Variant report

Variant	rs17499306
Chromosome Location	chr2:172547553-172547554
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr2:172544067..172546213-chr2:172547195..172550116,3	MCF-7	breast:

Variant related genes	Relation type
ENSG00000077380	Chromatin interaction

Extended variants
information (count: 28 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:27)

rs_ID	r²[population]
rs11673831	0.91[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs11675404	0.82[CEU][hapmap];0.83[GIH][hapmap];0.89[MEX][hapmap];1.00[MKK][hapmap]
rs11675891	0.94[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs12991441	0.85[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs13016580	0.87[CEU][hapmap];0.90[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs13017695	0.91[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs13021138	0.90[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs13024662	0.84[AMR][1000 genomes]
rs1554259	0.86[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs17427311	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17427473	1.00[CEU][hapmap];0.81[CHD][hapmap];0.95[GIH][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];0.96[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs17499502	0.93[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs17848721	0.90[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs1996424	1.00[CEU][hapmap];0.90[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs2102738	1.00[LWK][hapmap]
rs2138349	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2357062	0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34108287	0.90[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs34221876	0.90[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs34632749	0.93[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs34962243	0.90[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs35162284	0.82[AFR][1000 genomes];0.97[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs3770459	0.95[CEU][hapmap];0.91[GIH][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];0.98[TSI][hapmap];0.90[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs62184174	0.91[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs72889853	0.83[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs74173119	0.87[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs979955	0.81[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]

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

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv997638	chr2:172442205-172560406	Weak transcription Flanking Active TSS Genic enhancers Active TSS Enhancers Strong transcription ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region	13 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs17499306	B3GALT1	cis	cerebellum	SCAN
rs17499306	MAP1D	cis	parietal	SCAN
rs17499306	SLC25A12	cis	parietal	SCAN
rs17499306	SLC25A12	cis	cerebellum	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:172545000-172550600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
2	chr2:172545000-172550600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
3	chr2:172545000-172550600	Weak transcription	Lung	lung
4	chr2:172545000-172553600	Weak transcription	Esophagus	oesophagus
5	chr2:172545000-172553600	Weak transcription	Sigmoid Colon	Sigmoid Colon
6	chr2:172545000-172580200	Weak transcription	Pancreas	Pancrea
7	chr2:172545000-172580400	Weak transcription	Spleen	Spleen
8	chr2:172545000-172580800	Weak transcription	Gastric	stomach
9	chr2:172545200-172550600	Weak transcription	Left Ventricle	heart
10	chr2:172545200-172551600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
11	chr2:172545200-172611200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
12	chr2:172545400-172588000	Weak transcription	H9 Cell Line	embryonic stem cell
13	chr2:172545600-172547600	Weak transcription	Fetal Intestine Large	intestine
14	chr2:172545600-172550000	Weak transcription	Fetal Muscle Trunk	muscle
15	chr2:172545600-172550600	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
16	chr2:172545600-172550600	Weak transcription	Fetal Intestine Small	intestine
17	chr2:172545600-172551200	Weak transcription	Colonic Mucosa	Colon
18	chr2:172545800-172548000	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
19	chr2:172545800-172548800	Weak transcription	Primary neutrophils fromperipheralblood	blood
20	chr2:172545800-172550600	Weak transcription	Fetal Stomach	stomach
21	chr2:172545800-172550600	Weak transcription	Thymus	Thymus
22	chr2:172545800-172551000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
23	chr2:172545800-172551200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
24	chr2:172545800-172551400	Weak transcription	Skeletal Muscle Male	skeletal muscle
25	chr2:172545800-172553600	Weak transcription	Aorta	Aorta
26	chr2:172545800-172553800	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
27	chr2:172545800-172556600	Weak transcription	Ovary	ovary
28	chr2:172545800-172560200	Weak transcription	Rectal Smooth Muscle	rectum
29	chr2:172545800-172573000	Weak transcription	H1 Cell Line	embryonic stem cell
30	chr2:172545800-172575400	Weak transcription	Placenta Amnion	Placenta Amnion
31	chr2:172545800-172588000	Weak transcription	Right Ventricle	heart
32	chr2:172546000-172547600	Enhancers	Brain Hippocampus Middle	brain
33	chr2:172546000-172547800	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
34	chr2:172546000-172547800	Weak transcription	Brain Cingulate Gyrus	brain
35	chr2:172546000-172547800	Weak transcription	Skeletal Muscle Female	skeletal muscle
36	chr2:172546000-172548600	Weak transcription	Rectal Mucosa Donor 29	rectum
37	chr2:172546000-172549200	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
38	chr2:172546000-172551000	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
39	chr2:172546000-172551000	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
40	chr2:172546000-172551200	Weak transcription	Duodenum Smooth Muscle	Duodenum
41	chr2:172546000-172551200	Weak transcription	Stomach Smooth Muscle	stomach
42	chr2:172546000-172558600	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
43	chr2:172546000-172559200	Weak transcription	Psoas Muscle	Psoas
44	chr2:172546000-172559800	Weak transcription	Fetal Heart	heart
45	chr2:172546000-172560600	Weak transcription	Primary T killer memory cells from peripheral blood	blood
46	chr2:172546000-172563000	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
47	chr2:172546000-172567800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
48	chr2:172546000-172568600	Weak transcription	Hela-S3	cervix
49	chr2:172546200-172549600	Weak transcription	Breast Myoepithelial Primary Cells	Breast
50	chr2:172546200-172550000	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin

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