Variant report

Variant	rs10224320
Chromosome Location	chr7:16855007-16855008
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr7:16843083..16845664-chr7:16854797..16856624,2	MCF-7	breast:
2	chr7:16852860..16855364-chr7:16884704..16887275,2	MCF-7	breast:
3	chr7:16846231..16849111-chr7:16853009..16855819,2	K562	blood:
4	chr7:16853700..16855388-chr7:16865354..16867185,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000106541	Chromatin interaction

Extended variants
information (count: 58 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:46)

rs_ID	r²[population]
rs10085446	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10252977	0.92[AMR][1000 genomes];0.83[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10499476	1.00[CHB][hapmap];1.00[CHD][hapmap];0.80[GIH][hapmap];1.00[JPT][hapmap];0.99[ASN][1000 genomes]
rs12665886	1.00[CHB][hapmap];0.92[CHD][hapmap];1.00[JPT][hapmap];0.96[ASN][1000 genomes]
rs12665957	1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[ASN][1000 genomes]
rs12666607	0.81[CHB][hapmap];0.84[CHD][hapmap]
rs12667956	0.84[ASN][1000 genomes]
rs12672294	0.96[ASN][1000 genomes]
rs12672301	1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[ASN][1000 genomes]
rs12672400	0.96[ASN][1000 genomes]
rs12674385	0.87[ASN][1000 genomes]
rs13229262	0.95[ASN][1000 genomes]
rs13437970	0.86[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1525744	1.00[CHB][hapmap];0.96[CHD][hapmap];0.86[JPT][hapmap];0.81[ASN][1000 genomes]
rs17136670	0.96[ASN][1000 genomes]
rs17150186	1.00[CHB][hapmap];0.89[CHD][hapmap];1.00[JPT][hapmap];0.96[ASN][1000 genomes]
rs17629719	1.00[CHB][hapmap];0.88[CHD][hapmap];0.91[GIH][hapmap];1.00[JPT][hapmap];0.84[MEX][hapmap];0.81[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1917742	0.90[CHB][hapmap];0.84[CHD][hapmap]
rs28945075	0.87[ASN][1000 genomes]
rs28945079	0.86[AMR][1000 genomes];0.87[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs3757454	0.96[ASN][1000 genomes]
rs3757455	1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[ASN][1000 genomes]
rs3807501	1.00[CHB][hapmap];0.88[CHD][hapmap];1.00[JPT][hapmap];0.96[ASN][1000 genomes]
rs3807502	0.96[ASN][1000 genomes]
rs3807503	0.96[ASN][1000 genomes]
rs3817502	0.96[ASN][1000 genomes]
rs3817505	1.00[CHB][hapmap];0.92[CHD][hapmap];1.00[JPT][hapmap];0.96[ASN][1000 genomes]
rs3817506	0.93[ASN][1000 genomes]
rs3817507	0.93[ASN][1000 genomes]
rs3817508	0.92[ASN][1000 genomes]
rs3817509	1.00[CHB][hapmap];0.92[CHD][hapmap];1.00[JPT][hapmap];0.93[ASN][1000 genomes]
rs3817510	1.00[CHB][hapmap];0.92[CHD][hapmap];1.00[JPT][hapmap];0.96[ASN][1000 genomes]
rs3817512	0.89[CHB][hapmap];0.88[CHD][hapmap];1.00[JPT][hapmap];0.96[ASN][1000 genomes]
rs3823653	0.96[ASN][1000 genomes]
rs55824063	0.92[AMR][1000 genomes];0.85[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs56291875	0.96[ASN][1000 genomes]
rs57997528	0.96[ASN][1000 genomes]
rs61130271	0.97[ASN][1000 genomes]
rs62440423	0.96[ASN][1000 genomes]
rs62440424	0.93[ASN][1000 genomes]
rs62440425	0.96[ASN][1000 genomes]
rs62440459	0.97[ASN][1000 genomes]
rs73073559	0.96[ASN][1000 genomes]
rs73078122	0.87[ASN][1000 genomes]
rs73078127	0.87[ASN][1000 genomes]
rs73078130	0.87[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:12 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv887761	chr7:16834361-17732490	Enhancers Genic enhancers Weak transcription Flanking Active TSS Active TSS Strong transcription ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	34 gene(s)	inside rSNPs	diseases
2	nsv887762	chr7:16834361-17746628	Enhancers Genic enhancers Flanking Active TSS Active TSS Strong transcription Weak transcription Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	34 gene(s)	inside rSNPs	diseases
3	nsv887763	chr7:16834361-17750811	Weak transcription Active TSS Enhancers Strong transcription Flanking Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	34 gene(s)	inside rSNPs	diseases
4	nsv887764	chr7:16839835-17218800	Weak transcription Enhancers Active TSS Flanking Active TSS Genic enhancers Strong transcription Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	diseases
5	nsv887765	chr7:16839835-17750811	Enhancers Active TSS Flanking Active TSS Weak transcription ZNF genes & repeats Strong transcription Bivalent Enhancer Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	34 gene(s)	inside rSNPs	diseases
6	nsv1027284	chr7:16849986-17008167	Enhancers Flanking Active TSS Weak transcription Active TSS Strong transcription ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
7	nsv606339	chr7:16852808-17004301	Enhancers Weak transcription Strong transcription Flanking Active TSS ZNF genes & repeats Active TSS Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
8	nsv1016695	chr7:16854300-16991627	Weak transcription Strong transcription Enhancers Flanking Active TSS ZNF genes & repeats Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
9	nsv1017413	chr7:16854300-17125005	Enhancers Weak transcription Strong transcription Flanking Active TSS Active TSS ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases
10	nsv538749	chr7:16854300-17125005	Enhancers Weak transcription Flanking Active TSS Active TSS ZNF genes & repeats Strong transcription Bivalent Enhancer Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases
11	nsv1015831	chr7:16854300-17732227	Enhancers Weak transcription Active TSS Flanking Active TSS Strong transcription Genic enhancers ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	32 gene(s)	inside rSNPs	diseases
12	nsv538750	chr7:16854300-17732227	Enhancers Strong transcription Weak transcription Active TSS Flanking Active TSS Bivalent/Poised TSS ZNF genes & repeats Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	32 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:28 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:16848000-16858200	Enhancers	Stomach Mucosa	stomach
2	chr7:16849400-16857600	Weak transcription	Sigmoid Colon	Sigmoid Colon
3	chr7:16851800-16856200	Weak transcription	Hela-S3	cervix
4	chr7:16851800-16856400	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
5	chr7:16851800-16857200	Weak transcription	NH-A	brain
6	chr7:16851800-16858200	Enhancers	Rectal Mucosa Donor 31	rectum
7	chr7:16853200-16857200	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
8	chr7:16853200-16857800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
9	chr7:16853200-16858600	Enhancers	A549	lung
10	chr7:16853400-16855400	Weak transcription	Primary monocytes fromperipheralblood	blood
11	chr7:16853400-16855400	Weak transcription	Monocytes-CD14+_RO01746	blood
12	chr7:16853400-16856800	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
13	chr7:16853400-16857000	Weak transcription	Muscle Satellite Cultured Cells	--
14	chr7:16853400-16857400	Weak transcription	Osteobl	bone
15	chr7:16854400-16855600	Enhancers	Duodenum Mucosa	Duodenum
16	chr7:16854400-16856000	Enhancers	Rectal Mucosa Donor 29	rectum
17	chr7:16854400-16858000	Enhancers	Fetal Intestine Small	intestine
18	chr7:16854600-16857200	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
19	chr7:16854800-16855200	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
20	chr7:16854800-16855200	Enhancers	NHEK	skin
21	chr7:16854800-16856200	Enhancers	Brain Hippocampus Middle	brain
22	chr7:16854800-16858200	Enhancers	Primary hematopoietic stem cells short term culture	blood
23	chr7:16855000-16855400	Enhancers	Colonic Mucosa	Colon
24	chr7:16855000-16855600	Weak transcription	Pancreas	Pancrea
25	chr7:16855000-16856400	Weak transcription	Fetal Intestine Large	intestine
26	chr7:16855000-16857600	Weak transcription	HMEC	breast
27	chr7:16855000-16857800	Weak transcription	Esophagus	oesophagus
28	chr7:16855000-16858000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links