Variant report

Variant	rs2289506
Chromosome Location	chr3:100064902-100064903
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr3:100062699..100065082-chr3:100066080..100068778,2	K562	blood:
2	chr3:100053577..100055099-chr3:100063294..100065719,2	MCF-7	breast:
3	chr3:100064881..100067551-chr3:100115923..100118439,2	MCF-7	breast:
4	chr3:100057791..100061321-chr3:100063708..100069038,7	MCF-7	breast:

Variant related genes	Relation type
ENSG00000114021	Chromatin interaction

Extended variants
information (count: 28 )
Associated
traits (count: 7 )

rSNPs within LD-proxies of this variant (count:26)

rs_ID	r²[population]
rs1045206	0.84[CEU][hapmap];0.83[EUR][1000 genomes]
rs11714045	1.00[CEU][hapmap];0.94[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.83[MKK][hapmap];0.95[TSI][hapmap];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1214375	0.84[CEU][hapmap];0.87[GIH][hapmap];0.83[EUR][1000 genomes]
rs13071905	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[AMR][1000 genomes];0.90[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs13073252	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.87[GIH][hapmap];1.00[JPT][hapmap];0.90[MEX][hapmap];0.83[AMR][1000 genomes];0.90[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs13082297	1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1486308	1.00[ASW][hapmap];0.91[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];0.83[MKK][hapmap];0.88[AFR][1000 genomes];0.86[AMR][1000 genomes];0.90[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1561743	0.84[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs2289502	0.81[AMR][1000 genomes];0.84[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2289505	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34645158	0.88[AFR][1000 genomes];0.81[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35281373	0.88[AFR][1000 genomes];0.81[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35945684	0.83[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs3772693	1.00[ASW][hapmap];0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.87[GIH][hapmap];1.00[JPT][hapmap];0.90[MEX][hapmap];0.83[MKK][hapmap];0.81[TSI][hapmap];0.88[AFR][1000 genomes];0.84[AMR][1000 genomes];0.89[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs395399	0.83[EUR][1000 genomes]
rs4441690	0.83[ASN][1000 genomes]
rs4928123	0.88[AFR][1000 genomes];0.86[AMR][1000 genomes];0.90[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4928124	0.82[ASN][1000 genomes]
rs4928125	0.92[CEU][hapmap]
rs61436017	0.95[ASN][1000 genomes]
rs62274141	0.82[ASN][1000 genomes]
rs62274146	0.84[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62274147	0.88[AFR][1000 genomes];0.86[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73150352	0.84[ASN][1000 genomes]
rs756103	0.83[ASN][1000 genomes]
rs7649598	1.00[ASW][hapmap];0.96[CEU][hapmap];0.94[CHB][hapmap];1.00[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];0.97[TSI][hapmap];0.94[AFR][1000 genomes];0.96[AMR][1000 genomes];0.87[EUR][1000 genomes];0.95[ASN][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	nsv916476	chr3:99478229-100124625	Active TSS Weak transcription Flanking Active TSS Strong transcription Enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	46 gene(s)	inside rSNPs	diseases
2	nsv1003924	chr3:99933762-100112690	Strong transcription Weak transcription Enhancers Genic enhancers Bivalent/Poised TSS Flanking Active TSS Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	17 gene(s)	inside rSNPs	diseases

mRNA abundance (count:7)

SNP	Gene	Cis/trans	Tissue	Source
rs2289506	C3orf26	cis	cerebellum	SCAN
rs2289506	PCNP	cis	parietal	SCAN
rs2289506	FAM55C	cis	parietal	SCAN
rs2289506	NIT2	cis	parietal	SCAN
rs2289506	TMEM45A	Cis_1M	lymphoblastoid	RTeQTL
rs2289506	TOMM70A	Cis_1M	lymphoblastoid	RTeQTL
rs2289506	OR5H6	cis	cerebellum	SCAN

Chromatin state (count:125 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:100054000-100065000	Weak transcription	Spleen	Spleen
2	chr3:100054200-100081000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
3	chr3:100054400-100067600	Weak transcription	Psoas Muscle	Psoas
4	chr3:100054600-100102600	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
5	chr3:100054800-100067200	Weak transcription	Esophagus	oesophagus
6	chr3:100054800-100067400	Weak transcription	Small Intestine	intestine
7	chr3:100054800-100067600	Weak transcription	Colonic Mucosa	Colon
8	chr3:100054800-100068600	Weak transcription	Pancreas	Pancrea
9	chr3:100054800-100069000	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
10	chr3:100054800-100081000	Weak transcription	H1 Cell Line	embryonic stem cell
11	chr3:100054800-100097200	Weak transcription	Stomach Mucosa	stomach
12	chr3:100054800-100102200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
13	chr3:100055000-100068200	Weak transcription	iPS-20b Cell Line	embryonic stem cell
14	chr3:100055000-100068600	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
15	chr3:100055000-100082400	Weak transcription	iPS-15b Cell Line	embryonic stem cell
16	chr3:100055200-100068200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
17	chr3:100055200-100071000	Weak transcription	HepG2	liver
18	chr3:100057000-100069200	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
19	chr3:100057000-100069600	Strong transcription	Dnd41	blood
20	chr3:100057200-100066800	Strong transcription	HSMM	muscle
21	chr3:100057200-100069200	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
22	chr3:100057200-100069600	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
23	chr3:100057400-100069600	Strong transcription	Monocytes-CD14+_RO01746	blood
24	chr3:100057600-100066200	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
25	chr3:100057600-100069200	Strong transcription	Stomach Smooth Muscle	stomach
26	chr3:100057600-100069600	Strong transcription	Primary B cells from peripheral blood	blood
27	chr3:100057600-100069600	Strong transcription	Adipose Nuclei	Adipose
28	chr3:100057800-100066200	Strong transcription	HMEC	breast
29	chr3:100057800-100069600	Strong transcription	Duodenum Smooth Muscle	Duodenum
30	chr3:100057800-100071400	Weak transcription	Fetal Heart	heart
31	chr3:100058000-100065800	Strong transcription	A549	lung
32	chr3:100058000-100069600	Strong transcription	Primary monocytes fromperipheralblood	blood
33	chr3:100058000-100069600	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
34	chr3:100058000-100069600	Strong transcription	Skeletal Muscle Female	skeletal muscle
35	chr3:100058200-100065200	Strong transcription	HUES64 Cell Line	embryonic stem cell
36	chr3:100058200-100065800	Strong transcription	Placenta	Placenta
37	chr3:100058200-100069600	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
38	chr3:100058200-100069600	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
39	chr3:100058400-100065800	Strong transcription	Muscle Satellite Cultured Cells	--
40	chr3:100059200-100065000	Weak transcription	Gastric	stomach
41	chr3:100059200-100067600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
42	chr3:100059400-100069600	Strong transcription	Primary T cells fromperipheralblood	blood
43	chr3:100060000-100069600	Strong transcription	Cortex derived primary cultured neurospheres	brain
44	chr3:100060200-100067800	Weak transcription	H9 Cell Line	embryonic stem cell
45	chr3:100060200-100068400	Weak transcription	iPS-18 Cell Line	embryonic stem cell
46	chr3:100060200-100069600	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
47	chr3:100060800-100066400	Weak transcription	Right Ventricle	heart
48	chr3:100061000-100065000	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
49	chr3:100061000-100067000	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
50	chr3:100061000-100068600	Weak transcription	Pancreatic Islets	Pancreatic Islet

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