Variant report

Variant	rs10736683
Chromosome Location	chr11:57120621-57120622
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:8)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:8 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr11:57110145..57111927-chr11:57119276..57121800,2	K562	blood:
2	chr11:57120084..57121801-chr11:57123395..57125766,2	K562	blood:
3	chr11:57118779..57121066-chr11:57192252..57194028,2	K562	blood:
4	chr11:57111944..57114870-chr11:57120183..57122061,2	K562	blood:
5	chr11:57119644..57122336-chr11:57124896..57127727,2	K562	blood:
6	chr11:57119177..57122088-chr11:57123742..57126418,2	MCF-7	breast:
7	chr11:57109658..57111927-chr11:57120300..57122314,2	K562	blood:
8	chr11:57120084..57121849-chr11:57122754..57124895,2	K562	blood:

No data

Variant related genes	Relation type
ENSG00000134802	Chromatin interaction
ENSG00000266018	Chromatin interaction

Extended variants
information (count: 27 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:23)

rs_ID	r²[population]
rs10732882	0.81[CHD][hapmap];0.85[JPT][hapmap];0.81[ASN][1000 genomes]
rs10750859	0.94[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10792085	0.81[CHD][hapmap]
rs10896602	0.81[CHD][hapmap]
rs10896610	0.89[ASN][1000 genomes]
rs1837974	0.91[ASN][1000 genomes]
rs2003065	0.91[ASN][1000 genomes]
rs2013314	0.86[JPT][hapmap]
rs2276039	0.86[JPT][hapmap]
rs2276040	0.86[JPT][hapmap]
rs2276042	0.81[CHB][hapmap];0.88[CHD][hapmap];0.95[JPT][hapmap];0.89[ASN][1000 genomes]
rs3781899	0.86[JPT][hapmap]
rs3781901	0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3781902	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.96[MEX][hapmap];1.00[TSI][hapmap];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4570598	1.00[JPT][hapmap];0.93[MKK][hapmap];0.91[ASN][1000 genomes]
rs4939138	0.88[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4939140	0.86[JPT][hapmap]
rs4939141	0.86[JPT][hapmap]
rs55637147	0.81[ASN][1000 genomes]
rs56077100	0.91[ASN][1000 genomes]
rs879646	0.85[CHB][hapmap];0.88[CHD][hapmap];1.00[JPT][hapmap];0.91[ASN][1000 genomes]
rs894450	0.86[JPT][hapmap]
rs9667065	0.88[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	nsv915640	chr11:56814841-57139786	Weak transcription Transcr. at gene 5' and 3' Enhancers Genic enhancers Flanking Active TSS Strong transcription Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	34 gene(s)	inside rSNPs	diseases
2	nsv1044030	chr11:57073395-58035564	Transcr. at gene 5' and 3' Weak transcription Flanking Active TSS Strong transcription Enhancers Genic enhancers Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	136 gene(s)	inside rSNPs	diseases
3	nsv541047	chr11:57073395-58035564	Active TSS Enhancers Strong transcription Bivalent/Poised TSS Genic enhancers Flanking Active TSS Weak transcription Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	136 gene(s)	inside rSNPs	diseases
4	nsv541048	chr11:57076815-57120781	Flanking Active TSS Genic enhancers Active TSS Weak transcription Enhancers Strong transcription Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	29 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs10736683	LRRC55	cis	parietal	SCAN
rs10736683	OR5AN1	cis	parietal	SCAN
rs10736683	TMX2	cis	cerebellum	SCAN
rs10736683	OR5B12	cis	parietal	SCAN

Chromatin state (count:30 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:57117400-57120800	Weak transcription	Brain Cingulate Gyrus	brain
2	chr11:57117400-57122000	Weak transcription	Pancreas	Pancrea
3	chr11:57117600-57122000	Weak transcription	Skeletal Muscle Female	skeletal muscle
4	chr11:57117600-57126400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
5	chr11:57117600-57140000	Weak transcription	Right Atrium	heart
6	chr11:57117800-57120800	Weak transcription	H1 Cell Line	embryonic stem cell
7	chr11:57117800-57121000	Weak transcription	Brain Hippocampus Middle	brain
8	chr11:57117800-57122000	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
9	chr11:57117800-57122000	Weak transcription	Skeletal Muscle Male	skeletal muscle
10	chr11:57119400-57123600	Weak transcription	A549	lung
11	chr11:57119800-57124800	Enhancers	Fetal Brain Male	brain
12	chr11:57120000-57121000	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
13	chr11:57120000-57121600	Enhancers	Primary hematopoietic stem cells short term culture	blood
14	chr11:57120000-57121600	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
15	chr11:57120000-57126600	Enhancers	Primary hematopoietic stem cells	blood
16	chr11:57120000-57126800	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
17	chr11:57120200-57122600	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
18	chr11:57120200-57123400	Enhancers	Fetal Brain Female	brain
19	chr11:57120200-57123400	Enhancers	Fetal Muscle Leg	muscle
20	chr11:57120400-57120800	Enhancers	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
21	chr11:57120400-57121000	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
22	chr11:57120400-57121200	Enhancers	iPS-20b Cell Line	embryonic stem cell
23	chr11:57120400-57121600	Enhancers	iPS-15b Cell Line	embryonic stem cell
24	chr11:57120400-57122000	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
25	chr11:57120400-57122000	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
26	chr11:57120600-57121000	Enhancers	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
27	chr11:57120600-57121400	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
28	chr11:57120600-57121400	Enhancers	iPS-18 Cell Line	embryonic stem cell
29	chr11:57120600-57121400	Flanking Active TSS	K562	blood
30	chr11:57120600-57121600	Enhancers	HUES6 Cell Line	embryonic stem cell

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links