Variant report

Variant	rs13275653
Chromosome Location	chr8:102649681-102649682
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr8:102503148..102509288-chr8:102639386..102649682,19	MCF-7	breast:
2	chr8:102643444..102646539-chr8:102648297..102653448,5	MCF-7	breast:
3	chr8:102649060..102651936-chr8:102661670..102663613,2	MCF-7	breast:
4	chr8:102499850..102508532-chr8:102642696..102652505,26	MCF-7	breast:

Variant related genes	Relation type
ENSG00000254024	Chromatin interaction
ENSG00000083307	Chromatin interaction

Extended variants
information (count: 10 )
Associated
traits (count: 2 )

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

rs_ID	r²[population]
rs1357984	1.00[CEU][hapmap];0.83[TSI][hapmap];0.88[EUR][1000 genomes]
rs1917727	1.00[CEU][hapmap];0.83[TSI][hapmap];0.90[EUR][1000 genomes]
rs1917728	1.00[CEU][hapmap];0.91[EUR][1000 genomes]
rs2226399	0.88[CEU][hapmap]
rs2387625	0.86[EUR][1000 genomes]
rs3735712	0.86[EUR][1000 genomes]
rs6992430	1.00[CEU][hapmap];0.85[TSI][hapmap];0.87[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	esv2757285	chr8:102609474-102649681	Weak transcription Enhancers Flanking Active TSS Strong transcription Bivalent Enhancer Genic enhancers Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
2	esv2759635	chr8:102609474-102649681	Enhancers Weak transcription Strong transcription Bivalent Enhancer Flanking Active TSS Genic enhancers Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
3	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:2)

SNP	Gene	Cis/trans	Tissue	Source
rs13275653	ODF1	cis	parietal	SCAN
rs13275653	ALPK2	trans	cerebellum	SCAN

Chromatin state (count:46 , 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	chr8:102643000-102650800	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
3	chr8:102643800-102650000	Strong transcription	HUES48 Cell Line	embryonic stem cell
4	chr8:102644600-102651200	Weak transcription	Gastric	stomach
5	chr8:102644600-102652200	Strong transcription	HUES64 Cell Line	embryonic stem cell
6	chr8:102644600-102663800	Weak transcription	Lung	lung
7	chr8:102644800-102651400	Weak transcription	Fetal Kidney	kidney
8	chr8:102644800-102674600	Weak transcription	Ovary	ovary
9	chr8:102645000-102651600	Strong transcription	iPS-20b Cell Line	embryonic stem cell
10	chr8:102645000-102656000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
11	chr8:102645600-102653800	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
12	chr8:102645600-102655600	Strong transcription	Placenta	Placenta
13	chr8:102646000-102652000	Strong transcription	HUES6 Cell Line	embryonic stem cell
14	chr8:102646200-102650000	Strong transcription	H1 Cell Line	embryonic stem cell
15	chr8:102646200-102652400	Strong transcription	Rectal Mucosa Donor 29	rectum
16	chr8:102646200-102653600	Strong transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
17	chr8:102646600-102651000	Weak transcription	Duodenum Mucosa	Duodenum
18	chr8:102647000-102651000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
19	chr8:102647000-102651200	Weak transcription	Esophagus	oesophagus
20	chr8:102647000-102652200	Strong transcription	iPS-18 Cell Line	embryonic stem cell
21	chr8:102647200-102650600	Weak transcription	Pancreatic Islets	Pancreatic Islet
22	chr8:102647200-102655800	Weak transcription	Sigmoid Colon	Sigmoid Colon
23	chr8:102647800-102651000	Weak transcription	Aorta	Aorta
24	chr8:102648200-102655800	Weak transcription	Colonic Mucosa	Colon
25	chr8:102648600-102651800	Weak transcription	Small Intestine	intestine
26	chr8:102648600-102663600	Weak transcription	Rectal Smooth Muscle	rectum
27	chr8:102648800-102650400	Weak transcription	Colon Smooth Muscle	Colon
28	chr8:102648800-102650800	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
29	chr8:102648800-102650800	Weak transcription	Fetal Lung	lung
30	chr8:102648800-102650800	Weak transcription	Stomach Mucosa	stomach
31	chr8:102648800-102652000	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
32	chr8:102648800-102653200	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
33	chr8:102648800-102653600	Strong transcription	NHEK	skin
34	chr8:102648800-102654200	Weak transcription	A549	lung
35	chr8:102649000-102654200	Weak transcription	Fetal Intestine Small	intestine
36	chr8:102649200-102651400	Strong transcription	Placenta Amnion	Placenta Amnion
37	chr8:102649400-102649800	Strong transcription	Pancreas	Pancrea
38	chr8:102649400-102650000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
39	chr8:102649400-102650400	Weak transcription	Brain Germinal Matrix	brain
40	chr8:102649400-102650800	Weak transcription	Fetal Stomach	stomach
41	chr8:102649400-102651000	Weak transcription	H9 Cell Line	embryonic stem cell
42	chr8:102649400-102652200	Strong transcription	HMEC	breast
43	chr8:102649600-102650600	Weak transcription	Breast Myoepithelial Primary Cells	Breast
44	chr8:102649600-102651200	Weak transcription	Fetal Intestine Large	intestine
45	chr8:102649600-102651200	Weak transcription	Rectal Mucosa Donor 31	rectum
46	chr8:102649600-102651600	Weak transcription	GM12878-XiMat	blood

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links