Variant report

Variant	rs1119618
Chromosome Location	chr11:17528273-17528274
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	MAX	chr11:17528130-17528302	K562	blood:	n/a	n/a
2	MAX	chr11:17528011-17528344	K562	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr11:17499490..17502461-chr11:17527268..17529480,2	MCF-7	breast:
2	chr11:17403459..17408423-chr11:17525899..17528813,5	K562	blood:
3	chr11:17405209..17406183-chr11:17527113..17528432,4	MCF-7	breast:
4	chr11:17426028..17428651-chr11:17526756..17528624,2	MCF-7	breast:

Variant related genes	Relation type
USH1C	TF binding region
ENSG00000006071	Chromatin interaction
ENSG00000187486	Chromatin interaction

Extended variants
information (count: 14 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:13)

rs_ID	r²[population]
rs11024317	0.82[GIH][hapmap];0.83[TSI][hapmap]
rs12793661	0.88[GIH][hapmap]
rs16934376	1.00[CHB][hapmap];1.00[CHD][hapmap];0.85[JPT][hapmap];0.91[ASN][1000 genomes]
rs17703528	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.86[ASN][1000 genomes]
rs17714673	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.96[ASN][1000 genomes]
rs2073584	0.85[ASW][hapmap];0.80[CEU][hapmap];1.00[CHB][hapmap];0.86[GIH][hapmap]
rs4757538	0.91[ASN][1000 genomes]
rs7107406	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.96[ASN][1000 genomes]
rs7119876	0.94[GIH][hapmap];0.80[TSI][hapmap]
rs7129919	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.91[GIH][hapmap];1.00[JPT][hapmap];0.88[MEX][hapmap];1.00[TSI][hapmap];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72868496	0.96[ASN][1000 genomes]
rs878208	0.93[ASW][hapmap];0.80[CEU][hapmap];1.00[CHB][hapmap];0.87[LWK][hapmap];0.89[MKK][hapmap];0.93[YRI][hapmap];0.88[AFR][1000 genomes]
rs985575	1.00[CHB][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	nsv469895	chr11:17368270-17584220	Weak transcription Bivalent Enhancer Genic enhancers Enhancers Bivalent/Poised TSS Flanking Active TSS Active TSS ZNF genes & repeats Strong transcription Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	20 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs1119618	TMEM86A	cis	cerebellum	SCAN

Chromatin state (count:24 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:17512600-17530000	Weak transcription	Right Atrium	heart
2	chr11:17513600-17530600	Strong transcription	Fetal Intestine Small	intestine
3	chr11:17516800-17529600	Weak transcription	Sigmoid Colon	Sigmoid Colon
4	chr11:17516800-17553000	Weak transcription	Stomach Mucosa	stomach
5	chr11:17520000-17528600	Weak transcription	Gastric	stomach
6	chr11:17521400-17529800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
7	chr11:17521800-17529800	Weak transcription	Rectal Mucosa Donor 29	rectum
8	chr11:17522600-17531800	Weak transcription	Colonic Mucosa	Colon
9	chr11:17522800-17531200	Weak transcription	Rectal Mucosa Donor 31	rectum
10	chr11:17524600-17528400	Weak transcription	Fetal Intestine Large	intestine
11	chr11:17525400-17533600	Enhancers	Breast Myoepithelial Primary Cells	Breast
12	chr11:17526200-17539400	Weak transcription	Pancreas	Pancrea
13	chr11:17526600-17536600	Weak transcription	Brain Substantia Nigra	brain
14	chr11:17526600-17537200	Weak transcription	Brain Cingulate Gyrus	brain
15	chr11:17526800-17529800	Weak transcription	Colon Smooth Muscle	Colon
16	chr11:17526800-17529800	Weak transcription	Rectal Smooth Muscle	rectum
17	chr11:17526800-17529800	Weak transcription	HSMMtube	muscle
18	chr11:17527000-17528600	Weak transcription	Skeletal Muscle Female	skeletal muscle
19	chr11:17527000-17529200	Weak transcription	Fetal Heart	heart
20	chr11:17527600-17549200	Strong transcription	Duodenum Mucosa	Duodenum
21	chr11:17528000-17528400	Bivalent Enhancer	Foreskin Melanocyte Primary Cells skin01	Skin
22	chr11:17528200-17528400	Bivalent Enhancer	Fetal Adrenal Gland	Adrenal Gland
23	chr11:17528200-17528400	Enhancers	Ovary	ovary
24	chr11:17528200-17529800	Weak transcription	Spleen	Spleen

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links