Variant report

Variant	rs746179
Chromosome Location	chr2:174026324-174026325
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 46 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:43)

rs_ID	r²[population]
rs10497402	0.94[CHD][hapmap]
rs11680555	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11687539	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[AMR][1000 genomes];0.92[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12463612	0.87[CEU][hapmap]
rs1551249	0.83[CEU][hapmap]
rs16861363	0.88[CHD][hapmap]
rs17710065	0.93[CEU][hapmap];0.91[CHB][hapmap];1.00[JPT][hapmap];0.90[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs17710437	1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];0.83[TSI][hapmap];0.83[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1809139	0.93[CEU][hapmap];0.91[CHB][hapmap];0.91[JPT][hapmap];0.91[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs1973037	0.83[CEU][hapmap]
rs2043950	0.88[CEU][hapmap];1.00[CHB][hapmap];0.92[JPT][hapmap];0.88[ASN][1000 genomes]
rs2358088	0.88[ASN][1000 genomes]
rs3754739	0.92[ASN][1000 genomes]
rs3754747	1.00[CEU][hapmap];0.91[CHB][hapmap];0.88[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];0.83[TSI][hapmap]
rs3754749	0.81[CEU][hapmap]
rs3769159	0.88[CEU][hapmap];0.91[CHB][hapmap];0.94[CHD][hapmap];0.91[GIH][hapmap];1.00[JPT][hapmap];0.90[TSI][hapmap];0.90[YRI][hapmap];0.82[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs3769162	0.88[CEU][hapmap];0.91[CHB][hapmap];0.92[JPT][hapmap];0.86[ASN][1000 genomes]
rs3769163	1.00[JPT][hapmap];0.81[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs3769173	0.88[ASN][1000 genomes]
rs3769201	0.82[CEU][hapmap]
rs3769213	0.83[CEU][hapmap]
rs3820835	0.88[CEU][hapmap];0.91[CHB][hapmap];0.92[JPT][hapmap]
rs4399689	0.90[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4972529	0.88[CEU][hapmap];0.92[JPT][hapmap]
rs4972532	0.84[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs56980119	0.81[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs59500540	0.81[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs61264428	0.91[AFR][1000 genomes];0.88[ASN][1000 genomes]
rs62175824	0.81[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6433392	0.85[CEU][hapmap]
rs6717529	0.83[CEU][hapmap]
rs6717735	0.83[CEU][hapmap]
rs6742219	0.86[CEU][hapmap]
rs6759847	0.91[CHB][hapmap];0.92[JPT][hapmap]
rs722864	0.82[CHB][hapmap];0.81[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs734993	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.92[TSI][hapmap];0.90[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73974105	0.93[AFR][1000 genomes];0.84[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7567355	0.87[CEU][hapmap];0.82[CHB][hapmap];1.00[JPT][hapmap];0.81[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7575319	0.82[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7599340	0.94[CEU][hapmap]
rs7601536	0.82[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs935006	0.93[CEU][hapmap];1.00[CHB][hapmap];0.84[CHD][hapmap];0.83[GIH][hapmap];0.92[JPT][hapmap];0.89[MKK][hapmap];0.90[TSI][hapmap];0.83[AMR][1000 genomes];0.85[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs935007	0.87[CEU][hapmap];1.00[CHB][hapmap];0.83[GIH][hapmap];0.92[JPT][hapmap];0.86[MKK][hapmap];0.93[TSI][hapmap];0.83[EUR][1000 genomes];0.91[ASN][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	nsv1011724	chr2:173916482-174231908	Enhancers Flanking Bivalent TSS/Enh Strong transcription Flanking Active TSS Weak transcription Bivalent Enhancer Active TSS Bivalent/Poised TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	15 gene(s)	inside rSNPs	diseases
2	nsv834460	chr2:173919464-174085288	Strong transcription Enhancers ZNF genes & repeats Weak transcription Flanking Active TSS Transcr. at gene 5' and 3' Genic enhancers Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
3	nsv834461	chr2:173979734-174038471	Enhancers Weak transcription ZNF genes & repeats Strong transcription Flanking Active TSS Active TSS Bivalent Enhancer Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs746179	CYBRD1	cis	parietal	SCAN
rs746179	ZAK	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:58 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:174012800-174026600	Enhancers	Skeletal Muscle Female	skeletal muscle
2	chr2:174015400-174027400	Weak transcription	Fetal Muscle Leg	muscle
3	chr2:174015400-174047000	Weak transcription	Rectal Smooth Muscle	rectum
4	chr2:174016200-174048800	Weak transcription	K562	blood
5	chr2:174016400-174028200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
6	chr2:174021600-174027000	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
7	chr2:174021600-174027800	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
8	chr2:174021600-174030400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
9	chr2:174021800-174026400	Enhancers	Breast Myoepithelial Primary Cells	Breast
10	chr2:174022000-174027800	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
11	chr2:174022400-174026400	Enhancers	NHEK	skin
12	chr2:174022400-174026600	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
13	chr2:174022400-174026600	Enhancers	HMEC	breast
14	chr2:174023800-174026600	Enhancers	Primary monocytes fromperipheralblood	blood
15	chr2:174024000-174026600	Enhancers	Osteobl	bone
16	chr2:174024200-174026600	Flanking Active TSS	Primary neutrophils fromperipheralblood	blood
17	chr2:174024200-174026600	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
18	chr2:174024200-174026600	Enhancers	Adipose Nuclei	Adipose
19	chr2:174024200-174026600	Enhancers	Liver	Liver
20	chr2:174024200-174026600	Enhancers	Fetal Heart	heart
21	chr2:174024400-174026400	Enhancers	Colon Smooth Muscle	Colon
22	chr2:174024400-174026400	Enhancers	Stomach Smooth Muscle	stomach
23	chr2:174024800-174026400	Flanking Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
24	chr2:174024800-174037200	Weak transcription	Fetal Muscle Trunk	muscle
25	chr2:174025000-174026400	Enhancers	Duodenum Mucosa	Duodenum
26	chr2:174025000-174026600	Flanking Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
27	chr2:174025000-174028000	Weak transcription	Primary hematopoietic stem cells short term culture	blood
28	chr2:174025200-174026600	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
29	chr2:174025200-174029200	Weak transcription	HUVEC	blood vessel
30	chr2:174025400-174026400	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
31	chr2:174025400-174026400	Enhancers	Duodenum Smooth Muscle	Duodenum
32	chr2:174025400-174026400	Enhancers	Left Ventricle	heart
33	chr2:174025400-174026600	Enhancers	Psoas Muscle	Psoas
34	chr2:174025400-174026600	Enhancers	Sigmoid Colon	Sigmoid Colon
35	chr2:174025400-174027000	Enhancers	HepG2	liver
36	chr2:174025400-174027200	Enhancers	Fetal Intestine Large	intestine
37	chr2:174025600-174026600	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
38	chr2:174025800-174026400	Enhancers	Muscle Satellite Cultured Cells	--
39	chr2:174025800-174026600	Enhancers	A549	lung
40	chr2:174025800-174030000	Weak transcription	Ovary	ovary
41	chr2:174026000-174026400	Weak transcription	Esophagus	oesophagus
42	chr2:174026000-174026600	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
43	chr2:174026000-174026600	Active TSS	Right Ventricle	heart
44	chr2:174026000-174026600	Enhancers	NHDF-Ad	bronchial
45	chr2:174026000-174026800	Enhancers	Hela-S3	cervix
46	chr2:174026000-174027000	Enhancers	NHLF	lung
47	chr2:174026000-174029400	Weak transcription	Fetal Lung	lung
48	chr2:174026000-174030600	Weak transcription	Pancreas	Pancrea
49	chr2:174026000-174036800	Weak transcription	Small Intestine	intestine
50	chr2:174026000-174037400	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived

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