Variant report

Variant	rs17359001
Chromosome Location	chr15:83531468-83531469
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr15:83223614..83226484-chr15:83530714..83532470,2	MCF-7	breast:
2	chr15:83528501..83531527-chr15:83534305..83537461,3	K562	blood:

Variant related genes	Relation type
ENSG00000214575	Chromatin interaction
ENSG00000260836	Chromatin interaction

Extended variants
information (count: 24 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:21)

rs_ID	r²[population]
rs1010820	0.82[CEU][hapmap];0.80[TSI][hapmap];1.00[ASN][1000 genomes]
rs1105714	1.00[ASN][1000 genomes]
rs11259957	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11856299	1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12442894	0.86[ASW][hapmap];0.82[CEU][hapmap];0.89[GIH][hapmap];0.83[TSI][hapmap];0.81[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17358518	1.00[ASN][1000 genomes]
rs17359494	1.00[CEU][hapmap];1.00[GIH][hapmap];0.95[LWK][hapmap];0.95[MEX][hapmap];0.97[MKK][hapmap];1.00[TSI][hapmap];0.87[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs17361375	0.83[TSI][hapmap]
rs2019208	1.00[ASN][1000 genomes]
rs2055891	0.80[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs55800901	1.00[ASN][1000 genomes]
rs62011706	1.00[ASN][1000 genomes]
rs62011709	0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62011712	0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62011735	0.90[AMR][1000 genomes];0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62011742	1.00[ASN][1000 genomes]
rs62011744	1.00[ASN][1000 genomes]
rs67022650	1.00[ASN][1000 genomes]
rs7179000	1.00[ASN][1000 genomes]
rs72753993	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs8031723	0.83[TSI][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	nsv469557	chr15:83417763-83560629	Enhancers Genic enhancers Weak transcription Flanking Active TSS Strong transcription Active TSS ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	45 gene(s)	inside rSNPs	diseases
2	nsv482340	chr15:83417763-83560629	Strong transcription Weak transcription Active TSS Enhancers ZNF genes & repeats Flanking Active TSS Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	45 gene(s)	inside rSNPs	diseases
3	nsv471687	chr15:83417764-83560629	Enhancers Flanking Active TSS Genic enhancers Strong transcription Weak transcription Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	45 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs17359001	C15orf40	cis	parietal	SCAN
rs17359001	WHAMM	cis	parietal	SCAN

Chromatin state (count:32 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:83504600-83549400	Weak transcription	Psoas Muscle	Psoas
2	chr15:83506200-83543800	Weak transcription	Pancreatic Islets	Pancreatic Islet
3	chr15:83507200-83539400	Weak transcription	Fetal Intestine Small	intestine
4	chr15:83513200-83532000	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
5	chr15:83514400-83542800	Weak transcription	Primary T cells from cord blood	blood
6	chr15:83519000-83535800	Weak transcription	HUES48 Cell Line	embryonic stem cell
7	chr15:83519000-83541400	Weak transcription	Brain Anterior Caudate	brain
8	chr15:83519200-83536200	Weak transcription	HUES6 Cell Line	embryonic stem cell
9	chr15:83519800-83544400	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
10	chr15:83520000-83543600	Weak transcription	HSMM	muscle
11	chr15:83520000-83549800	Weak transcription	Brain Cingulate Gyrus	brain
12	chr15:83520000-83563800	Weak transcription	Brain Hippocampus Middle	brain
13	chr15:83520200-83542000	Weak transcription	Brain Angular Gyrus	brain
14	chr15:83520200-83547000	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
15	chr15:83522400-83543400	Weak transcription	Fetal Muscle Trunk	muscle
16	chr15:83522600-83542200	Weak transcription	Fetal Muscle Leg	muscle
17	chr15:83523400-83540000	Weak transcription	Breast Myoepithelial Primary Cells	Breast
18	chr15:83523400-83540800	Weak transcription	Stomach Smooth Muscle	stomach
19	chr15:83523600-83541400	Weak transcription	Fetal Stomach	stomach
20	chr15:83523600-83558000	Weak transcription	Esophagus	oesophagus
21	chr15:83523800-83535600	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
22	chr15:83524600-83567800	Weak transcription	Left Ventricle	heart
23	chr15:83524800-83534400	Weak transcription	Adipose Nuclei	Adipose
24	chr15:83524800-83563800	Weak transcription	Cortex derived primary cultured neurospheres	brain
25	chr15:83526000-83541800	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
26	chr15:83527200-83539600	Weak transcription	HSMMtube	muscle
27	chr15:83528000-83531600	Weak transcription	Pancreas	Pancrea
28	chr15:83528000-83540400	Weak transcription	Skeletal Muscle Male	skeletal muscle
29	chr15:83528000-83540800	Weak transcription	Gastric	stomach
30	chr15:83528000-83542000	Weak transcription	Skeletal Muscle Female	skeletal muscle
31	chr15:83528000-83544000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
32	chr15:83530800-83533000	Strong transcription	Liver	Liver

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links