Variant report

Variant	rs6696225
Chromosome Location	chr1:216705965-216705966
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	chr1:216705301..216708105-chr1:216716452..216719098,3	MCF-7	breast:

Extended variants
information (count: 41 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:37)

rs_ID	r²[population]
rs10442683	0.81[JPT][hapmap];0.81[ASN][1000 genomes]
rs10442688	0.85[ASN][1000 genomes]
rs10495027	0.85[CHD][hapmap];0.87[ASN][1000 genomes]
rs10495029	0.85[CHD][hapmap];0.85[ASN][1000 genomes]
rs10863250	0.89[ASN][1000 genomes]
rs11117612	0.84[CHD][hapmap];0.87[ASN][1000 genomes]
rs11117613	0.85[CHD][hapmap];0.80[JPT][hapmap];0.87[ASN][1000 genomes]
rs12067809	0.87[ASN][1000 genomes]
rs12130540	0.88[ASN][1000 genomes]
rs12137616	0.84[JPT][hapmap]
rs12145418	0.87[CHD][hapmap];0.89[ASN][1000 genomes]
rs12757165	0.80[JPT][hapmap];0.89[ASN][1000 genomes]
rs1566223	0.87[ASN][1000 genomes]
rs17611421	0.87[CHD][hapmap];0.80[JPT][hapmap];0.85[ASN][1000 genomes]
rs17667808	0.87[ASN][1000 genomes]
rs1833036	0.90[CHB][hapmap];0.92[CHD][hapmap];0.84[GIH][hapmap];0.95[JPT][hapmap];0.81[AMR][1000 genomes];0.99[ASN][1000 genomes]
rs1846223	0.89[CEU][hapmap];0.90[CHB][hapmap];0.90[JPT][hapmap];0.92[YRI][hapmap];0.86[AFR][1000 genomes];0.97[AMR][1000 genomes];0.93[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2377098	0.87[CHD][hapmap];0.89[GIH][hapmap];0.80[JPT][hapmap];0.89[ASN][1000 genomes]
rs3929399	0.84[CHD][hapmap];0.87[ASN][1000 genomes]
rs4147269	0.85[CHD][hapmap];0.87[ASN][1000 genomes]
rs4147270	0.88[ASN][1000 genomes]
rs4147271	0.85[CHD][hapmap];0.87[ASN][1000 genomes]
rs4294475	0.87[ASN][1000 genomes]
rs4462218	0.87[ASN][1000 genomes]
rs4846520	0.85[ASN][1000 genomes]
rs4846521	0.89[AFR][1000 genomes];0.97[AMR][1000 genomes];0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4846524	0.85[CEU][hapmap];0.90[CHB][hapmap];0.84[CHD][hapmap];0.94[GIH][hapmap];0.90[JPT][hapmap];0.89[LWK][hapmap];0.82[MEX][hapmap];0.88[MKK][hapmap];0.91[YRI][hapmap];0.87[AFR][1000 genomes];0.92[AMR][1000 genomes];0.90[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4846525	0.86[ASN][1000 genomes]
rs6604634	0.83[ASW][hapmap];0.85[CEU][hapmap];0.90[CHB][hapmap];0.85[CHD][hapmap];0.94[GIH][hapmap];0.90[JPT][hapmap];0.84[LWK][hapmap];0.83[MEX][hapmap];0.90[MKK][hapmap];0.85[TSI][hapmap];0.92[YRI][hapmap];0.86[AFR][1000 genomes];0.91[AMR][1000 genomes];0.90[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6604635	0.85[CEU][hapmap];0.90[CHB][hapmap];0.85[CHD][hapmap];0.94[GIH][hapmap];0.90[JPT][hapmap];0.85[TSI][hapmap];0.87[AMR][1000 genomes];0.91[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6658528	0.85[CHD][hapmap];0.84[GIH][hapmap];0.80[JPT][hapmap];0.87[ASN][1000 genomes]
rs6658786	0.88[CHB][hapmap];0.94[JPT][hapmap]
rs6673295	0.80[JPT][hapmap];0.87[ASN][1000 genomes]
rs6673524	0.80[JPT][hapmap];0.87[ASN][1000 genomes]
rs6676984	0.91[AMR][1000 genomes];0.91[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7542009	0.92[YRI][hapmap]
rs7544765	0.96[CEU][hapmap];0.90[CHB][hapmap];0.89[JPT][hapmap];0.92[YRI][hapmap];0.89[AFR][1000 genomes];0.97[AMR][1000 genomes];0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv549199	chr1:216384908-216814702	Weak transcription Enhancers Flanking Active TSS Active TSS Bivalent/Poised TSS Strong transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region	4 gene(s)	inside rSNPs	diseases
2	nsv1003815	chr1:216504235-216836498	Active TSS Weak transcription Enhancers ZNF genes & repeats Flanking Active TSS Bivalent/Poised TSS Bivalent Enhancer Strong transcription Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region	4 gene(s)	inside rSNPs	diseases
3	nsv535289	chr1:216504235-216836498	Enhancers Active TSS Weak transcription Bivalent/Poised TSS Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats Strong transcription	TF binding region CpG island Chromatin interactive region	4 gene(s)	inside rSNPs	diseases
4	nsv1008939	chr1:216688284-216712570	Weak transcription Enhancers Active TSS Flanking Active TSS Bivalent/Poised TSS Bivalent Enhancer Strong transcription Flanking Bivalent TSS/Enh	Chromatin interactive region	n/a	inside rSNPs	diseases

No data

Chromatin state (count:21 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:216704200-216706200	Active TSS	Pancreatic Islets	Pancreatic Islet
2	chr1:216704400-216706000	Active TSS	Brain Angular Gyrus	brain
3	chr1:216704400-216706000	Active TSS	Brain Anterior Caudate	brain
4	chr1:216704400-216706000	Active TSS	Brain Cingulate Gyrus	brain
5	chr1:216704600-216706000	Active TSS	Brain Hippocampus Middle	brain
6	chr1:216705000-216714400	Weak transcription	Gastric	stomach
7	chr1:216705200-216706000	Enhancers	Fetal Muscle Leg	muscle
8	chr1:216705200-216706000	Enhancers	Small Intestine	intestine
9	chr1:216705400-216707200	Weak transcription	Fetal Heart	heart
10	chr1:216705400-216708000	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
11	chr1:216705400-216708200	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
12	chr1:216705400-216721000	Weak transcription	Pancreas	Pancrea
13	chr1:216705400-216734800	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
14	chr1:216705600-216706000	Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
15	chr1:216705600-216711800	Weak transcription	Right Atrium	heart
16	chr1:216705800-216706000	Enhancers	Cortex derived primary cultured neurospheres	brain
17	chr1:216705800-216706000	Flanking Active TSS	Brain Germinal Matrix	brain
18	chr1:216705800-216706000	Enhancers	Psoas Muscle	Psoas
19	chr1:216705800-216707400	Weak transcription	Skeletal Muscle Female	skeletal muscle
20	chr1:216705800-216708000	Weak transcription	Left Ventricle	heart
21	chr1:216705800-216708600	Weak transcription	Skeletal Muscle Male	skeletal muscle

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links