Fetal Intestine Small	intestine
50	chr8:125736200-125737200	Weak transcription	Primary hematopoietic stem cells	blood

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links