Variant report

Variant	rs17499544
Chromosome Location	chr2:172640734-172640735
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr2:172637502..172642511-chr2:172648363..172652969,5	K562	blood:
2	chr2:172639886..172641878-chr2:172646463..172647982,2	K562	blood:

Extended variants
information (count: 20 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:19)

rs_ID	r²[population]
rs12619041	1.00[MEX][hapmap]
rs12622895	1.00[MEX][hapmap]
rs17499593	0.88[CEU][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.91[AFR][1000 genomes];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17615262	0.84[MEX][hapmap]
rs3736499	0.92[MEX][hapmap]
rs3765166	1.00[MEX][hapmap]
rs3770448	0.89[MEX][hapmap]
rs3770455	1.00[MEX][hapmap]
rs55681218	0.81[AFR][1000 genomes];0.82[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs56049564	0.83[AFR][1000 genomes];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62181740	0.91[AFR][1000 genomes];0.87[AMR][1000 genomes];0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62181741	0.91[AFR][1000 genomes];0.87[AMR][1000 genomes];0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62181743	0.91[AFR][1000 genomes];0.87[AMR][1000 genomes];0.82[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62182368	0.90[ASN][1000 genomes]
rs62182401	0.88[AMR][1000 genomes];0.91[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs62182404	0.91[AFR][1000 genomes];0.86[AMR][1000 genomes];0.88[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs62182425	0.81[AFR][1000 genomes];0.82[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs62182432	0.84[AMR][1000 genomes]
rs72881959	1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[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	nsv834457	chr2:172564939-172770901	Strong transcription Genic enhancers Enhancers Weak transcription Active TSS Flanking Active TSS Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	14 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs17499544	SLC25A12	cis	parietal	SCAN

Chromatin state (count:121 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:172587800-172640800	Weak transcription	Psoas Muscle	Psoas
2	chr2:172593200-172645000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
3	chr2:172603000-172688400	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
4	chr2:172604400-172641200	Weak transcription	Colon Smooth Muscle	Colon
5	chr2:172610200-172651400	Weak transcription	Placenta Amnion	Placenta Amnion
6	chr2:172618400-172641000	Weak transcription	Aorta	Aorta
7	chr2:172618800-172640800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
8	chr2:172619000-172641000	Weak transcription	Spleen	Spleen
9	chr2:172619200-172640800	Weak transcription	Rectal Smooth Muscle	rectum
10	chr2:172619200-172641000	Weak transcription	Thymus	Thymus
11	chr2:172619200-172641600	Weak transcription	Gastric	stomach
12	chr2:172619200-172641800	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
13	chr2:172620200-172641400	Weak transcription	NHEK	skin
14	chr2:172620400-172641000	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
15	chr2:172620400-172641600	Weak transcription	HUVEC	blood vessel
16	chr2:172620400-172641800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
17	chr2:172620800-172640800	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
18	chr2:172621000-172648000	Weak transcription	HSMMtube	muscle
19	chr2:172633400-172646200	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
20	chr2:172633800-172641600	Weak transcription	H9 Cell Line	embryonic stem cell
21	chr2:172635400-172640800	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
22	chr2:172635400-172640800	Weak transcription	Brain Angular Gyrus	brain
23	chr2:172635400-172647600	Weak transcription	NHDF-Ad	bronchial
24	chr2:172635400-172654800	Weak transcription	A549	lung
25	chr2:172635600-172641600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
26	chr2:172635600-172643000	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
27	chr2:172635600-172654600	Weak transcription	Liver	Liver
28	chr2:172636400-172641600	Weak transcription	Fetal Intestine Large	intestine
29	chr2:172636800-172654800	Weak transcription	Small Intestine	intestine
30	chr2:172637800-172640800	Weak transcription	iPS-20b Cell Line	embryonic stem cell
31	chr2:172637800-172641600	Weak transcription	K562	blood
32	chr2:172638000-172650200	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
33	chr2:172638200-172645000	Strong transcription	Breast Myoepithelial Primary Cells	Breast
34	chr2:172638400-172641000	Weak transcription	Fetal Stomach	stomach
35	chr2:172638600-172641000	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
36	chr2:172638600-172641000	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
37	chr2:172638600-172641000	Weak transcription	HMEC	breast
38	chr2:172638600-172641000	Weak transcription	NHLF	lung
39	chr2:172638600-172641400	Weak transcription	H1 Cell Line	embryonic stem cell
40	chr2:172638600-172642200	Strong transcription	HSMM	muscle
41	chr2:172638600-172644600	Strong transcription	Skeletal Muscle Female	skeletal muscle
42	chr2:172638600-172645600	Strong transcription	Primary B cells from cord blood	blood
43	chr2:172638600-172648400	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
44	chr2:172638600-172650600	Strong transcription	Stomach Smooth Muscle	stomach
45	chr2:172638800-172640800	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
46	chr2:172638800-172641000	Weak transcription	Primary neutrophils fromperipheralblood	blood
47	chr2:172638800-172641600	Strong transcription	Fetal Kidney	kidney
48	chr2:172638800-172642400	Strong transcription	Primary hematopoietic stem cells	blood
49	chr2:172638800-172642400	Strong transcription	Brain Hippocampus Middle	brain
50	chr2:172638800-172642600	Strong transcription	Cortex derived primary cultured neurospheres	brain

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