Variant report

Variant	rs7596172
Chromosome Location	chr2:110339623-110339624
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr2:110337969..110339732-chr2:110347344..110349136,2	MCF-7	breast:

Extended variants
information (count: 41 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:36)

rs_ID	r²[population]
rs10175432	0.87[ASN][1000 genomes]
rs11541143	0.95[ASN][1000 genomes]
rs12998808	0.84[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs1434167	0.81[EUR][1000 genomes]
rs2018352	0.85[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2043462	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2060402	0.97[AFR][1000 genomes];0.98[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2060403	0.81[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs28544318	0.97[ASN][1000 genomes]
rs28567471	0.89[AMR][1000 genomes];0.89[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs28583991	0.95[ASN][1000 genomes]
rs28615410	0.97[AFR][1000 genomes];0.98[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs28728215	0.94[ASN][1000 genomes]
rs34557890	0.93[AFR][1000 genomes];0.98[AMR][1000 genomes];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs3923006	0.92[ASN][1000 genomes]
rs3934873	0.84[AMR][1000 genomes];0.85[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4953760	0.96[AMR][1000 genomes];0.92[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4953784	0.81[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4953843	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4953850	0.87[ASN][1000 genomes]
rs56364682	0.93[AFR][1000 genomes];0.98[AMR][1000 genomes];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs56402128	0.92[AFR][1000 genomes];0.97[AMR][1000 genomes];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6594037	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6594049	0.89[AFR][1000 genomes];0.98[AMR][1000 genomes];0.84[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs6723295	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6726252	0.97[AMR][1000 genomes];0.83[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs6745809	0.81[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6748632	0.86[ASN][1000 genomes]
rs72938271	0.81[ASN][1000 genomes]
rs747445	0.85[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs892460	0.85[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs892464	0.81[ASN][1000 genomes]
rs919941	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9330311	0.85[ASN][1000 genomes]
rs9330320	0.84[AMR][1000 genomes];0.84[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs9330324	0.81[AFR][1000 genomes];0.88[AMR][1000 genomes];0.84[EUR][1000 genomes];0.91[ASN][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	nsv874777	chr2:109825516-110693317	Strong transcription Flanking Bivalent TSS/Enh Weak transcription Enhancers Flanking Active TSS Genic enhancers Bivalent Enhancer ZNF genes & repeats Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	33 gene(s)	inside rSNPs	diseases
2	nsv874780	chr2:110078080-110432886	Active TSS Enhancers Weak transcription Bivalent Enhancer Strong transcription Flanking Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	24 gene(s)	inside rSNPs	diseases
3	nsv1011456	chr2:110290958-110980402	Active TSS Weak transcription Enhancers Flanking Active TSS Genic enhancers ZNF genes & repeats Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	60 gene(s)	inside rSNPs	diseases
4	nsv535861	chr2:110290958-110980402	Weak transcription Active TSS Flanking Active TSS Strong transcription Enhancers Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	60 gene(s)	inside rSNPs	diseases
5	nsv482469	chr2:110302488-110452580	Enhancers Weak transcription Flanking Active TSS Strong transcription ZNF genes & repeats Active TSS Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	21 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs7596172	SEPT10	cis	Muscle Skeletal	GTEx

Chromatin state (count:87 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:110293400-110352200	Weak transcription	Gastric	stomach
2	chr2:110297400-110351600	Weak transcription	Brain Germinal Matrix	brain
3	chr2:110302200-110357600	Weak transcription	iPS-15b Cell Line	embryonic stem cell
4	chr2:110302400-110343000	Weak transcription	Psoas Muscle	Psoas
5	chr2:110308400-110363400	Weak transcription	Brain Inferior Temporal Lobe	brain
6	chr2:110308600-110358600	Weak transcription	Small Intestine	intestine
7	chr2:110309000-110347400	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
8	chr2:110309800-110351600	Weak transcription	Pancreas	Pancrea
9	chr2:110310200-110351600	Weak transcription	Fetal Brain Male	brain
10	chr2:110310400-110342000	Weak transcription	Brain Hippocampus Middle	brain
11	chr2:110310400-110351600	Weak transcription	Rectal Smooth Muscle	rectum
12	chr2:110310400-110351800	Weak transcription	Fetal Brain Female	brain
13	chr2:110310400-110353800	Weak transcription	Skeletal Muscle Male	skeletal muscle
14	chr2:110310400-110363800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
15	chr2:110310600-110341400	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
16	chr2:110318200-110348400	Weak transcription	Placenta Amnion	Placenta Amnion
17	chr2:110319200-110367400	Weak transcription	HSMMtube	muscle
18	chr2:110319400-110358200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
19	chr2:110320600-110354600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
20	chr2:110323400-110343800	Weak transcription	Aorta	Aorta
21	chr2:110323400-110348000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
22	chr2:110323400-110348200	Weak transcription	Rectal Mucosa Donor 31	rectum
23	chr2:110323600-110341000	Weak transcription	Duodenum Mucosa	Duodenum
24	chr2:110323600-110344200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
25	chr2:110324000-110342800	Weak transcription	Sigmoid Colon	Sigmoid Colon
26	chr2:110324000-110348400	Weak transcription	Hela-S3	cervix
27	chr2:110324000-110370400	Weak transcription	Esophagus	oesophagus
28	chr2:110324200-110342800	Weak transcription	H1 Cell Line	embryonic stem cell
29	chr2:110324200-110348600	Weak transcription	iPS-18 Cell Line	embryonic stem cell
30	chr2:110324600-110362200	Weak transcription	Skeletal Muscle Female	skeletal muscle
31	chr2:110325200-110341000	Weak transcription	HUES48 Cell Line	embryonic stem cell
32	chr2:110325400-110343800	Weak transcription	Duodenum Smooth Muscle	Duodenum
33	chr2:110325800-110342800	Weak transcription	A549	lung
34	chr2:110328800-110349000	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
35	chr2:110329000-110369000	Weak transcription	Ovary	ovary
36	chr2:110329200-110341200	Weak transcription	Fetal Kidney	kidney
37	chr2:110329200-110342400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
38	chr2:110329200-110359400	Weak transcription	NHLF	lung
39	chr2:110329200-110369400	Weak transcription	Rectal Mucosa Donor 29	rectum
40	chr2:110329400-110341000	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
41	chr2:110329400-110359600	Weak transcription	NHDF-Ad	bronchial
42	chr2:110329600-110351200	Weak transcription	HMEC	breast
43	chr2:110329600-110351600	Weak transcription	Stomach Smooth Muscle	stomach
44	chr2:110329800-110351600	Weak transcription	Colon Smooth Muscle	Colon
45	chr2:110331400-110341000	Weak transcription	Muscle Satellite Cultured Cells	--
46	chr2:110331400-110341000	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
47	chr2:110331600-110341200	Weak transcription	HUES6 Cell Line	embryonic stem cell
48	chr2:110331800-110341200	Weak transcription	iPS-20b Cell Line	embryonic stem cell
49	chr2:110331800-110341400	Weak transcription	HUVEC	blood vessel
50	chr2:110331800-110342800	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links