Variant report

Variant	rs4930305
Chromosome Location	chr11:65464000-65464001
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:0)
CpG islands
(count:0)
Chromatin interactive
region (count:9)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:9 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr11:65462860..65464502-chr11:65486006..65488122,2	MCF-7	breast:
2	chr11:65463670..65466251-chr11:65542574..65544907,2	K562	blood:
3	chr11:65461869..65464366-chr11:65623666..65626207,3	MCF-7	breast:
4	chr11:65445422..65447498-chr11:65463363..65465929,2	MCF-7	breast:
5	chr11:65460118..65463457-chr11:65463620..65467916,5	K562	blood:
6	chr11:65429955..65431628-chr11:65463619..65466319,2	MCF-7	breast:
7	chr11:65429766..65432533-chr11:65462094..65464981,2	MCF-7	breast:
8	chr11:65403783..65405933-chr11:65463116..65465453,2	K562	blood:
9	chr11:65463676..65466407-chr11:65650763..65652793,2	MCF-7	breast:

No data

Variant related genes	Relation type
ENSG00000172757	Chromatin interaction
ENSG00000172922	Chromatin interaction
ENSG00000173039	Chromatin interaction
ENSG00000213445	Chromatin interaction
ENSG00000172732	Chromatin interaction
ENSG00000172977	Chromatin interaction
ENSG00000239356	Chromatin interaction

Extended variants
information (count: 20 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:11)

rs_ID	r²[population]
rs10400292	0.90[AMR][1000 genomes];0.90[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11227259	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];0.85[LWK][hapmap];1.00[MEX][hapmap];0.93[TSI][hapmap];0.89[YRI][hapmap];0.83[AFR][1000 genomes];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11227277	0.87[EUR][1000 genomes]
rs11820062	0.85[CEU][hapmap];0.95[CHB][hapmap];0.98[CHD][hapmap];0.82[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.87[TSI][hapmap];0.91[AMR][1000 genomes];0.87[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12576802	0.92[AMR][1000 genomes];0.92[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12787843	0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2127507	0.88[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[YRI][hapmap];0.82[AFR][1000 genomes];0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2170082	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.89[GIH][hapmap];1.00[JPT][hapmap];0.85[LWK][hapmap];1.00[MEX][hapmap];0.93[TSI][hapmap];0.89[YRI][hapmap];0.83[AFR][1000 genomes];0.97[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4244812	1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];0.89[GIH][hapmap];0.91[JPT][hapmap];1.00[MEX][hapmap];0.88[MKK][hapmap];0.95[TSI][hapmap];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7926512	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7932857	0.81[AFR][1000 genomes];0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:9 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv897716	chr11:65083491-65481166	Weak transcription Enhancers Genic enhancers Flanking Active TSS Strong transcription Transcr. at gene 5' and 3' Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	999 gene(s)	inside rSNPs	diseases
2	nsv897718	chr11:65140209-65577516	Enhancers Active TSS Flanking Active TSS Weak transcription Strong transcription Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	1003 gene(s)	inside rSNPs	diseases
3	nsv897723	chr11:65294830-65481166	Transcr. at gene 5' and 3' Enhancers Weak transcription Flanking Active TSS Active TSS Bivalent Enhancer Genic enhancers Strong transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	107 gene(s)	inside rSNPs	diseases
4	nsv897735	chr11:65335705-65481166	Flanking Active TSS Enhancers Strong transcription Genic enhancers 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 miRNA miRNA target site	98 gene(s)	inside rSNPs	diseases
5	nsv897736	chr11:65335705-65676516	Flanking Active TSS Active TSS Enhancers Weak transcription Strong transcription Transcr. at gene 5' and 3' Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	227 gene(s)	inside rSNPs	diseases
6	nsv897747	chr11:65353906-65481166	Weak transcription Enhancers Active TSS Bivalent/Poised TSS Genic enhancers Strong transcription Flanking Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	78 gene(s)	inside rSNPs	diseases
7	nsv897748	chr11:65392695-65466911	Active TSS Weak transcription Genic enhancers Bivalent/Poised TSS Flanking Active TSS Strong transcription Transcr. at gene 5' and 3' Enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	61 gene(s)	inside rSNPs	diseases
8	nsv897755	chr11:65405300-65481166	Strong transcription Active TSS Flanking Active TSS Enhancers Bivalent/Poised TSS Weak transcription Transcr. at gene 5' and 3' Genic enhancers Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	67 gene(s)	inside rSNPs	diseases
9	nsv430401	chr11:65419324-65788024	Enhancers Weak transcription Flanking Active TSS Strong transcription Transcr. at gene 5' and 3' Genic enhancers Flanking Bivalent TSS/Enh Active TSS Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	224 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs4930305	MRGPRD	cis	parietal	SCAN
rs4930305	SIPA1	cis	cerebellum	SCAN
rs4930305	RNASEH2C	cis	parietal	SCAN
rs4930305	SLC22A11	cis	cerebellum	SCAN

Chromatin state (count:26 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:65459400-65466200	Enhancers	Stomach Mucosa	stomach
2	chr11:65461200-65465000	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
3	chr11:65461800-65465600	Weak transcription	K562	blood
4	chr11:65462000-65465600	Weak transcription	Esophagus	oesophagus
5	chr11:65462000-65465800	Weak transcription	Gastric	stomach
6	chr11:65462400-65468000	Enhancers	Brain Hippocampus Middle	brain
7	chr11:65462600-65464400	Enhancers	Brain Cingulate Gyrus	brain
8	chr11:65462600-65464600	Enhancers	Brain Substantia Nigra	brain
9	chr11:65462600-65467800	Enhancers	Brain Inferior Temporal Lobe	brain
10	chr11:65463000-65464000	Enhancers	Adipose Nuclei	Adipose
11	chr11:65463000-65464000	Enhancers	Brain Dorsolateral Prefrontal Cortex	brain
12	chr11:65463000-65464000	Enhancers	Duodenum Smooth Muscle	Duodenum
13	chr11:65463000-65464000	Enhancers	HUVEC	blood vessel
14	chr11:65463000-65464200	Enhancers	Fetal Adrenal Gland	Adrenal Gland
15	chr11:65463000-65464600	Enhancers	Rectal Mucosa Donor 29	rectum
16	chr11:65463000-65464600	Enhancers	Sigmoid Colon	Sigmoid Colon
17	chr11:65463000-65464600	Enhancers	Skeletal Muscle Male	skeletal muscle
18	chr11:65463000-65464800	Enhancers	Brain Angular Gyrus	brain
19	chr11:65463000-65465200	Enhancers	Foreskin Melanocyte Primary Cells skin01	Skin
20	chr11:65463200-65464000	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
21	chr11:65463200-65464200	Enhancers	Fetal Muscle Trunk	muscle
22	chr11:65463400-65465000	Enhancers	Brain Anterior Caudate	brain
23	chr11:65463400-65465600	Weak transcription	Duodenum Mucosa	Duodenum
24	chr11:65463800-65464600	Weak transcription	Rectal Mucosa Donor 31	rectum
25	chr11:65463800-65474000	Weak transcription	Pancreas	Pancrea
26	chr11:65464000-65467400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links