Variant report

Variant	rs2967
Chromosome Location	chr6:33689534-33689535
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr6:33687230..33690069-chr6:34119183..34120791,2	MCF-7	breast:
2	chr6:33678022..33679887-chr6:33687741..33690570,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000137288	Chromatin interaction

Extended variants
information (count: 33 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:30)

rs_ID	r²[population]
rs10672	0.93[ASW][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.80[LWK][hapmap]
rs10947436	1.00[JPT][hapmap]
rs1536501	1.00[JPT][hapmap]
rs1998949	1.00[JPT][hapmap]
rs2182659	1.00[JPT][hapmap]
rs2395401	1.00[JPT][hapmap]
rs2395448	1.00[JPT][hapmap]
rs4711350	1.00[JPT][hapmap]
rs498114	1.00[JPT][hapmap]
rs530614	1.00[JPT][hapmap]
rs549652	0.83[CHD][hapmap];1.00[JPT][hapmap];0.80[ASN][1000 genomes]
rs597386	1.00[JPT][hapmap]
rs602399	1.00[JPT][hapmap]
rs608971	1.00[JPT][hapmap]
rs623813	1.00[JPT][hapmap]
rs6457740	0.96[CEU][hapmap];0.83[CHD][hapmap];0.86[LWK][hapmap];1.00[TSI][hapmap];0.81[YRI][hapmap];0.85[AFR][1000 genomes];0.98[EUR][1000 genomes]
rs654682	1.00[JPT][hapmap]
rs658087	1.00[JPT][hapmap];0.80[ASN][1000 genomes]
rs684119	0.83[CHD][hapmap];1.00[JPT][hapmap];0.80[ASN][1000 genomes]
rs688209	1.00[CHB][hapmap];1.00[JPT][hapmap];0.80[ASN][1000 genomes]
rs6913517	1.00[JPT][hapmap]
rs6915136	1.00[JPT][hapmap]
rs751727	1.00[JPT][hapmap]
rs764753	1.00[JPT][hapmap]
rs943463	1.00[JPT][hapmap]
rs943464	1.00[JPT][hapmap]
rs943472	1.00[JPT][hapmap]
rs9461905	1.00[JPT][hapmap]
rs9469542	1.00[JPT][hapmap]
rs9469583	0.81[YRI][hapmap]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv830638	chr6:33551202-33711346	Enhancers Weak transcription Active TSS Flanking Active TSS Genic enhancers Bivalent/Poised TSS Strong transcription ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA	46 gene(s)	inside rSNPs	diseases
2	nsv830639	chr6:33592022-33711346	Strong transcription Enhancers Flanking Active TSS Weak transcription Transcr. at gene 5' and 3' Active TSS Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA	30 gene(s)	inside rSNPs	diseases
3	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

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs2967	LEMD2	cis	cerebellum	SCAN
rs2967	C6orf125	cis	cerebellum	SCAN
rs2967	C6orf227	cis	parietal	SCAN

Chromatin state (count:39 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:33680000-33690000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
2	chr6:33680000-33690200	Weak transcription	Psoas Muscle	Psoas
3	chr6:33680000-33693000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
4	chr6:33680000-33695200	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
5	chr6:33680000-33695800	Weak transcription	Spleen	Spleen
6	chr6:33680000-33696200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
7	chr6:33680000-33698400	Weak transcription	Placenta Amnion	Placenta Amnion
8	chr6:33680000-33705000	Weak transcription	Brain Angular Gyrus	brain
9	chr6:33685200-33693400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
10	chr6:33686200-33700200	Weak transcription	Liver	Liver
11	chr6:33686400-33689600	Weak transcription	Brain Hippocampus Middle	brain
12	chr6:33686400-33689600	Weak transcription	Placenta	Placenta
13	chr6:33686400-33691600	Weak transcription	Brain Cingulate Gyrus	brain
14	chr6:33686400-33691800	Weak transcription	Colon Smooth Muscle	Colon
15	chr6:33686400-33710600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
16	chr6:33686600-33689600	Weak transcription	Fetal Muscle Trunk	muscle
17	chr6:33686600-33689600	Weak transcription	Skeletal Muscle Male	skeletal muscle
18	chr6:33686600-33689800	Weak transcription	Skeletal Muscle Female	skeletal muscle
19	chr6:33686600-33690000	Weak transcription	Rectal Smooth Muscle	rectum
20	chr6:33686600-33690600	Weak transcription	Right Ventricle	heart
21	chr6:33686600-33695800	Weak transcription	Right Atrium	heart
22	chr6:33686600-33698600	Weak transcription	Muscle Satellite Cultured Cells	--
23	chr6:33687400-33691200	Weak transcription	Duodenum Smooth Muscle	Duodenum
24	chr6:33687400-33692600	Enhancers	Stomach Mucosa	stomach
25	chr6:33687400-33694000	Weak transcription	Brain Anterior Caudate	brain
26	chr6:33687800-33693200	Weak transcription	Brain Inferior Temporal Lobe	brain
27	chr6:33688000-33692000	Weak transcription	Brain Substantia Nigra	brain
28	chr6:33688200-33689600	Weak transcription	Fetal Brain Male	brain
29	chr6:33688200-33690200	Weak transcription	Fetal Lung	lung
30	chr6:33688600-33690000	Enhancers	Primary B cells from peripheral blood	blood
31	chr6:33688800-33689800	Strong transcription	Left Ventricle	heart
32	chr6:33688800-33690000	Weak transcription	Gastric	stomach
33	chr6:33688800-33698200	Weak transcription	Lung	lung
34	chr6:33688800-33700000	Strong transcription	HSMM	muscle
35	chr6:33689200-33689600	Weak transcription	Pancreas	Pancrea
36	chr6:33689200-33696800	Strong transcription	HSMMtube	muscle
37	chr6:33689400-33689600	Flanking Bivalent TSS/Enh	GM12878-XiMat	blood
38	chr6:33689400-33689800	Bivalent Enhancer	Primary B cells from cord blood	blood
39	chr6:33689400-33695000	Strong transcription	Foreskin Melanocyte Primary Cells skin01	Skin

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