Variant report

Variant	rs1517682
Chromosome Location	chr2:99450831-99450832
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr2:99449234..99452452-chr2:99458195..99461216,3	MCF-7	breast:
2	chr2:99344923..99349258-chr2:99450100..99455296,6	MCF-7	breast:

Variant related genes	Relation type
ENSG00000071073	Chromatin interaction

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

rSNPs within LD-proxies of this variant (count:5)

rs_ID	r²[population]
rs10175560	0.85[AFR][1000 genomes]
rs11900176	0.89[ASW][hapmap];0.81[LWK][hapmap];0.81[MKK][hapmap];0.84[AFR][1000 genomes]
rs11900524	0.86[AFR][1000 genomes]
rs12990579	0.86[YRI][hapmap];0.88[AFR][1000 genomes]
rs7565736	0.86[AFR][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	nsv1011278	chr2:99280928-99638376	Weak transcription Enhancers Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Flanking Active TSS Strong transcription Active TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	18 gene(s)	inside rSNPs	diseases
2	nsv535835	chr2:99280928-99638376	Enhancers Weak transcription Bivalent Enhancer Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Strong transcription Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	18 gene(s)	inside rSNPs	diseases
3	nsv582517	chr2:99440917-99487972	Weak transcription Enhancers Active TSS Bivalent/Poised TSS Strong transcription Flanking Active TSS Bivalent Enhancer ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region	6 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs1517682	C2orf15	cis	cerebellum	SCAN

Chromatin state (count:42 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:99440000-99460600	Weak transcription	Placenta Amnion	Placenta Amnion
2	chr2:99440400-99453800	Weak transcription	Brain Cingulate Gyrus	brain
3	chr2:99440400-99463400	Weak transcription	Fetal Intestine Large	intestine
4	chr2:99440600-99453800	Weak transcription	Brain Inferior Temporal Lobe	brain
5	chr2:99444200-99451000	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
6	chr2:99446400-99451600	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
7	chr2:99446400-99451600	Weak transcription	Primary T killer memory cells from peripheral blood	blood
8	chr2:99446800-99452000	Weak transcription	Primary T cells from cord blood	blood
9	chr2:99447600-99451000	Enhancers	Left Ventricle	heart
10	chr2:99448400-99451000	Enhancers	Lung	lung
11	chr2:99448400-99454000	Enhancers	Fetal Thymus	thymus
12	chr2:99448600-99451000	Enhancers	Primary T cells fromperipheralblood	blood
13	chr2:99448800-99452400	Enhancers	HUVEC	blood vessel
14	chr2:99449000-99451000	Enhancers	Primary T cells effector/memory enriched fromperipheralblood	blood
15	chr2:99449000-99451000	Enhancers	Brain Anterior Caudate	brain
16	chr2:99449000-99452200	Enhancers	Dnd41	blood
17	chr2:99449200-99451400	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
18	chr2:99449400-99451000	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
19	chr2:99449400-99451000	Enhancers	Spleen	Spleen
20	chr2:99449400-99454000	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
21	chr2:99449600-99452200	Weak transcription	Esophagus	oesophagus
22	chr2:99449800-99451000	Enhancers	Primary T helper cells PMA-I stimulated	--
23	chr2:99450000-99454600	Weak transcription	Brain Angular Gyrus	brain
24	chr2:99450000-99468400	Weak transcription	Fetal Intestine Small	intestine
25	chr2:99450200-99451000	Enhancers	Right Atrium	heart
26	chr2:99450200-99451800	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
27	chr2:99450400-99452400	Weak transcription	Cortex derived primary cultured neurospheres	brain
28	chr2:99450400-99452400	Weak transcription	Rectal Mucosa Donor 31	rectum
29	chr2:99450400-99453800	Weak transcription	Duodenum Mucosa	Duodenum
30	chr2:99450600-99451600	Weak transcription	Primary T helper naive cells from peripheral blood	blood
31	chr2:99450600-99453600	Weak transcription	Monocytes-CD14+_RO01746	blood
32	chr2:99450600-99455200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
33	chr2:99450600-99455200	Weak transcription	HMEC	breast
34	chr2:99450600-99456200	Weak transcription	Rectal Mucosa Donor 29	rectum
35	chr2:99450800-99451200	Weak transcription	Primary T helper cells fromperipheralblood	blood
36	chr2:99450800-99451800	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
37	chr2:99450800-99451800	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
38	chr2:99450800-99452200	Weak transcription	HepG2	liver
39	chr2:99450800-99452600	Weak transcription	Adipose Nuclei	Adipose
40	chr2:99450800-99452800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
41	chr2:99450800-99453600	Weak transcription	Primary neutrophils fromperipheralblood	blood
42	chr2:99450800-99462800	Weak transcription	Gastric	stomach

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