Variant report

Variant	rs3806108
Chromosome Location	chr6:33767579-33767580
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

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:

Variant related genes	Relation type
ENSG00000096395	Chromatin interaction

Extended variants
information (count: 45 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:40)

rs_ID	r²[population]
rs11752297	0.96[CEU][hapmap];1.00[CHB][hapmap];0.89[JPT][hapmap];0.92[AMR][1000 genomes];0.94[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs1359781	1.00[CEU][hapmap];0.94[CHB][hapmap];0.94[JPT][hapmap];0.90[AMR][1000 genomes];0.98[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2013365	0.85[AMR][1000 genomes];0.97[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2013381	0.89[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs2281816	0.93[ASW][hapmap];0.81[MEX][hapmap]
rs2296743	1.00[ASW][hapmap];1.00[CEU][hapmap];0.94[CHB][hapmap];0.96[CHD][hapmap];1.00[GIH][hapmap];0.94[JPT][hapmap];0.92[LWK][hapmap];0.98[MKK][hapmap];0.95[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2296744	0.81[ASW][hapmap];0.92[LWK][hapmap];0.88[YRI][hapmap];0.88[AFR][1000 genomes]
rs2296746	0.90[AMR][1000 genomes];0.97[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2296747	0.85[AMR][1000 genomes];0.98[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2296748	0.93[ASW][hapmap];1.00[CEU][hapmap];0.94[CHB][hapmap];0.88[CHD][hapmap];0.89[GIH][hapmap];0.94[JPT][hapmap];0.86[MEX][hapmap];0.95[TSI][hapmap];0.90[AMR][1000 genomes];0.98[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2395402	0.81[ASW][hapmap]
rs2395449	0.96[CEU][hapmap];1.00[CHB][hapmap];0.89[JPT][hapmap];0.90[AMR][1000 genomes];0.93[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs3763260	0.93[ASW][hapmap]
rs3793079	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]
rs3806109	1.00[ASW][hapmap];0.92[CEU][hapmap];0.94[CHB][hapmap];0.96[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];0.89[TSI][hapmap];0.86[AFR][1000 genomes];0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs3806110	1.00[ASW][hapmap];0.84[CEU][hapmap];0.82[CHB][hapmap];0.82[GIH][hapmap];0.83[JPT][hapmap];0.90[MEX][hapmap];0.84[AFR][1000 genomes];0.94[AMR][1000 genomes];0.87[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs4342423	0.96[CEU][hapmap];1.00[CHB][hapmap];0.89[JPT][hapmap];0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs4711351	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4713681	0.85[AMR][1000 genomes];0.98[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs4713682	0.89[AMR][1000 genomes];0.98[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs4713683	0.92[CEU][hapmap];0.92[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs4713684	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4713686	0.80[MEX][hapmap]
rs6904716	0.88[CHB][hapmap]
rs6904991	0.96[CEU][hapmap];1.00[CHB][hapmap];0.89[JPT][hapmap];0.90[AMR][1000 genomes];0.94[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs6920075	0.92[AMR][1000 genomes];0.94[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs6925273	0.83[AMR][1000 genomes];0.94[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs747695	0.88[AMR][1000 genomes];0.95[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs751726	0.90[AMR][1000 genomes];0.98[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs751728	0.85[AMR][1000 genomes];0.98[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs755496	0.96[CEU][hapmap];1.00[CHB][hapmap];0.96[CHD][hapmap];0.93[GIH][hapmap];0.89[JPT][hapmap];0.95[MEX][hapmap];0.87[TSI][hapmap];0.92[AMR][1000 genomes];0.94[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs756137	0.92[CEU][hapmap];0.92[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs9366829	0.83[JPT][hapmap]
rs9380376	0.89[JPT][hapmap];0.81[MEX][hapmap]
rs9380378	0.85[AMR][1000 genomes];0.95[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs9394165	0.96[CEU][hapmap];1.00[CHB][hapmap];0.89[JPT][hapmap];0.92[AMR][1000 genomes];0.94[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs9394166	1.00[CEU][hapmap];0.94[CHB][hapmap];0.94[JPT][hapmap];0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs9394168	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs943467	0.94[CHB][hapmap];0.85[CHD][hapmap]
rs943477	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]

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:4)

SNP	Gene	Cis/trans	Tissue	Source
rs3806108	C6orf89	cis	parietal	SCAN
rs3806108	DEF6	cis	cerebellum	SCAN
rs3806108	ITPR3	cis	multi-tissue	Pritchard
rs3806108	PPARD	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	chr6:33764600-33767600	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
5	chr6:33765800-33769200	Weak transcription	Brain Germinal Matrix	brain
6	chr6:33765800-33770200	Weak transcription	iPS-15b Cell Line	embryonic stem cell
7	chr6:33766000-33769200	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
8	chr6:33766000-33770200	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
9	chr6:33766000-33776000	Weak transcription	HUES48 Cell Line	embryonic stem cell
10	chr6:33766200-33769000	Weak transcription	Cortex derived primary cultured neurospheres	brain
11	chr6:33766600-33770000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
12	chr6:33766800-33767600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
13	chr6:33766800-33768800	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
14	chr6:33766800-33769800	Weak transcription	HUES6 Cell Line	embryonic stem cell
15	chr6:33766800-33776400	Weak transcription	HUES64 Cell Line	embryonic stem cell
16	chr6:33767000-33768000	Enhancers	Adipose Nuclei	Adipose
17	chr6:33767000-33768200	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
18	chr6:33767000-33768600	Enhancers	Fetal Muscle Leg	muscle
19	chr6:33767200-33767600	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
20	chr6:33767200-33768200	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
21	chr6:33767200-33768200	Enhancers	Osteobl	bone
22	chr6:33767200-33768400	Enhancers	NHDF-Ad	bronchial
23	chr6:33767200-33768600	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
24	chr6:33767400-33768000	Enhancers	Right Ventricle	heart
25	chr6:33767400-33768400	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
26	chr6:33767400-33768400	Bivalent Enhancer	Fetal Muscle Trunk	muscle

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