Variant report

Variant	rs17145372
Chromosome Location	chr5:118747588-118747589
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:0)
CpG islands
(count:0)
Chromatin interactive
region (count:19)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:19 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr5:118357259..118357861-chr5:118747519..118748249,2	K562	blood:
2	chr5:118322603..118326136-chr5:118745091..118748767,5	MCF-7	breast:
3	chr5:118323616..118324642-chr5:118747407..118748119,4	MCF-7	breast:
4	chr5:118745362..118747706-chr5:118750248..118751868,2	K562	blood:
5	chr5:118651201..118652914-chr5:118746753..118748686,2	K562	blood:
6	chr5:118648170..118648715-chr5:118747416..118748172,2	K562	blood:
7	chr5:118357310..118358382-chr5:118747153..118748053,5	MCF-7	breast:
8	chr5:118323682..118324344-chr5:118747438..118748180,2	Hela-S3	cervix:
9	chr5:118323143..118324569-chr5:118747458..118748790,7	MCF-7	breast:
10	chr5:118604013..118605667-chr5:118746438..118748354,2	MCF-7	breast:
11	chr5:118323769..118324283-chr5:118747494..118748090,2	MCF-7	breast:
12	chr5:118747505..118748328-chr5:118770657..118771776,5	MCF-7	breast:
13	chr5:118323688..118325465-chr5:118745878..118747588,2	MCF-7	breast:
14	chr5:118668038..118668652-chr5:118747446..118748001,2	MCF-7	breast:
15	chr5:118747162..118749496-chr5:118752473..118755239,2	K562	blood:
16	chr5:118357582..118358760-chr5:118747481..118748200,3	MCF-7	breast:
17	chr5:118602609..118607395-chr5:118746240..118749056,4	MCF-7	breast:
18	chr5:118323105..118324704-chr5:118747352..118748403,7	K562	blood:
19	chr5:118746206..118749496-chr5:118750368..118755239,5	K562	blood:

No data

Variant related genes	Relation type
ENSG00000169570	Chromatin interaction
ENSG00000145779	Chromatin interaction

Extended variants
information (count: 89 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:86)

rs_ID	r²[population]
rs10041464	1.00[ASN][1000 genomes]
rs10053031	1.00[ASN][1000 genomes]
rs10055743	1.00[JPT][hapmap];0.81[MEX][hapmap];1.00[ASN][1000 genomes]
rs10060971	0.81[MEX][hapmap]
rs10064524	1.00[GIH][hapmap];1.00[JPT][hapmap];0.90[MEX][hapmap];1.00[ASN][1000 genomes]
rs10064668	1.00[ASN][1000 genomes]
rs10064783	1.00[GIH][hapmap];1.00[JPT][hapmap];0.81[MEX][hapmap];1.00[ASN][1000 genomes]
rs10069480	1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs10519575	1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs10519576	1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs11539471	1.00[JPT][hapmap]
rs11746780	1.00[JPT][hapmap];0.87[YRI][hapmap]
rs11748477	0.89[ASW][hapmap];1.00[JPT][hapmap];0.83[LWK][hapmap];0.90[YRI][hapmap]
rs11748530	1.00[JPT][hapmap];0.89[YRI][hapmap]
rs11957255	1.00[JPT][hapmap]
rs17145194	1.00[JPT][hapmap]
rs17145196	1.00[JPT][hapmap]
rs17145259	1.00[GIH][hapmap];1.00[JPT][hapmap];0.81[MEX][hapmap];1.00[ASN][1000 genomes]
rs17145471	1.00[JPT][hapmap]
rs17145473	1.00[JPT][hapmap]
rs17145475	1.00[JPT][hapmap]
rs17145476	1.00[JPT][hapmap]
rs17385942	1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[TSI][hapmap];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2560718	1.00[JPT][hapmap]
rs3797344	1.00[GIH][hapmap];1.00[JPT][hapmap];0.90[MEX][hapmap];1.00[ASN][1000 genomes]
rs3797345	1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[ASN][1000 genomes]
rs3813305	1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs3850201	1.00[JPT][hapmap]
rs4895192	0.85[AFR][1000 genomes];0.92[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs4895374	0.82[AFR][1000 genomes];0.92[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs55796175	1.00[ASN][1000 genomes]
rs55933899	1.00[ASN][1000 genomes]
rs55986996	0.91[AFR][1000 genomes]
rs56194667	0.88[AFR][1000 genomes];0.92[AMR][1000 genomes]
rs56206018	1.00[ASN][1000 genomes]
rs56303741	1.00[ASN][1000 genomes]
rs57598751	1.00[ASN][1000 genomes]
rs57722161	1.00[ASN][1000 genomes]
rs59034186	1.00[ASN][1000 genomes]
rs59119324	1.00[ASN][1000 genomes]
rs60795377	0.84[AFR][1000 genomes];1.00[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs60832077	1.00[ASN][1000 genomes]
rs61412235	1.00[ASN][1000 genomes]
rs61415411	0.93[AFR][1000 genomes];0.92[AMR][1000 genomes];0.81[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6595184	1.00[ASN][1000 genomes]
rs66534333	1.00[ASN][1000 genomes]
rs67967956	1.00[ASN][1000 genomes]
rs68024523	1.00[ASN][1000 genomes]
rs6860034	1.00[ASN][1000 genomes]
rs6862941	1.00[ASN][1000 genomes]
rs6869623	1.00[ASN][1000 genomes]
rs6883394	1.00[JPT][hapmap]
rs6891981	1.00[ASN][1000 genomes]
rs72786113	1.00[ASN][1000 genomes]
rs72786116	1.00[ASN][1000 genomes]
rs72786125	1.00[ASN][1000 genomes]
rs72786136	1.00[ASN][1000 genomes]
rs72786143	1.00[ASN][1000 genomes]
rs72786161	1.00[ASN][1000 genomes]
rs72788123	1.00[ASN][1000 genomes]
rs72788136	1.00[ASN][1000 genomes]
rs72788144	0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72788145	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72788146	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72788148	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72788162	0.87[AFR][1000 genomes];0.92[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs72788163	0.87[AFR][1000 genomes];0.88[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs72788165	1.00[ASN][1000 genomes]
rs72788177	1.00[ASN][1000 genomes]
rs72788186	1.00[ASN][1000 genomes]
rs73237289	1.00[ASN][1000 genomes]
rs73790852	1.00[ASN][1000 genomes]
rs73790862	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73794110	1.00[ASN][1000 genomes]
rs7701561	1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[ASN][1000 genomes]
rs7701688	1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs7704291	1.00[JPT][hapmap]
rs7704487	1.00[JPT][hapmap]
rs7722172	1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs7723390	1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs7723933	1.00[ASN][1000 genomes]
rs7725244	1.00[ASN][1000 genomes]
rs7729690	1.00[ASN][1000 genomes]
rs7734378	1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs7737934	1.00[JPT][hapmap]
rs9327100	0.81[MEX][hapmap]

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	nsv1030717	chr5:118709310-118836951	Active TSS Strong transcription Enhancers Genic enhancers Weak transcription Flanking Active TSS Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases
2	nsv427732	chr5:118730999-119034741	Strong transcription Weak transcription Enhancers Flanking Active TSS Bivalent/Poised TSS ZNF genes & repeats Genic enhancers Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	19 gene(s)	inside rSNPs	diseases
3	nsv965533	chr5:118738884-118762384	Enhancers Weak transcription Flanking Active TSS Active TSS Bivalent/Poised TSS Bivalent Enhancer	Chromatin interactive region	7 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:120 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:118707600-118754600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
2	chr5:118723000-118747600	Weak transcription	Pancreas	Pancrea
3	chr5:118745200-118747600	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
4	chr5:118746200-118747600	Enhancers	Stomach Mucosa	stomach
5	chr5:118746400-118747600	Weak transcription	Sigmoid Colon	Sigmoid Colon
6	chr5:118746800-118747600	Flanking Active TSS	Muscle Satellite Cultured Cells	--
7	chr5:118747000-118747600	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
8	chr5:118747000-118747600	Weak transcription	Esophagus	oesophagus
9	chr5:118747000-118747600	Enhancers	Small Intestine	intestine
10	chr5:118747000-118748000	Active TSS	ES-I3 Cell Line	embryonic stem cell
11	chr5:118747000-118748000	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
12	chr5:118747000-118748000	Active TSS	NHDF-Ad	bronchial
13	chr5:118747200-118747600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
14	chr5:118747200-118747600	Flanking Active TSS	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
15	chr5:118747200-118747600	Flanking Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
16	chr5:118747200-118747600	Flanking Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
17	chr5:118747200-118747600	Flanking Active TSS	Foreskin Melanocyte Primary Cells skin03	Skin
18	chr5:118747200-118747600	Flanking Active TSS	Brain Hippocampus Middle	brain
19	chr5:118747200-118747600	Flanking Active TSS	Colon Smooth Muscle	Colon
20	chr5:118747200-118747600	Enhancers	Fetal Brain Male	brain
21	chr5:118747200-118747800	Flanking Active TSS	Cortex derived primary cultured neurospheres	brain
22	chr5:118747200-118747800	Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
23	chr5:118747200-118748000	Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
24	chr5:118747200-118748000	Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
25	chr5:118747200-118748000	Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
26	chr5:118747200-118748000	Active TSS	Right Atrium	heart
27	chr5:118747200-118748000	Active TSS	Right Ventricle	heart
28	chr5:118747200-118748000	Active TSS	Stomach Smooth Muscle	stomach
29	chr5:118747200-118748000	Flanking Active TSS	Hela-S3	cervix
30	chr5:118747200-118748000	Active TSS	HSMM	muscle
31	chr5:118747200-118748000	Active TSS	Osteobl	bone
32	chr5:118747400-118747600	Flanking Active TSS	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
33	chr5:118747400-118747600	Flanking Active TSS	H9 Derived Neuron Cultured Cells	ES cell derived
34	chr5:118747400-118747600	Flanking Active TSS	HUES64 Cell Line	embryonic stem cell
35	chr5:118747400-118747600	Flanking Active TSS	iPS-18 Cell Line	embryonic stem cell
36	chr5:118747400-118747600	Flanking Active TSS	iPS-20b Cell Line	embryonic stem cell
37	chr5:118747400-118747600	Enhancers	Primary hematopoietic stem cells short term culture	blood
38	chr5:118747400-118747600	Enhancers	Primary T regulatory cells fromperipheralblood	blood
39	chr5:118747400-118747600	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
40	chr5:118747400-118747600	Active TSS	Primary T killer memory cells from peripheral blood	blood
41	chr5:118747400-118747600	Enhancers	Primary mononuclear cells fromperipheralblood	Blood
42	chr5:118747400-118747600	Flanking Active TSS	Adipose Nuclei	Adipose
43	chr5:118747400-118747600	Flanking Active TSS	Brain Angular Gyrus	brain
44	chr5:118747400-118747600	Flanking Active TSS	Brain Inferior Temporal Lobe	brain
45	chr5:118747400-118747600	Flanking Active TSS	Duodenum Smooth Muscle	Duodenum
46	chr5:118747400-118747600	Flanking Active TSS	Fetal Brain Female	brain
47	chr5:118747400-118747600	Flanking Active TSS	Fetal Heart	heart
48	chr5:118747400-118747600	Flanking Active TSS	Fetal Muscle Leg	muscle
49	chr5:118747400-118747600	Flanking Active TSS	Placenta Amnion	Placenta Amnion
50	chr5:118747400-118747600	Enhancers	Dnd41	blood

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links