Variant report

Variant	rs17252498
Chromosome Location	chr3:136014198-136014199
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr3:136012746..136014476-chr3:136025907..136027620,2	K562	blood:
2	chr3:135913637..135916357-chr3:136011519..136014362,3	MCF-7	breast:

Variant related genes	Relation type
ENSG00000174579	Chromatin interaction

Extended variants
information (count: 34 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:31)

rs_ID	r²[population]
rs1145101	1.00[CHD][hapmap];1.00[JPT][hapmap];0.94[MEX][hapmap];0.90[TSI][hapmap];0.82[EUR][1000 genomes]
rs1145106	0.88[MEX][hapmap]
rs1154988	0.83[CEU][hapmap]
rs11715257	0.88[MEX][hapmap]
rs1279840	0.83[MEX][hapmap]
rs13068119	0.83[CEU][hapmap];0.88[MEX][hapmap];0.90[TSI][hapmap]
rs13071085	1.00[ASN][1000 genomes]
rs1394092	0.83[MEX][hapmap]
rs34498968	1.00[JPT][hapmap]
rs35087366	1.00[CHD][hapmap];1.00[JPT][hapmap]
rs3755636	0.82[CEU][hapmap]
rs3821445	1.00[ASW][hapmap];0.94[CEU][hapmap];1.00[CHD][hapmap];0.96[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.94[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.93[AFR][1000 genomes];0.98[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs483465	0.88[MEX][hapmap]
rs489398	0.92[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs503973	1.00[JPT][hapmap]
rs548288	0.83[MEX][hapmap]
rs571513	0.83[MEX][hapmap]
rs576771	0.88[MEX][hapmap]
rs610860	0.94[CEU][hapmap];1.00[JPT][hapmap];0.80[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs61789601	0.85[EUR][1000 genomes]
rs645040	0.83[CEU][hapmap]
rs667920	0.88[MEX][hapmap]
rs684773	0.83[CEU][hapmap];0.88[MEX][hapmap]
rs687339	0.83[CEU][hapmap]
rs695983	0.83[MEX][hapmap]
rs696516	0.94[MEX][hapmap]
rs696517	0.94[CEU][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.88[MEX][hapmap];1.00[TSI][hapmap];0.92[EUR][1000 genomes]
rs698270	0.88[MEX][hapmap]
rs8045	1.00[ASW][hapmap];0.83[CEU][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.83[MEX][hapmap];0.81[MKK][hapmap];1.00[TSI][hapmap];0.91[YRI][hapmap];0.86[AMR][1000 genomes]
rs866782	0.84[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs9883916	0.83[CEU][hapmap];0.88[MEX][hapmap];0.90[TSI][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	nsv869409	chr3:135649101-136164174	Strong transcription Genic enhancers Enhancers Active TSS Weak transcription ZNF genes & repeats Flanking Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	50 gene(s)	inside rSNPs	diseases
2	nsv508246	chr3:135922023-136038622	Active TSS Enhancers Genic enhancers ZNF genes & repeats Strong transcription Weak transcription Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
3	nsv948461	chr3:135969755-136349636	Enhancers ZNF genes & repeats Flanking Active TSS Weak transcription Genic enhancers Strong transcription Active TSS Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	9 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs17252498	MSL2	cis	cerebellum	SCAN

Chromatin state (count:122 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:135970600-136039400	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
2	chr3:135976200-136016400	Weak transcription	Colonic Mucosa	Colon
3	chr3:135976200-136021600	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
4	chr3:135981200-136052000	Weak transcription	NH-A	brain
5	chr3:135981600-136020400	Weak transcription	HUVEC	blood vessel
6	chr3:135996800-136016000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
7	chr3:135997400-136015200	Weak transcription	iPS-15b Cell Line	embryonic stem cell
8	chr3:135998000-136040200	Weak transcription	Muscle Satellite Cultured Cells	--
9	chr3:135999800-136016200	Weak transcription	Esophagus	oesophagus
10	chr3:135999800-136016800	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
11	chr3:135999800-136019000	Weak transcription	NHEK	skin
12	chr3:135999800-136038200	Weak transcription	Fetal Brain Male	brain
13	chr3:135999800-136061200	Weak transcription	Hela-S3	cervix
14	chr3:136000000-136016600	Weak transcription	Thymus	Thymus
15	chr3:136000000-136024600	Weak transcription	Pancreatic Islets	Pancreatic Islet
16	chr3:136000200-136038200	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
17	chr3:136001200-136016400	Weak transcription	Primary T helper naive cells from peripheral blood	blood
18	chr3:136001200-136019200	Weak transcription	Colon Smooth Muscle	Colon
19	chr3:136002000-136017400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
20	chr3:136002200-136014800	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
21	chr3:136002200-136015600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
22	chr3:136003000-136016400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
23	chr3:136004200-136016000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
24	chr3:136004200-136016200	Weak transcription	H9 Cell Line	embryonic stem cell
25	chr3:136004400-136015600	Weak transcription	Fetal Lung	lung
26	chr3:136004600-136021400	Weak transcription	HMEC	breast
27	chr3:136004600-136022000	Weak transcription	NHDF-Ad	bronchial
28	chr3:136005000-136016000	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
29	chr3:136005200-136014800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
30	chr3:136005200-136015800	Weak transcription	iPS-18 Cell Line	embryonic stem cell
31	chr3:136005200-136019200	Weak transcription	Osteobl	bone
32	chr3:136005600-136016000	Weak transcription	Rectal Smooth Muscle	rectum
33	chr3:136005600-136016200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
34	chr3:136005800-136016200	Weak transcription	H1 Cell Line	embryonic stem cell
35	chr3:136006200-136014200	Weak transcription	HUES64 Cell Line	embryonic stem cell
36	chr3:136006600-136015800	Weak transcription	Primary T cells fromperipheralblood	blood
37	chr3:136009400-136023000	Strong transcription	Dnd41	blood
38	chr3:136010000-136017800	Strong transcription	Primary T cells from cord blood	blood
39	chr3:136010000-136021000	Strong transcription	Primary hematopoietic stem cells short term culture	blood
40	chr3:136010000-136021000	Strong transcription	Liver	Liver
41	chr3:136010200-136015400	Strong transcription	Primary hematopoietic stem cells	blood
42	chr3:136010200-136021200	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
43	chr3:136010400-136021000	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
44	chr3:136010400-136021000	Strong transcription	Fetal Muscle Leg	muscle
45	chr3:136010400-136021000	Strong transcription	Fetal Stomach	stomach
46	chr3:136010600-136018000	Weak transcription	Fetal Heart	heart
47	chr3:136010600-136031400	Weak transcription	Stomach Mucosa	stomach
48	chr3:136010800-136016400	Weak transcription	Gastric	stomach
49	chr3:136010800-136020600	Strong transcription	Cortex derived primary cultured neurospheres	brain
50	chr3:136011000-136024600	Weak transcription	Psoas Muscle	Psoas

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