Variant report

Variant	rs943466
Chromosome Location	chr6:33731787-33731788
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr6:33730661..33732317-chr6:33745927..33748398,2	MCF-7	breast:
2	chr6:33728564..33732066-chr6:33733725..33737558,5	MCF-7	breast:
3	chr6:33731707..33733377-chr6:33739681..33741307,2	K562	blood:
4	chr6:33730312..33733510-chr6:33847562..33850265,3	K562	blood:
5	chr6:33678876..33680749-chr6:33729962..33732135,3	K562	blood:

Variant related genes	Relation type
ENSG00000137288	Chromatin interaction
ENSG00000161904	Chromatin interaction

Extended variants
information (count: 44 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:39)

rs_ID	r²[population]
rs1075379	0.90[CEU][hapmap];0.82[CHB][hapmap];0.90[JPT][hapmap];0.86[MEX][hapmap];0.86[TSI][hapmap];0.94[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs11753083	0.95[EUR][1000 genomes]
rs11754690	1.00[CEU][hapmap];0.90[CHB][hapmap];0.86[JPT][hapmap];0.96[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs11755593	0.82[AMR][1000 genomes];0.96[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs11757524	0.95[EUR][1000 genomes]
rs11758463	0.94[EUR][1000 genomes]
rs12524768	0.86[CEU][hapmap];0.89[JPT][hapmap];0.93[EUR][1000 genomes]
rs12524835	0.90[CHB][hapmap];1.00[JPT][hapmap];0.85[AMR][1000 genomes];0.99[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs1887340	1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2281819	0.94[CEU][hapmap];0.87[EUR][1000 genomes]
rs2281820	0.82[CHB][hapmap]
rs2395400	1.00[CEU][hapmap];0.90[JPT][hapmap];0.91[EUR][1000 genomes]
rs2894342	0.94[CEU][hapmap];0.86[EUR][1000 genomes]
rs3763253	0.94[CEU][hapmap];0.86[EUR][1000 genomes]
rs3828783	0.82[CHB][hapmap];0.83[CHD][hapmap];0.90[JPT][hapmap]
rs4711346	1.00[CEU][hapmap];0.91[CHB][hapmap];1.00[JPT][hapmap];0.90[AMR][1000 genomes];0.99[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs4713677	0.97[LWK][hapmap];0.92[YRI][hapmap];0.89[AFR][1000 genomes]
rs55775340	0.94[EUR][1000 genomes]
rs59137082	0.94[EUR][1000 genomes]
rs61394483	0.95[EUR][1000 genomes]
rs61662306	0.95[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs6910736	0.90[EUR][1000 genomes]
rs6921487	0.93[EUR][1000 genomes]
rs6930201	0.93[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs6933174	0.95[EUR][1000 genomes]
rs6933568	0.94[EUR][1000 genomes]
rs6933607	1.00[CEU][hapmap];0.91[CHB][hapmap];0.83[CHD][hapmap];0.84[GIH][hapmap];0.90[JPT][hapmap];0.87[MEX][hapmap];0.92[TSI][hapmap];0.96[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs6940353	0.95[EUR][1000 genomes]
rs72880511	0.84[AMR][1000 genomes];0.98[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs73412140	0.95[EUR][1000 genomes]
rs73746509	0.88[AMR][1000 genomes];0.99[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs747692	1.00[CEU][hapmap];0.91[CHB][hapmap];0.83[CHD][hapmap];0.84[GIH][hapmap];1.00[JPT][hapmap];0.87[MEX][hapmap];0.92[TSI][hapmap];0.82[AMR][1000 genomes];0.96[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs747693	1.00[JPT][hapmap]
rs751096	0.95[CEU][hapmap];0.82[CHB][hapmap];0.81[CHD][hapmap];0.90[JPT][hapmap];0.91[MEX][hapmap];0.85[TSI][hapmap];0.94[EUR][1000 genomes]
rs755495	1.00[CEU][hapmap];0.91[CHB][hapmap];0.83[CHD][hapmap];0.84[GIH][hapmap];1.00[JPT][hapmap];0.87[MEX][hapmap];0.97[TSI][hapmap];0.83[AMR][1000 genomes];0.96[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs7755323	0.95[CEU][hapmap];0.82[CHB][hapmap];0.83[CHD][hapmap];0.90[JPT][hapmap];0.86[MEX][hapmap];0.86[TSI][hapmap];0.93[EUR][1000 genomes]
rs943461	0.95[EUR][1000 genomes]
rs943462	1.00[CEU][hapmap];0.91[CHB][hapmap];0.90[JPT][hapmap];0.95[EUR][1000 genomes]
rs943465	0.81[YRI][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
rs943466	LEMD2	cis	parietal	SCAN
rs943466	LEMD2	cis	multi-tissue	Pritchard

Chromatin state (count:25 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:33715200-33737800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
2	chr6:33723400-33736600	Weak transcription	H1 Cell Line	embryonic stem cell
3	chr6:33726400-33738200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
4	chr6:33728000-33732000	Enhancers	Fetal Muscle Trunk	muscle
5	chr6:33729000-33736200	Weak transcription	HSMM	muscle
6	chr6:33729200-33732000	Enhancers	Placenta	Placenta
7	chr6:33729800-33734800	Weak transcription	HSMMtube	muscle
8	chr6:33730000-33731800	Enhancers	Skeletal Muscle Female	skeletal muscle
9	chr6:33730000-33738600	Weak transcription	A549	lung
10	chr6:33730200-33733200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
11	chr6:33730200-33736400	Weak transcription	Breast Myoepithelial Primary Cells	Breast
12	chr6:33730200-33737800	Weak transcription	Right Atrium	heart
13	chr6:33730200-33738200	Weak transcription	Colonic Mucosa	Colon
14	chr6:33730200-33738400	Weak transcription	Rectal Mucosa Donor 29	rectum
15	chr6:33730600-33731800	Weak transcription	Brain Cingulate Gyrus	brain
16	chr6:33730600-33738600	Weak transcription	Rectal Mucosa Donor 31	rectum
17	chr6:33730800-33732000	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
18	chr6:33730800-33736000	Weak transcription	Muscle Satellite Cultured Cells	--
19	chr6:33730800-33736600	Weak transcription	Brain Substantia Nigra	brain
20	chr6:33730800-33737600	Weak transcription	Duodenum Smooth Muscle	Duodenum
21	chr6:33730800-33738600	Weak transcription	Liver	Liver
22	chr6:33731000-33731800	Bivalent Enhancer	IMR90 fetal lung fibroblasts Cell Line	lung
23	chr6:33731400-33738400	Weak transcription	Spleen	Spleen
24	chr6:33731600-33731800	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
25	chr6:33731600-33738200	Weak transcription	Right Ventricle	heart

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