Variant report

Variant	rs3793080
Chromosome Location	chr6:33767803-33767804
allele	A/G
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	chr6:33766337..33768230-chr6:33769399..33771793,3	MCF-7	breast:
2	chr6:33758412..33760501-chr6:33767524..33770306,2	MCF-7	breast:
3	chr6:33765705..33768539-chr6:33770119..33775506,6	K562	blood:
4	chr6:33700010..33701892-chr6:33765256..33768196,2	MCF-7	breast:
5	chr6:33767158..33770119-chr6:33775833..33777551,2	MCF-7	breast:
6	chr6:33762823..33764594-chr6:33767158..33770034,2	K562	blood:
7	chr6:33765957..33768539-chr6:33771317..33775505,3	K562	blood:
8	chr6:33767719..33770571-chr6:33780655..33782252,3	K562	blood:

No data

Variant related genes	Relation type
ENSG00000096395	Chromatin interaction

Extended variants
information (count: 60 )
Associated
traits (count: 5 )

rSNPs within LD-proxies of this variant (count:56)

rs_ID	r²[population]
rs10456420	0.97[EUR][1000 genomes]
rs10456421	0.91[EUR][1000 genomes]
rs10947432	0.80[TSI][hapmap]
rs12153877	0.95[EUR][1000 genomes]
rs12189725	1.00[CEU][hapmap];0.86[JPT][hapmap];0.83[TSI][hapmap];0.83[EUR][1000 genomes]
rs12192035	0.89[CEU][hapmap];0.91[EUR][1000 genomes]
rs12192087	0.89[EUR][1000 genomes]
rs12193658	1.00[CEU][hapmap];0.83[EUR][1000 genomes]
rs12195409	0.97[EUR][1000 genomes]
rs12198383	0.89[CEU][hapmap];0.92[EUR][1000 genomes]
rs12199132	0.83[EUR][1000 genomes]
rs12203688	0.80[TSI][hapmap]
rs12204620	0.97[EUR][1000 genomes]
rs12204992	0.97[EUR][1000 genomes]
rs12211490	1.00[CEU][hapmap];0.86[JPT][hapmap];0.90[TSI][hapmap];0.95[EUR][1000 genomes]
rs12211554	1.00[CEU][hapmap];0.86[JPT][hapmap];0.95[EUR][1000 genomes]
rs12211565	0.95[EUR][1000 genomes]
rs12215329	0.90[EUR][1000 genomes]
rs12660955	0.82[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs12662447	0.83[EUR][1000 genomes]
rs13200063	1.00[CEU][hapmap];0.86[JPT][hapmap];0.96[EUR][1000 genomes]
rs13204162	0.80[TSI][hapmap]
rs13206228	0.92[EUR][1000 genomes]
rs13207666	0.81[EUR][1000 genomes]
rs13213889	0.94[EUR][1000 genomes]
rs2274459	1.00[CEU][hapmap];0.86[JPT][hapmap];0.93[TSI][hapmap];0.82[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs2281831	0.80[TSI][hapmap]
rs2281918	0.80[TSI][hapmap]
rs2281919	0.80[TSI][hapmap]
rs2296749	1.00[CEU][hapmap];0.97[EUR][1000 genomes]
rs34139049	0.90[EUR][1000 genomes]
rs34339105	0.94[EUR][1000 genomes]
rs34460651	0.96[EUR][1000 genomes]
rs34472165	0.82[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs34869648	0.95[EUR][1000 genomes]
rs34884883	0.82[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs35274562	0.90[EUR][1000 genomes]
rs35328423	0.86[EUR][1000 genomes]
rs35366046	0.89[EUR][1000 genomes]
rs35445446	0.90[EUR][1000 genomes]
rs35646598	0.90[EUR][1000 genomes]
rs35721478	0.92[EUR][1000 genomes]
rs35797388	0.96[EUR][1000 genomes]
rs35964955	0.80[EUR][1000 genomes]
rs36122085	0.82[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs3806107	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.84[MEX][hapmap];0.98[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3818532	0.80[TSI][hapmap]
rs66617522	0.92[EUR][1000 genomes]
rs66670017	0.82[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs68168863	0.82[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs6925337	0.81[CEU][hapmap];0.82[CHB][hapmap];0.86[JPT][hapmap];0.93[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs729376	1.00[CEU][hapmap];0.85[JPT][hapmap];0.83[EUR][1000 genomes]
rs751095	0.97[EUR][1000 genomes]
rs755239	0.82[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs877187	1.00[CEU][hapmap];0.86[JPT][hapmap];0.83[TSI][hapmap];0.83[EUR][1000 genomes]
rs9296097	0.80[TSI][hapmap]

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	nsv462897	chr6:33717770-33778964	Genic enhancers Enhancers Weak transcription Bivalent Enhancer Strong transcription Flanking Active TSS Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
2	nsv602839	chr6:33717770-33778964	Enhancers Genic enhancers Flanking Active TSS Active TSS Weak transcription Strong transcription Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
3	nsv462898	chr6:33723383-33768897	Weak transcription Active TSS Strong transcription Flanking Active TSS Enhancers Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region	11 gene(s)	inside rSNPs	diseases
4	nsv602840	chr6:33723383-33768897	Enhancers Flanking Active TSS Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Weak transcription Genic enhancers Strong transcription ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region	11 gene(s)	inside rSNPs	diseases

mRNA abundance (count:5)

SNP	Gene	Cis/trans	Tissue	Source
rs3793080	LEMD2	cis	parietal	SCAN
rs3793080	ITPR3	cis	multi-tissue	Pritchard
rs3793080	LEMD2	cis	cerebellum	SCAN
rs3793080	C6orf125	cis	cerebellum	SCAN
rs3793080	C6orf227	cis	parietal	SCAN

Chromatin state (count:27 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:33757600-33775800	Weak transcription	Right Atrium	heart
2	chr6:33763600-33771600	Weak transcription	Fetal Intestine Small	intestine
3	chr6:33765800-33769200	Weak transcription	Brain Germinal Matrix	brain
4	chr6:33765800-33770200	Weak transcription	iPS-15b Cell Line	embryonic stem cell
5	chr6:33766000-33769200	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
6	chr6:33766000-33770200	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
7	chr6:33766000-33776000	Weak transcription	HUES48 Cell Line	embryonic stem cell
8	chr6:33766200-33769000	Weak transcription	Cortex derived primary cultured neurospheres	brain
9	chr6:33766600-33770000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
10	chr6:33766800-33768800	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
11	chr6:33766800-33769800	Weak transcription	HUES6 Cell Line	embryonic stem cell
12	chr6:33766800-33776400	Weak transcription	HUES64 Cell Line	embryonic stem cell
13	chr6:33767000-33768000	Enhancers	Adipose Nuclei	Adipose
14	chr6:33767000-33768200	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
15	chr6:33767000-33768600	Enhancers	Fetal Muscle Leg	muscle
16	chr6:33767200-33768200	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
17	chr6:33767200-33768200	Enhancers	Osteobl	bone
18	chr6:33767200-33768400	Enhancers	NHDF-Ad	bronchial
19	chr6:33767200-33768600	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
20	chr6:33767400-33768000	Enhancers	Right Ventricle	heart
21	chr6:33767400-33768400	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
22	chr6:33767400-33768400	Bivalent Enhancer	Fetal Muscle Trunk	muscle
23	chr6:33767600-33768200	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
24	chr6:33767800-33768000	Bivalent Enhancer	Skeletal Muscle Female	skeletal muscle
25	chr6:33767800-33768200	Bivalent/Poised TSS	Foreskin Fibroblast Primary Cells skin02	Skin
26	chr6:33767800-33768800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
27	chr6:33767800-33769000	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived

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