Variant report

Variant	rs4907086
Chromosome Location	chr1:85107858-85107859
allele	A/C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr1:85087799..85089777-chr1:85107656..85110506,2	K562	blood:
2	chr1:85107451..85110887-chr1:85114026..85115969,4	K562	blood:
3	chr1:85107610..85110415-chr1:85125132..85127856,2	K562	blood:

Extended variants
information (count: 31 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:31)

rs_ID	r²[population]
rs1057746	0.95[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap];0.85[TSI][hapmap];0.81[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs10874453	0.88[JPT][hapmap]
rs10874454	0.82[CEU][hapmap];0.93[CHB][hapmap];1.00[JPT][hapmap];0.81[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs11161435	0.84[CHB][hapmap];0.88[JPT][hapmap]
rs11161436	0.84[CHB][hapmap];0.81[CHD][hapmap];0.88[JPT][hapmap]
rs11164031	0.81[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs11164032	0.94[CHB][hapmap];1.00[JPT][hapmap];0.81[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs11164033	0.81[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs11164034	0.95[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap];0.85[TSI][hapmap];0.86[ASN][1000 genomes]
rs11164036	0.81[ASN][1000 genomes]
rs11164041	0.80[ASN][1000 genomes]
rs11164048	0.85[CHB][hapmap];0.89[JPT][hapmap]
rs12044089	0.87[ASN][1000 genomes]
rs12049262	0.85[CHB][hapmap];0.89[JPT][hapmap]
rs12137124	0.95[CHB][hapmap];0.93[CHD][hapmap];0.88[JPT][hapmap];0.80[ASN][1000 genomes]
rs12730273	0.80[ASN][1000 genomes]
rs2911561	0.81[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs2911562	1.00[CHB][hapmap];1.00[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];0.81[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs2911563	0.91[ASN][1000 genomes]
rs2911564	0.94[CHB][hapmap];0.93[JPT][hapmap];0.81[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs2911565	0.81[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs2911566	1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs3768239	0.95[CEU][hapmap];0.95[CHB][hapmap];0.98[CHD][hapmap];0.95[GIH][hapmap];0.94[JPT][hapmap];0.95[MEX][hapmap];0.94[TSI][hapmap];0.90[AMR][1000 genomes];0.93[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs3768240	0.81[ASN][1000 genomes]
rs3768241	0.81[ASN][1000 genomes]
rs3768242	0.95[CHB][hapmap];1.00[JPT][hapmap];0.86[ASN][1000 genomes]
rs3768243	0.95[CHB][hapmap];0.93[CHD][hapmap];1.00[JPT][hapmap];0.86[ASN][1000 genomes]
rs4537578	0.95[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap];0.85[TSI][hapmap];0.81[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs57636989	0.86[ASN][1000 genomes]
rs6681911	0.95[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap];0.81[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs7524511	0.80[CHB][hapmap];0.85[JPT][hapmap]

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs4907086	COL24A1	cis	parietal	SCAN

Chromatin state (count:40 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:85087000-85147400	Weak transcription	Gastric	stomach
2	chr1:85099000-85109600	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
3	chr1:85099000-85115600	Weak transcription	Cortex derived primary cultured neurospheres	brain
4	chr1:85099000-85123400	Weak transcription	H9 Cell Line	embryonic stem cell
5	chr1:85099200-85109200	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
6	chr1:85099200-85109800	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
7	chr1:85099200-85115000	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
8	chr1:85099200-85121400	Weak transcription	NHDF-Ad	bronchial
9	chr1:85099200-85138200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
10	chr1:85099400-85115000	Weak transcription	Osteobl	bone
11	chr1:85099400-85131200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
12	chr1:85099600-85122600	Weak transcription	Fetal Brain Male	brain
13	chr1:85100600-85112400	Weak transcription	Rectal Mucosa Donor 31	rectum
14	chr1:85100600-85116800	Weak transcription	Rectal Mucosa Donor 29	rectum
15	chr1:85101000-85123200	Weak transcription	Fetal Kidney	kidney
16	chr1:85101000-85124400	Weak transcription	Hela-S3	cervix
17	chr1:85101400-85109000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
18	chr1:85101600-85121000	Weak transcription	Placenta	Placenta
19	chr1:85103000-85115000	Weak transcription	HMEC	breast
20	chr1:85104600-85116000	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
21	chr1:85104800-85111600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
22	chr1:85105000-85119000	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
23	chr1:85105800-85115000	Weak transcription	Small Intestine	intestine
24	chr1:85106000-85110800	Weak transcription	Fetal Thymus	thymus
25	chr1:85106000-85116600	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
26	chr1:85106200-85108000	Weak transcription	Fetal Intestine Large	intestine
27	chr1:85106200-85108200	Weak transcription	K562	blood
28	chr1:85106200-85112400	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
29	chr1:85106200-85115000	Weak transcription	Breast Myoepithelial Primary Cells	Breast
30	chr1:85106200-85140400	Weak transcription	NHEK	skin
31	chr1:85106400-85114800	Weak transcription	Fetal Brain Female	brain
32	chr1:85106400-85155400	Weak transcription	Sigmoid Colon	Sigmoid Colon
33	chr1:85106600-85114800	Weak transcription	Duodenum Mucosa	Duodenum
34	chr1:85106600-85116800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
35	chr1:85107200-85110000	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
36	chr1:85107200-85110000	Enhancers	Fetal Intestine Small	intestine
37	chr1:85107400-85110000	Enhancers	Fetal Heart	heart
38	chr1:85107600-85114800	Weak transcription	Primary B cells from cord blood	blood
39	chr1:85107600-85115000	Weak transcription	Primary T cells from cord blood	blood
40	chr1:85107800-85115400	Weak transcription	Brain Cingulate Gyrus	brain

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links