Variant report

Variant	rs17500199
Chromosome Location	chr2:172929537-172929538
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	SPI1	chr2:172929353-172929597	GM12891	blood:	n/a	chr2:172929476-172929485

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr2:172928306..172931524-chr2:172948301..172950748,4	MCF-7	breast:
2	chr2:172911399..172913242-chr2:172927772..172930159,2	K562	blood:

Variant related genes	Relation type
METAP1D	TF binding region
ENSG00000144355	Chromatin interaction

Extended variants
information (count: 9 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:6)

rs_ID	r²[population]
rs11681005	0.85[JPT][hapmap]
rs11688839	0.80[CEU][hapmap];0.86[JPT][hapmap]
rs11695630	0.84[CEU][hapmap]
rs12996935	0.85[JPT][hapmap]
rs13013988	0.92[CEU][hapmap];0.83[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs72892894	0.83[AMR][1000 genomes];0.85[EUR][1000 genomes]

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	nsv875411	chr2:172693780-172942448	Strong transcription Weak transcription Enhancers Flanking Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Active TSS Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	22 gene(s)	inside rSNPs	diseases
2	esv2830399	chr2:172781830-172952526	Weak transcription Enhancers Transcr. at gene 5' and 3' Flanking Active TSS Flanking Bivalent TSS/Enh Strong transcription ZNF genes & repeats Active TSS Bivalent Enhancer Bivalent/Poised TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	26 gene(s)	inside rSNPs	diseases
3	nsv875412	chr2:172903124-172942448	Enhancers Active TSS Weak transcription Strong transcription Flanking Active TSS Bivalent Enhancer ZNF genes & repeats Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:49 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:172911000-172930000	Weak transcription	Primary T cells from cord blood	blood
2	chr2:172911200-172947200	Weak transcription	HSMM	muscle
3	chr2:172914000-172937000	Weak transcription	Pancreas	Pancrea
4	chr2:172917400-172934800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
5	chr2:172917800-172932000	Weak transcription	iPS-18 Cell Line	embryonic stem cell
6	chr2:172917800-172944800	Weak transcription	Brain Substantia Nigra	brain
7	chr2:172918000-172930400	Weak transcription	Brain Cingulate Gyrus	brain
8	chr2:172918000-172932800	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
9	chr2:172918600-172935600	Weak transcription	Fetal Kidney	kidney
10	chr2:172918600-172935800	Weak transcription	Cortex derived primary cultured neurospheres	brain
11	chr2:172921800-172937200	Weak transcription	HepG2	liver
12	chr2:172923600-172939800	Weak transcription	Psoas Muscle	Psoas
13	chr2:172924200-172935800	Weak transcription	Adipose Nuclei	Adipose
14	chr2:172924400-172931400	Weak transcription	Primary B cells from cord blood	blood
15	chr2:172925600-172931000	Weak transcription	HSMMtube	muscle
16	chr2:172925600-172932400	Weak transcription	Dnd41	blood
17	chr2:172925800-172930200	Weak transcription	Stomach Smooth Muscle	stomach
18	chr2:172925800-172937200	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
19	chr2:172925800-172937400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
20	chr2:172925800-172942400	Weak transcription	Primary T helper cells fromperipheralblood	blood
21	chr2:172926000-172931000	Weak transcription	Breast Myoepithelial Primary Cells	Breast
22	chr2:172926000-172932000	Weak transcription	Brain Hippocampus Middle	brain
23	chr2:172926200-172933200	Weak transcription	Aorta	Aorta
24	chr2:172926200-172933400	Weak transcription	Right Ventricle	heart
25	chr2:172926400-172929800	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
26	chr2:172926400-172935200	Weak transcription	Primary T helper cells PMA-I stimulated	--
27	chr2:172926600-172933400	Weak transcription	Duodenum Smooth Muscle	Duodenum
28	chr2:172926800-172929800	Weak transcription	Fetal Muscle Leg	muscle
29	chr2:172927000-172933800	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
30	chr2:172927200-172931400	Weak transcription	Primary hematopoietic stem cells	blood
31	chr2:172927200-172931600	Strong transcription	Skeletal Muscle Female	skeletal muscle
32	chr2:172927200-172941600	Weak transcription	Gastric	stomach
33	chr2:172927400-172929600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
34	chr2:172927600-172933200	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
35	chr2:172927600-172933400	Weak transcription	Fetal Muscle Trunk	muscle
36	chr2:172927800-172929800	Weak transcription	Osteobl	bone
37	chr2:172927800-172931400	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
38	chr2:172927800-172936800	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
39	chr2:172928200-172935800	Weak transcription	Primary hematopoietic stem cells short term culture	blood
40	chr2:172928400-172932200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
41	chr2:172928400-172932600	Weak transcription	Fetal Heart	heart
42	chr2:172928600-172933600	Weak transcription	Spleen	Spleen
43	chr2:172928600-172937400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
44	chr2:172928600-172940000	Weak transcription	Left Ventricle	heart
45	chr2:172929000-172931000	Weak transcription	K562	blood
46	chr2:172929000-172933000	Weak transcription	Brain Inferior Temporal Lobe	brain
47	chr2:172929200-172929600	Weak transcription	Brain Germinal Matrix	brain
48	chr2:172929200-172931000	Weak transcription	Ovary	ovary
49	chr2:172929400-172933400	Weak transcription	GM12878-XiMat	blood

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links