Variant report

Variant	rs13214874
Chromosome Location	chr6:33686368-33686369
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:9)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:9 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr6:33684071..33687779-chr6:33863332..33865982,3	MCF-7	breast:
2	chr6:33684529..33686540-chr6:33729478..33731636,2	MCF-7	breast:
3	chr6:33670443..33672859-chr6:33684999..33687830,2	K562	blood:
4	chr6:33680227..33683145-chr6:33684696..33687420,2	K562	blood:
5	chr6:33674250..33675922-chr6:33684521..33687700,3	K562	blood:
6	chr6:33676188..33679535-chr6:33684532..33687209,3	MCF-7	breast:
7	chr6:33684753..33687394-chr6:33728535..33731247,2	MCF-7	breast:
8	chr6:33680227..33683293-chr6:33684221..33688907,5	K562	blood:
9	chr6:33686168..33688632-chr6:33755438..33757308,2	MCF-7	breast:

No data

Variant related genes	Relation type
ENSG00000249346	Chromatin interaction
ENSG00000137288	Chromatin interaction
ENSG00000161904	Chromatin interaction

Extended variants
information (count: 68 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:65)

rs_ID	r²[population]
rs10456075	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10947415	0.84[CEU][hapmap]
rs10947426	0.87[AFR][1000 genomes]
rs10947427	0.83[GIH][hapmap]
rs10947432	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];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10947441	1.00[LWK][hapmap];0.95[MKK][hapmap]
rs11757379	1.00[ASW][hapmap];1.00[LWK][hapmap]
rs12153870	0.87[AFR][1000 genomes]
rs12189725	1.00[ASW][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.85[JPT][hapmap];1.00[LWK][hapmap];0.91[MEX][hapmap];1.00[MKK][hapmap];0.97[TSI][hapmap];0.83[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs12190155	1.00[CEU][hapmap];1.00[JPT][hapmap];0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12193658	0.83[EUR][1000 genomes]
rs12195707	0.84[CEU][hapmap];0.87[AFR][1000 genomes]
rs12199132	0.83[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs12203688	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];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12205398	0.80[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12205667	0.87[AFR][1000 genomes]
rs12207382	0.85[JPT][hapmap]
rs12211490	1.00[ASW][hapmap];1.00[CHD][hapmap];0.85[JPT][hapmap];1.00[LWK][hapmap];0.81[MEX][hapmap];1.00[MKK][hapmap];0.90[TSI][hapmap];0.82[ASN][1000 genomes]
rs12211554	0.85[JPT][hapmap];0.82[ASN][1000 genomes]
rs12211565	0.82[ASN][1000 genomes]
rs12214669	1.00[LWK][hapmap]
rs12215329	0.82[ASN][1000 genomes]
rs12660955	0.82[ASN][1000 genomes]
rs12661400	1.00[AFR][1000 genomes];0.80[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12662447	0.83[EUR][1000 genomes]
rs13200063	0.85[JPT][hapmap];0.82[ASN][1000 genomes]
rs13203745	1.00[LWK][hapmap];0.95[MKK][hapmap]
rs13204162	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.91[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[AFR][1000 genomes];0.82[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs13204975	1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];0.92[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs13206228	0.82[ASN][1000 genomes]
rs13207666	0.81[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs13220421	0.87[AFR][1000 genomes]
rs2274459	1.00[ASW][hapmap];0.85[JPT][hapmap];1.00[LWK][hapmap];0.81[MEX][hapmap];0.91[MKK][hapmap];0.87[TSI][hapmap];0.82[ASN][1000 genomes]
rs2281831	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.85[JPT][hapmap];0.82[MEX][hapmap];0.91[MKK][hapmap];1.00[TSI][hapmap];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2281917	0.85[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[AMR][1000 genomes];0.94[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2281918	1.00[ASW][hapmap];0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.85[JPT][hapmap];0.91[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];0.89[AFR][1000 genomes];0.98[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2281919	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap];1.00[TSI][hapmap];0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2296737	0.88[AMR][1000 genomes];0.94[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2296749	0.82[ASN][1000 genomes]
rs34139049	0.88[ASN][1000 genomes]
rs34339105	0.82[ASN][1000 genomes]
rs34472165	0.82[ASN][1000 genomes]
rs34517899	0.87[AFR][1000 genomes]
rs34778247	1.00[AFR][1000 genomes];0.95[EUR][1000 genomes]
rs34869648	0.82[ASN][1000 genomes]
rs35088242	0.87[AFR][1000 genomes]
rs35095444	1.00[AFR][1000 genomes];0.88[EUR][1000 genomes]
rs35274562	0.88[ASN][1000 genomes]
rs35646598	0.88[ASN][1000 genomes]
rs35698850	1.00[AFR][1000 genomes];0.80[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs35721478	0.82[ASN][1000 genomes]
rs35797388	0.82[ASN][1000 genomes]
rs36097803	0.87[AFR][1000 genomes]
rs3818526	0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs3818532	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[LWK][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[AFR][1000 genomes];0.80[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs4559081	1.00[LWK][hapmap]
rs66670017	0.82[ASN][1000 genomes]
rs68168863	0.82[ASN][1000 genomes]
rs6925337	0.85[JPT][hapmap]
rs729376	1.00[CHB][hapmap];0.82[JPT][hapmap];0.83[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs751095	0.82[ASN][1000 genomes]
rs755239	0.82[ASN][1000 genomes]
rs877187	1.00[ASW][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.85[JPT][hapmap];1.00[LWK][hapmap];0.91[MEX][hapmap];0.95[MKK][hapmap];0.97[TSI][hapmap];0.83[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs9296097	0.92[CEU][hapmap];1.00[CHB][hapmap];0.94[GIH][hapmap];1.00[JPT][hapmap];0.84[MEX][hapmap];1.00[TSI][hapmap];0.90[AMR][1000 genomes];0.93[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs9469554	0.92[CEU][hapmap];0.94[GIH][hapmap];0.91[MEX][hapmap];1.00[MKK][hapmap];0.90[TSI][hapmap];0.85[AMR][1000 genomes];0.87[EUR][1000 genomes]

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
rs13214874	LEMD2	cis	parietal	SCAN
rs13214874	C6orf125	cis	cerebellum	SCAN
rs13214874	LEMD2	cis	cerebellum	SCAN

Chromatin state (count:57 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:33680000-33689400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
2	chr6:33680000-33690000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
3	chr6:33680000-33690200	Weak transcription	Psoas Muscle	Psoas
4	chr6:33680000-33693000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
5	chr6:33680000-33695200	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
6	chr6:33680000-33695800	Weak transcription	Spleen	Spleen
7	chr6:33680000-33696200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
8	chr6:33680000-33698400	Weak transcription	Placenta Amnion	Placenta Amnion
9	chr6:33680000-33705000	Weak transcription	Brain Angular Gyrus	brain
10	chr6:33681800-33689200	Enhancers	Pancreas	Pancrea
11	chr6:33683000-33686600	Enhancers	Stomach Mucosa	stomach
12	chr6:33684000-33686600	Enhancers	Left Ventricle	heart
13	chr6:33684000-33687000	Enhancers	HMEC	breast
14	chr6:33684200-33687400	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
15	chr6:33684200-33688200	Enhancers	Fetal Lung	lung
16	chr6:33684400-33688000	Weak transcription	Gastric	stomach
17	chr6:33684600-33688200	Enhancers	Fetal Brain Male	brain
18	chr6:33684600-33688600	Weak transcription	Rectal Mucosa Donor 31	rectum
19	chr6:33684800-33686400	Enhancers	Colon Smooth Muscle	Colon
20	chr6:33684800-33686600	Enhancers	Rectal Smooth Muscle	rectum
21	chr6:33685000-33686400	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
22	chr6:33685000-33686400	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
23	chr6:33685000-33686600	Enhancers	Breast Myoepithelial Primary Cells	Breast
24	chr6:33685000-33686600	Bivalent Enhancer	Foreskin Fibroblast Primary Cells skin01	Skin
25	chr6:33685000-33686600	Enhancers	Fetal Stomach	stomach
26	chr6:33685000-33686600	Enhancers	Skeletal Muscle Male	skeletal muscle
27	chr6:33685000-33686800	Enhancers	Fetal Muscle Leg	muscle
28	chr6:33685000-33687400	Enhancers	Duodenum Smooth Muscle	Duodenum
29	chr6:33685200-33686400	Enhancers	Brain Hippocampus Middle	brain
30	chr6:33685200-33686600	Enhancers	Fetal Muscle Trunk	muscle
31	chr6:33685200-33688000	Weak transcription	GM12878-XiMat	blood
32	chr6:33685200-33693400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
33	chr6:33685600-33686400	Enhancers	Brain Cingulate Gyrus	brain
34	chr6:33685600-33686400	Enhancers	Placenta	Placenta
35	chr6:33685600-33686600	Enhancers	Brain Germinal Matrix	brain
36	chr6:33685800-33686400	Weak transcription	Skeletal Muscle Female	skeletal muscle
37	chr6:33685800-33686600	Enhancers	Right Atrium	heart
38	chr6:33685800-33687000	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
39	chr6:33685800-33687000	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
40	chr6:33686000-33686400	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
41	chr6:33686000-33686600	Bivalent Enhancer	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
42	chr6:33686000-33686600	Enhancers	Muscle Satellite Cultured Cells	--
43	chr6:33686000-33686600	Enhancers	Brain Anterior Caudate	brain
44	chr6:33686000-33686600	Enhancers	Fetal Brain Female	brain
45	chr6:33686000-33686600	Enhancers	Right Ventricle	heart
46	chr6:33686000-33686800	Enhancers	Primary hematopoietic stem cells short term culture	blood
47	chr6:33686000-33686800	Enhancers	Lung	lung
48	chr6:33686000-33688000	Enhancers	Brain Substantia Nigra	brain
49	chr6:33686200-33686400	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
50	chr6:33686200-33686400	Enhancers	Brain Dorsolateral Prefrontal Cortex	brain

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