Variant report

Variant	rs17219416
Chromosome Location	chr2:172200099-172200100
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 8 )
Associated
traits (count: 1 )

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

rs_ID	r²[population]
rs10490603	0.82[JPT][hapmap]
rs16823212	1.00[CHB][hapmap]
rs16859370	1.00[CEU][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.90[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs72880576	0.82[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs72880595	0.85[AMR][1000 genomes]
rs72882305	0.89[AMR][1000 genomes];0.89[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv3382346	chr2:172062677-172363892	Weak transcription Enhancers Active TSS ZNF genes & repeats Strong transcription Flanking Active TSS Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	29 gene(s)	inside rSNPs	diseases
2	nsv1003130	chr2:172189196-172237268	ZNF genes & repeats Enhancers Weak transcription Flanking Active TSS Strong transcription Transcr. at gene 5' and 3' Genic enhancers Active TSS	TF binding region CpG island Chromatin interactive region	5 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs17219416	SCRN3	cis	parietal	SCAN

Chromatin state (count:31 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:172171800-172211600	Weak transcription	Fetal Intestine Small	intestine
2	chr2:172172800-172222400	Weak transcription	Fetal Muscle Trunk	muscle
3	chr2:172180600-172203400	Weak transcription	Breast Myoepithelial Primary Cells	Breast
4	chr2:172181000-172203800	Weak transcription	HMEC	breast
5	chr2:172181000-172221600	Weak transcription	K562	blood
6	chr2:172181200-172204200	Weak transcription	NHEK	skin
7	chr2:172184000-172203400	Weak transcription	NH-A	brain
8	chr2:172184600-172203200	Weak transcription	Primary T helper cells fromperipheralblood	blood
9	chr2:172184800-172203200	Weak transcription	Fetal Thymus	thymus
10	chr2:172184800-172203200	Weak transcription	Rectal Smooth Muscle	rectum
11	chr2:172185000-172200400	Weak transcription	iPS-18 Cell Line	embryonic stem cell
12	chr2:172185000-172202200	Weak transcription	iPS-20b Cell Line	embryonic stem cell
13	chr2:172187000-172204200	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
14	chr2:172187600-172203000	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
15	chr2:172189400-172204200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
16	chr2:172191000-172203200	Weak transcription	Left Ventricle	heart
17	chr2:172191600-172203400	Weak transcription	Stomach Smooth Muscle	stomach
18	chr2:172193600-172218200	Weak transcription	HepG2	liver
19	chr2:172193800-172203400	Weak transcription	Primary B cells from peripheral blood	blood
20	chr2:172194000-172200600	Weak transcription	Primary B cells from cord blood	blood
21	chr2:172194200-172203000	Weak transcription	A549	lung
22	chr2:172196000-172201200	Weak transcription	Cortex derived primary cultured neurospheres	brain
23	chr2:172198400-172202600	Weak transcription	Rectal Mucosa Donor 31	rectum
24	chr2:172198600-172203600	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
25	chr2:172198800-172200600	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
26	chr2:172198800-172202800	Weak transcription	Primary hematopoietic stem cells	blood
27	chr2:172198800-172202800	Weak transcription	Sigmoid Colon	Sigmoid Colon
28	chr2:172199400-172202600	Weak transcription	Primary hematopoietic stem cells short term culture	blood
29	chr2:172199600-172200200	Weak transcription	GM12878-XiMat	blood
30	chr2:172199600-172202600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
31	chr2:172199600-172202800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links