Variant report

Variant	rs2226399
Chromosome Location	chr8:102654182-102654183
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr8:102505361..102507168-chr8:102652647..102654652,2	MCF-7	breast:
2	chr8:102501541..102504149-chr8:102653315..102655059,2	MCF-7	breast:
3	chr8:102503246..102506384-chr8:102653850..102656829,3	MCF-7	breast:
4	chr8:102647973..102651609-chr8:102651902..102654799,4	MCF-7	breast:
5	chr8:102562014..102564447-chr8:102652332..102655161,2	MCF-7	breast:
6	chr8:102652172..102654283-chr8:102658129..102660211,2	K562	blood:

Variant related genes	Relation type
ENSG00000254024	Chromatin interaction
ENSG00000083307	Chromatin interaction

Extended variants
information (count: 8 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:7)

rs_ID	r²[population]
rs13275653	0.88[CEU][hapmap]
rs1357984	0.88[CEU][hapmap]
rs1917727	0.88[CEU][hapmap]
rs1917728	0.88[CEU][hapmap]
rs2387625	0.85[CHB][hapmap];0.90[JPT][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];0.90[AMR][1000 genomes];0.91[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs3735712	0.85[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];0.90[AMR][1000 genomes];0.91[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs6992430	0.88[CEU][hapmap]

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	esv3401576	chr8:102640273-102724495	Weak transcription Genic enhancers Enhancers Strong transcription ZNF genes & repeats Active TSS Bivalent Enhancer Flanking Active TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region	4 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs2226399	ALPK2	trans	cerebellum	SCAN
rs2226399	HRSP12	cis	parietal	SCAN
rs2226399	ODF1	cis	parietal	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr8:102619800-102656200	Weak transcription	iPS-15b Cell Line	embryonic stem cell
2	chr8:102644600-102663800	Weak transcription	Lung	lung
3	chr8:102644800-102674600	Weak transcription	Ovary	ovary
4	chr8:102645000-102656000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
5	chr8:102645600-102655600	Strong transcription	Placenta	Placenta
6	chr8:102647200-102655800	Weak transcription	Sigmoid Colon	Sigmoid Colon
7	chr8:102648200-102655800	Weak transcription	Colonic Mucosa	Colon
8	chr8:102648600-102663600	Weak transcription	Rectal Smooth Muscle	rectum
9	chr8:102648800-102654200	Weak transcription	A549	lung
10	chr8:102649000-102654200	Weak transcription	Fetal Intestine Small	intestine
11	chr8:102650600-102664400	Strong transcription	Breast Myoepithelial Primary Cells	Breast
12	chr8:102650800-102662400	Strong transcription	H1 Cell Line	embryonic stem cell
13	chr8:102650800-102664600	Strong transcription	HUES48 Cell Line	embryonic stem cell
14	chr8:102651200-102658800	Weak transcription	Pancreatic Islets	Pancreatic Islet
15	chr8:102651400-102681200	Weak transcription	Stomach Mucosa	stomach
16	chr8:102651600-102654400	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
17	chr8:102651600-102654800	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
18	chr8:102651600-102656000	Weak transcription	iPS-20b Cell Line	embryonic stem cell
19	chr8:102651800-102655800	Weak transcription	Fetal Stomach	stomach
20	chr8:102652000-102655600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
21	chr8:102652000-102655600	Weak transcription	Gastric	stomach
22	chr8:102652000-102655800	Weak transcription	HUES6 Cell Line	embryonic stem cell
23	chr8:102652200-102656200	Weak transcription	HUES64 Cell Line	embryonic stem cell
24	chr8:102652200-102658800	Weak transcription	iPS-18 Cell Line	embryonic stem cell
25	chr8:102652400-102655800	Weak transcription	H9 Cell Line	embryonic stem cell
26	chr8:102652800-102654800	Enhancers	GM12878-XiMat	blood
27	chr8:102652800-102657800	Weak transcription	Fetal Heart	heart
28	chr8:102653000-102655800	Weak transcription	Esophagus	oesophagus
29	chr8:102653200-102658600	Weak transcription	Fetal Muscle Leg	muscle
30	chr8:102653200-102661000	Strong transcription	Placenta Amnion	Placenta Amnion
31	chr8:102653400-102655200	Genic enhancers	HMEC	breast
32	chr8:102653400-102656000	Weak transcription	Fetal Intestine Large	intestine
33	chr8:102653600-102654200	Genic enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
34	chr8:102653800-102654800	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
35	chr8:102653800-102654800	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
36	chr8:102653800-102654800	Enhancers	NHEK	skin
37	chr8:102653800-102655200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
38	chr8:102654000-102655600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
39	chr8:102654000-102655600	Weak transcription	Duodenum Mucosa	Duodenum
40	chr8:102654000-102655600	Weak transcription	Rectal Mucosa Donor 29	rectum
41	chr8:102654000-102656200	Weak transcription	Pancreas	Pancrea
42	chr8:102654000-102658600	Weak transcription	Rectal Mucosa Donor 31	rectum

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