Variant report

Variant	rs2749732
Chromosome Location	chr1:93565123-93565124
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr1:93560323..93561849-chr1:93563032..93565508,2	K562	blood:
2	chr1:93559141..93562193-chr1:93563032..93566364,5	K562	blood:
3	chr1:93551871..93559721-chr1:93563340..93568184,9	K562	blood:
4	chr1:93548731..93551569-chr1:93563538..93565587,2	MCF-7	breast:
5	chr1:93563011..93566516-chr1:93567594..93571757,4	K562	blood:

Extended variants
information (count: 49 )
Associated
traits (count: 5 )

rSNPs within LD-proxies of this variant (count:46)

rs_ID	r²[population]
rs1010476	1.00[ASW][hapmap];0.85[CEU][hapmap];0.95[CHB][hapmap];0.97[CHD][hapmap];0.88[GIH][hapmap];0.94[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];0.89[TSI][hapmap];1.00[YRI][hapmap];0.91[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs1060622	0.85[CHD][hapmap]
rs11164876	0.81[CHB][hapmap];0.85[CHD][hapmap]
rs12030843	0.90[CHB][hapmap]
rs12038699	0.87[CHD][hapmap]
rs12044557	0.90[CHB][hapmap];0.85[CHD][hapmap]
rs12118262	0.87[CHD][hapmap]
rs12128131	0.84[CHB][hapmap]
rs1335679	0.85[CHD][hapmap]
rs1474927	0.87[CHD][hapmap]
rs1572343	0.85[CHD][hapmap]
rs1856027	0.85[CHD][hapmap]
rs2255722	1.00[ASW][hapmap];0.95[CHB][hapmap];0.95[CHD][hapmap];0.85[GIH][hapmap];0.88[JPT][hapmap];0.87[LWK][hapmap];0.93[MEX][hapmap];0.84[MKK][hapmap];0.89[TSI][hapmap];0.80[ASN][1000 genomes]
rs2281524	0.85[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];0.88[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.89[TSI][hapmap];0.91[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs2281525	0.85[CHB][hapmap]
rs2295423	0.87[CHD][hapmap]
rs2484486	1.00[CHB][hapmap];0.92[CHD][hapmap];0.83[GIH][hapmap];0.88[JPT][hapmap];0.90[MKK][hapmap];0.83[TSI][hapmap];0.81[ASN][1000 genomes]
rs2765545	0.86[CHD][hapmap]
rs2783489	0.81[CHB][hapmap];0.84[CHD][hapmap]
rs2783490	1.00[ASW][hapmap];0.95[CHB][hapmap];0.95[CHD][hapmap];0.85[GIH][hapmap];0.88[JPT][hapmap];0.87[LWK][hapmap];0.93[MEX][hapmap];0.96[MKK][hapmap];0.89[TSI][hapmap];1.00[YRI][hapmap];0.83[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs2783493	0.83[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs2783495	1.00[ASW][hapmap];0.95[CHB][hapmap];0.95[CHD][hapmap];0.86[GIH][hapmap];0.88[JPT][hapmap];0.87[LWK][hapmap];0.93[MEX][hapmap];0.96[MKK][hapmap];0.89[TSI][hapmap];1.00[YRI][hapmap];0.80[ASN][1000 genomes]
rs2783496	0.80[ASN][1000 genomes]
rs2783497	0.80[ASN][1000 genomes]
rs2783499	0.90[CHB][hapmap];0.85[CHD][hapmap]
rs2783500	0.95[CHB][hapmap]
rs2783501	0.90[CHB][hapmap]
rs2815406	0.88[CHB][hapmap];1.00[YRI][hapmap];0.83[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs2815429	1.00[ASW][hapmap];0.85[CEU][hapmap];0.90[CHB][hapmap];0.95[CHD][hapmap];0.88[GIH][hapmap];0.94[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];0.89[TSI][hapmap];1.00[YRI][hapmap];0.91[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs3904665	0.82[CHB][hapmap]
rs3904666	1.00[ASW][hapmap];0.95[CHB][hapmap];0.95[CHD][hapmap];0.86[GIH][hapmap];0.88[JPT][hapmap];0.86[MEX][hapmap];0.83[TSI][hapmap]
rs4484937	0.90[CHB][hapmap];0.85[CHD][hapmap]
rs4847235	0.81[CHB][hapmap];0.85[CHD][hapmap]
rs4847399	0.87[CHD][hapmap]
rs489183	0.81[AFR][1000 genomes];0.91[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs531358	0.85[CHD][hapmap]
rs556446	0.89[AFR][1000 genomes];0.91[AMR][1000 genomes];0.99[ASN][1000 genomes]
rs579138	0.85[AFR][1000 genomes];0.94[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs61799470	0.81[ASN][1000 genomes]
rs6541404	0.85[CHD][hapmap]
rs6682670	0.85[CHD][hapmap]
rs693737	0.85[CHD][hapmap]
rs7513705	0.81[CHB][hapmap]
rs7517363	0.85[CHD][hapmap]
rs7535628	0.81[CHB][hapmap];0.83[CHD][hapmap]
rs7539307	0.81[CHB][hapmap]

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	nsv1008602	chr1:93176811-93640808	Enhancers Weak transcription Strong transcription Active TSS Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	51 gene(s)	inside rSNPs	diseases
2	nsv830614	chr1:93465978-93678700	Strong transcription Weak transcription Enhancers Active TSS Genic enhancers ZNF genes & repeats Flanking Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	34 gene(s)	inside rSNPs	diseases
3	nsv508404	chr1:93547383-93580012	Weak transcription Active TSS Enhancers Genic enhancers Strong transcription ZNF genes & repeats Flanking Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases

mRNA abundance (count:5)

SNP	Gene	Cis/trans	Tissue	Source
rs2749732	GLMN	cis	cerebellum	SCAN
rs2749732	DR1	cis	parietal	SCAN
rs2749732	CCDC18	cis	parietal	SCAN
rs2749732	HSP90B3P	cis	cerebellum	SCAN
rs2749732	TMEM190	trans	parietal	SCAN

Chromatin state (count:104 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:93545800-93568000	Weak transcription	Gastric	stomach
2	chr1:93545800-93578400	Weak transcription	Pancreas	Pancrea
3	chr1:93546000-93573000	Weak transcription	Placenta	Placenta
4	chr1:93546200-93602200	Weak transcription	Aorta	Aorta
5	chr1:93546400-93567200	Weak transcription	Right Atrium	heart
6	chr1:93546400-93569400	Weak transcription	Ovary	ovary
7	chr1:93547200-93576800	Weak transcription	Skeletal Muscle Female	skeletal muscle
8	chr1:93547400-93581800	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
9	chr1:93547600-93580600	Weak transcription	Adipose Nuclei	Adipose
10	chr1:93547600-93580600	Weak transcription	Brain Inferior Temporal Lobe	brain
11	chr1:93547600-93600000	Weak transcription	HSMMtube	muscle
12	chr1:93547800-93575400	Weak transcription	Hela-S3	cervix
13	chr1:93547800-93580600	Weak transcription	Fetal Kidney	kidney
14	chr1:93548000-93601800	Weak transcription	NHLF	lung
15	chr1:93548200-93576600	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
16	chr1:93548200-93576600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
17	chr1:93548200-93576800	Weak transcription	Osteobl	bone
18	chr1:93548200-93578400	Weak transcription	Lung	lung
19	chr1:93548600-93569400	Weak transcription	Duodenum Smooth Muscle	Duodenum
20	chr1:93548800-93581600	Weak transcription	Small Intestine	intestine
21	chr1:93549000-93576800	Weak transcription	Primary neutrophils fromperipheralblood	blood
22	chr1:93549000-93582400	Weak transcription	HMEC	breast
23	chr1:93549000-93582800	Weak transcription	NHEK	skin
24	chr1:93550600-93572600	Weak transcription	Fetal Muscle Leg	muscle
25	chr1:93551400-93579800	Weak transcription	Rectal Mucosa Donor 31	rectum
26	chr1:93551600-93570800	Weak transcription	HUVEC	blood vessel
27	chr1:93551600-93571000	Weak transcription	Fetal Intestine Large	intestine
28	chr1:93551600-93573000	Weak transcription	Fetal Muscle Trunk	muscle
29	chr1:93551600-93578400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
30	chr1:93551800-93565800	Weak transcription	H1 Cell Line	embryonic stem cell
31	chr1:93551800-93565800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
32	chr1:93551800-93569400	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
33	chr1:93551800-93571200	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
34	chr1:93551800-93572400	Weak transcription	Brain Germinal Matrix	brain
35	chr1:93551800-93572600	Weak transcription	Duodenum Mucosa	Duodenum
36	chr1:93551800-93576600	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
37	chr1:93551800-93579800	Weak transcription	Rectal Mucosa Donor 29	rectum
38	chr1:93552000-93572600	Weak transcription	Sigmoid Colon	Sigmoid Colon
39	chr1:93552000-93580000	Weak transcription	NH-A	brain
40	chr1:93552200-93573600	Weak transcription	Fetal Lung	lung
41	chr1:93552400-93569400	Weak transcription	Primary T cells fromperipheralblood	blood
42	chr1:93552600-93573000	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
43	chr1:93552800-93569200	Weak transcription	Cortex derived primary cultured neurospheres	brain
44	chr1:93553200-93567000	Weak transcription	Primary hematopoietic stem cells	blood
45	chr1:93553800-93566200	Weak transcription	K562	blood
46	chr1:93555400-93581000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
47	chr1:93555600-93565800	Weak transcription	Spleen	Spleen
48	chr1:93555600-93569600	Weak transcription	Fetal Intestine Small	intestine
49	chr1:93555600-93570800	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
50	chr1:93555600-93572600	Weak transcription	HSMM	muscle

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