Variant report

Variant	rs236358
Chromosome Location	chr6:36800611-36800612
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr6:36799434..36803274-chr6:36828928..36832166,3	MCF-7	breast:
2	chr6:36799628..36801268-chr6:36817100..36819975,2	K562	blood:
3	chr6:36798286..36801016-chr6:36828535..36830113,2	MCF-7	breast:
4	chr6:36795234..36797828-chr6:36799282..36801814,2	MCF-7	breast:

Extended variants
information (count: 11 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:7)

rs_ID	r²[population]
rs12528273	0.85[CEU][hapmap];0.95[JPT][hapmap];0.86[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs236357	0.84[CEU][hapmap];0.86[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs236373	0.80[JPT][hapmap]
rs460539	0.84[JPT][hapmap]
rs6910832	0.80[JPT][hapmap]
rs9366917	0.82[CHB][hapmap];0.85[JPT][hapmap];0.85[ASN][1000 genomes]
rs9394384	0.83[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[AMR][1000 genomes];0.88[EUR][1000 genomes];0.98[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1023171	chr6:36686935-36880899	Enhancers Flanking Active TSS Weak transcription Active TSS Strong transcription Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	27 gene(s)	inside rSNPs	diseases
2	nsv538202	chr6:36686935-36880899	Enhancers Weak transcription Strong transcription Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	27 gene(s)	inside rSNPs	diseases
3	nsv1033261	chr6:36687424-36837315	Weak transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh Enhancers Strong transcription Genic enhancers Flanking Active TSS Active TSS Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	16 gene(s)	inside rSNPs	diseases
4	nsv5262	chr6:36799329-36826210	Weak transcription Bivalent Enhancer Enhancers Flanking Active TSS Active TSS Strong transcription Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	9 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs236358	C6orf89	cis	parietal	SCAN
rs236358	C6orf89	cis	cerebellum	SCAN

Chromatin state (count:29 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:36788400-36802400	Weak transcription	Fetal Kidney	kidney
2	chr6:36789800-36802200	Weak transcription	H1 Cell Line	embryonic stem cell
3	chr6:36791200-36805800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
4	chr6:36795200-36802600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
5	chr6:36795800-36801800	Weak transcription	Primary neutrophils fromperipheralblood	blood
6	chr6:36795800-36802200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
7	chr6:36796400-36802200	Weak transcription	Placenta	Placenta
8	chr6:36798200-36802600	Weak transcription	Brain Substantia Nigra	brain
9	chr6:36798600-36802200	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
10	chr6:36798600-36802400	Weak transcription	Brain Angular Gyrus	brain
11	chr6:36798600-36802400	Weak transcription	Brain Inferior Temporal Lobe	brain
12	chr6:36798600-36802400	Weak transcription	Fetal Brain Male	brain
13	chr6:36798600-36802800	Weak transcription	Left Ventricle	heart
14	chr6:36798600-36805400	Weak transcription	Right Ventricle	heart
15	chr6:36798600-36805400	Weak transcription	HUVEC	blood vessel
16	chr6:36798600-36806800	Weak transcription	Ovary	ovary
17	chr6:36798800-36802200	Weak transcription	Fetal Brain Female	brain
18	chr6:36798800-36802200	Weak transcription	Fetal Stomach	stomach
19	chr6:36798800-36802400	Weak transcription	Brain Germinal Matrix	brain
20	chr6:36798800-36802400	Enhancers	HepG2	liver
21	chr6:36798800-36802800	Weak transcription	Breast Myoepithelial Primary Cells	Breast
22	chr6:36798800-36804000	Weak transcription	Brain Anterior Caudate	brain
23	chr6:36798800-36805600	Weak transcription	Right Atrium	heart
24	chr6:36800000-36801200	ZNF genes & repeats	Fetal Intestine Small	intestine
25	chr6:36800000-36801600	Genic enhancers	Cortex derived primary cultured neurospheres	brain
26	chr6:36800000-36802200	Weak transcription	Fetal Heart	heart
27	chr6:36800200-36801400	ZNF genes & repeats	Fetal Muscle Leg	muscle
28	chr6:36800400-36801200	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
29	chr6:36800400-36801800	Weak transcription	Fetal Muscle Trunk	muscle

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links