Variant report

Variant	rs6717735
Chromosome Location	chr2:173912865-173912866
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr2:173907898..173920360-chr2:173936226..173946823,30	MCF-7	breast:

Variant related genes	Relation type
ENSG00000091436	Chromatin interaction

Extended variants
information (count: 25 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:24)

rs_ID	r²[population]
rs1020599	0.94[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[AMR][1000 genomes];0.90[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10497403	0.94[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];0.95[GIH][hapmap];0.94[JPT][hapmap];0.86[MEX][hapmap];0.91[TSI][hapmap];0.84[AMR][1000 genomes];0.87[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs11687539	0.83[CEU][hapmap]
rs12463612	0.83[CEU][hapmap];0.83[GIH][hapmap]
rs12464956	0.82[ASW][hapmap];0.94[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.86[MEX][hapmap];0.97[TSI][hapmap];0.85[AMR][1000 genomes];0.89[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12474338	0.81[AFR][1000 genomes];0.92[AMR][1000 genomes];0.89[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs12474484	0.99[AMR][1000 genomes];0.95[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs1551248	0.84[CEU][hapmap]
rs1551249	0.94[ASW][hapmap];1.00[CEU][hapmap];0.93[CHD][hapmap];0.91[GIH][hapmap];0.84[JPT][hapmap];0.82[MKK][hapmap];0.89[TSI][hapmap];0.81[AFR][1000 genomes];0.85[AMR][1000 genomes];0.90[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs17710437	0.82[CEU][hapmap]
rs1973037	0.94[ASW][hapmap];1.00[CEU][hapmap];0.82[CHB][hapmap];0.93[CHD][hapmap];0.91[GIH][hapmap];0.84[JPT][hapmap];0.82[MKK][hapmap];0.89[TSI][hapmap];0.81[AFR][1000 genomes];0.83[AMR][1000 genomes];0.90[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2012213	0.88[ASW][hapmap];0.84[CEU][hapmap];0.84[GIH][hapmap];0.85[MKK][hapmap];0.86[TSI][hapmap]
rs3754747	0.83[CEU][hapmap]
rs3769210	0.84[CEU][hapmap];0.81[CHB][hapmap];0.86[CHD][hapmap];0.83[JPT][hapmap];0.84[ASN][1000 genomes]
rs3769211	0.84[CEU][hapmap];0.81[CHB][hapmap];0.83[JPT][hapmap];0.84[ASN][1000 genomes]
rs3769213	0.94[ASW][hapmap];1.00[CEU][hapmap];0.91[CHD][hapmap];1.00[GIH][hapmap];0.90[MEX][hapmap];0.92[MKK][hapmap];1.00[TSI][hapmap];0.82[AFR][1000 genomes];0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs3820835	0.82[CEU][hapmap]
rs4972529	0.82[CEU][hapmap]
rs60121307	0.81[AFR][1000 genomes];0.90[AMR][1000 genomes];0.92[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs6717489	0.84[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6717529	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.88[MKK][hapmap];1.00[TSI][hapmap];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6742219	1.00[CEU][hapmap];0.81[CHB][hapmap];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs734993	0.82[CEU][hapmap]
rs746179	0.83[CEU][hapmap]

Variant overlapped rSNPs/rCNVs (count:1 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv834459	chr2:173735192-173926750	Enhancers Weak transcription Strong transcription Active TSS Flanking Active TSS Bivalent Enhancer Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs6717735	CYBRD1	cis	parietal	SCAN
rs6717735	ZAK	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:46 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:173893000-173913200	Weak transcription	Brain Cingulate Gyrus	brain
2	chr2:173893200-173922000	Weak transcription	Brain Anterior Caudate	brain
3	chr2:173901000-173918000	Weak transcription	Brain Angular Gyrus	brain
4	chr2:173904400-173921400	Weak transcription	Ovary	ovary
5	chr2:173904600-173913000	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
6	chr2:173906800-173913000	Weak transcription	Skeletal Muscle Male	skeletal muscle
7	chr2:173908600-173916800	Enhancers	Fetal Intestine Large	intestine
8	chr2:173908600-173921400	Weak transcription	Left Ventricle	heart
9	chr2:173908800-173914400	Weak transcription	Liver	Liver
10	chr2:173908800-173924200	Weak transcription	Cortex derived primary cultured neurospheres	brain
11	chr2:173909000-173916800	Enhancers	Fetal Intestine Small	intestine
12	chr2:173909800-173915000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
13	chr2:173909800-173915200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
14	chr2:173910200-173913000	Weak transcription	Colon Smooth Muscle	Colon
15	chr2:173910400-173913000	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
16	chr2:173910600-173913000	Weak transcription	Fetal Lung	lung
17	chr2:173910600-173913000	Weak transcription	Rectal Smooth Muscle	rectum
18	chr2:173910600-173913200	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
19	chr2:173911800-173913800	Enhancers	Hela-S3	cervix
20	chr2:173911800-173918200	Weak transcription	Fetal Heart	heart
21	chr2:173912000-173914600	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
22	chr2:173912200-173914400	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
23	chr2:173912600-173913400	Enhancers	HMEC	breast
24	chr2:173912600-173913600	Enhancers	Breast Myoepithelial Primary Cells	Breast
25	chr2:173912600-173914400	Enhancers	NHEK	skin
26	chr2:173912600-173914400	Enhancers	NHLF	lung
27	chr2:173912800-173913000	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
28	chr2:173912800-173913200	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
29	chr2:173912800-173913200	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
30	chr2:173912800-173913200	Enhancers	Small Intestine	intestine
31	chr2:173912800-173913400	Enhancers	Pancreatic Islets	Pancreatic Islet
32	chr2:173912800-173913600	Enhancers	Duodenum Mucosa	Duodenum
33	chr2:173912800-173913600	Flanking Active TSS	A549	lung
34	chr2:173912800-173913800	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
35	chr2:173912800-173913800	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
36	chr2:173912800-173913800	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
37	chr2:173912800-173913800	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
38	chr2:173912800-173914200	Enhancers	NH-A	brain
39	chr2:173912800-173914200	Enhancers	NHDF-Ad	bronchial
40	chr2:173912800-173914200	Enhancers	Osteobl	bone
41	chr2:173912800-173914400	Enhancers	Muscle Satellite Cultured Cells	--
42	chr2:173912800-173914800	Enhancers	Skeletal Muscle Female	skeletal muscle
43	chr2:173912800-173915200	Enhancers	HepG2	liver
44	chr2:173912800-173915600	Enhancers	Stomach Mucosa	stomach
45	chr2:173912800-173916000	Enhancers	Monocytes-CD14+_RO01746	blood
46	chr2:173912800-173917000	Enhancers	Primary monocytes fromperipheralblood	blood

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links