Variant report

Variant	rs3828783
Chromosome Location	chr6:33767727-33767728
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: 41 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:36)

rs_ID	r²[population]
rs1075379	0.82[CHB][hapmap];0.94[CHD][hapmap];1.00[JPT][hapmap];0.81[ASN][1000 genomes]
rs11753083	0.91[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs11754690	0.83[CEU][hapmap];0.90[CHB][hapmap];1.00[JPT][hapmap];0.88[AMR][1000 genomes];0.84[ASN][1000 genomes]
rs11755593	0.84[AMR][1000 genomes];0.84[ASN][1000 genomes]
rs11757524	0.92[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs11758463	0.91[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs11759011	0.87[GIH][hapmap]
rs12524768	1.00[JPT][hapmap];0.82[AMR][1000 genomes];0.84[ASN][1000 genomes]
rs12524835	0.90[CHB][hapmap];0.88[JPT][hapmap];0.83[AMR][1000 genomes]
rs1887340	0.89[CHB][hapmap];0.90[JPT][hapmap]
rs2281820	0.82[CHB][hapmap];0.83[CHD][hapmap]
rs2395400	1.00[JPT][hapmap];0.88[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs2894342	0.83[CHD][hapmap]
rs3763253	0.83[CHD][hapmap]
rs4711346	0.81[CEU][hapmap];0.90[CHB][hapmap];0.88[JPT][hapmap]
rs55775340	0.89[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs61394483	0.91[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs61662306	0.88[AMR][1000 genomes];0.84[ASN][1000 genomes]
rs6910736	0.83[ASN][1000 genomes]
rs6921487	0.84[ASN][1000 genomes]
rs6930201	0.81[ASN][1000 genomes]
rs6933174	0.91[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs6933568	0.91[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs6933607	0.90[CHB][hapmap];1.00[CHD][hapmap];0.83[GIH][hapmap];1.00[JPT][hapmap];0.86[MEX][hapmap];0.88[AMR][1000 genomes];0.84[ASN][1000 genomes]
rs6940353	0.91[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs72880511	0.84[AMR][1000 genomes]
rs73412140	0.91[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs747692	0.90[CHB][hapmap];1.00[CHD][hapmap];0.83[GIH][hapmap];0.90[JPT][hapmap];0.86[MEX][hapmap];0.84[AMR][1000 genomes];0.81[ASN][1000 genomes]
rs747693	1.00[CHB][hapmap]
rs751096	0.82[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.83[ASN][1000 genomes]
rs755495	0.90[CHB][hapmap];1.00[CHD][hapmap];0.83[GIH][hapmap];0.90[JPT][hapmap];0.86[MEX][hapmap];0.81[AMR][1000 genomes];0.81[ASN][1000 genomes]
rs7755323	0.82[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.82[AMR][1000 genomes];0.84[ASN][1000 genomes]
rs942636	0.84[GIH][hapmap]
rs943461	0.91[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs943462	0.90[CHB][hapmap];1.00[JPT][hapmap];0.91[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs943466	0.82[CHB][hapmap];0.83[CHD][hapmap];0.90[JPT][hapmap]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv885772	chr6:33638180-33767727	Bivalent Enhancer Genic enhancers Strong transcription Enhancers Weak transcription Transcr. at gene 5' and 3' Flanking Active TSS Active TSS Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA	28 gene(s)	inside rSNPs	diseases
2	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
3	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
4	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
5	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:2)

SNP	Gene	Cis/trans	Tissue	Source
rs3828783	DEF6	cis	parietal	SCAN
rs3828783	LEMD2	cis	parietal	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:33757600-33775800	Weak transcription	Right Atrium	heart
2	chr6:33762400-33767800	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
3	chr6:33763600-33771600	Weak transcription	Fetal Intestine Small	intestine
4	chr6:33765800-33769200	Weak transcription	Brain Germinal Matrix	brain
5	chr6:33765800-33770200	Weak transcription	iPS-15b Cell Line	embryonic stem cell
6	chr6:33766000-33769200	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
7	chr6:33766000-33770200	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
8	chr6:33766000-33776000	Weak transcription	HUES48 Cell Line	embryonic stem cell
9	chr6:33766200-33769000	Weak transcription	Cortex derived primary cultured neurospheres	brain
10	chr6:33766600-33770000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
11	chr6:33766800-33768800	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
12	chr6:33766800-33769800	Weak transcription	HUES6 Cell Line	embryonic stem cell
13	chr6:33766800-33776400	Weak transcription	HUES64 Cell Line	embryonic stem cell
14	chr6:33767000-33768000	Enhancers	Adipose Nuclei	Adipose
15	chr6:33767000-33768200	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
16	chr6:33767000-33768600	Enhancers	Fetal Muscle Leg	muscle
17	chr6:33767200-33768200	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
18	chr6:33767200-33768200	Enhancers	Osteobl	bone
19	chr6:33767200-33768400	Enhancers	NHDF-Ad	bronchial
20	chr6:33767200-33768600	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
21	chr6:33767400-33768000	Enhancers	Right Ventricle	heart
22	chr6:33767400-33768400	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
23	chr6:33767400-33768400	Bivalent Enhancer	Fetal Muscle Trunk	muscle
24	chr6:33767600-33767800	Enhancers	iPS DF 6.9 Cell Line	embryonic stem cell
25	chr6:33767600-33767800	Bivalent Enhancer	Skeletal Muscle Male	skeletal muscle
26	chr6:33767600-33768200	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived

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