Variant report

Variant	rs200849
Chromosome Location	chr6:5095696-5095697
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr6:5095410..5098025-chr6:5107266..5109190,2	MCF-7	breast:
2	chr6:5094149..5096887-chr6:5098967..5101711,2	K562	blood:
3	chr6:5082435..5084667-chr6:5094252..5095807,2	K562	blood:

Extended variants
information (count: 53 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:41)

rs_ID	r²[population]
rs127119	0.95[ASN][1000 genomes]
rs127120	0.95[ASN][1000 genomes]
rs200847	0.83[EUR][1000 genomes]
rs200848	0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs200850	0.87[ASN][1000 genomes]
rs200851	0.95[ASN][1000 genomes]
rs200863	0.80[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs364878	0.95[ASN][1000 genomes]
rs365609	0.95[ASN][1000 genomes]
rs374733	0.92[ASN][1000 genomes]
rs376334	0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs385315	0.88[AMR][1000 genomes];0.91[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs386688	0.95[ASN][1000 genomes]
rs389691	0.95[ASN][1000 genomes]
rs389707	0.95[ASN][1000 genomes]
rs394683	0.95[ASN][1000 genomes]
rs394761	0.95[ASN][1000 genomes]
rs402103	0.95[ASN][1000 genomes]
rs402541	0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs413219	0.95[ASN][1000 genomes]
rs421473	0.95[ASN][1000 genomes]
rs424493	0.95[ASN][1000 genomes]
rs428513	0.87[ASN][1000 genomes]
rs435175	0.87[ASN][1000 genomes]
rs435545	0.95[ASN][1000 genomes]
rs438298	0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs439091	0.95[ASN][1000 genomes]
rs445204	0.80[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs449200	0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs452658	0.95[ASN][1000 genomes]
rs455504	0.95[ASN][1000 genomes]
rs457759	0.85[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs460551	0.92[ASN][1000 genomes]
rs461144	0.91[ASN][1000 genomes]
rs461698	0.89[AMR][1000 genomes];0.94[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs462749	0.83[ASN][1000 genomes]
rs463951	0.82[EUR][1000 genomes]
rs464681	0.89[AMR][1000 genomes];0.94[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs466368	0.92[ASN][1000 genomes]
rs683261	0.80[EUR][1000 genomes]
rs9606	0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];0.89[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:12 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1023527	chr6:4729592-5387176	Strong transcription Weak transcription Enhancers Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent/Poised TSS Bivalent Enhancer Genic enhancers ZNF genes & repeats Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	29 gene(s)	inside rSNPs	diseases
2	nsv462622	chr6:4904380-5172009	Active TSS Enhancers Strong transcription Weak transcription Flanking Active TSS Flanking Bivalent TSS/Enh Genic enhancers Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	19 gene(s)	inside rSNPs	diseases
3	nsv600871	chr6:4904380-5172009	Enhancers Active TSS Flanking Active TSS Weak transcription ZNF genes & repeats Strong transcription Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	19 gene(s)	inside rSNPs	diseases
4	nsv600872	chr6:4975313-5342190	Weak transcription Active TSS Strong transcription Flanking Active TSS Enhancers Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	24 gene(s)	inside rSNPs	diseases
5	nsv1031837	chr6:4996667-5418726	Enhancers Weak transcription ZNF genes & repeats Genic enhancers Flanking Active TSS Active TSS Strong transcription Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA	23 gene(s)	inside rSNPs	diseases
6	nsv1017380	chr6:5007870-5152551	Enhancers Weak transcription Active TSS Strong transcription Flanking Active TSS Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA	15 gene(s)	inside rSNPs	diseases
7	nsv1017373	chr6:5066785-5128943	Weak transcription Bivalent Enhancer Bivalent/Poised TSS Enhancers Genic enhancers Flanking Bivalent TSS/Enh Active TSS Flanking Active TSS Strong transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
8	nsv538112	chr6:5066785-5128943	Enhancers Bivalent Enhancer Active TSS Weak transcription Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Genic enhancers Strong transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
9	nsv1034681	chr6:5070351-5387176	Enhancers Weak transcription Active TSS Flanking Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Strong transcription ZNF genes & repeats Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	15 gene(s)	inside rSNPs	diseases
10	nsv538113	chr6:5070351-5387176	Enhancers Genic enhancers Weak transcription Strong transcription Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	15 gene(s)	inside rSNPs	diseases
11	nsv1018152	chr6:5077025-5387176	Flanking Active TSS Weak transcription Enhancers Strong transcription ZNF genes & repeats Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	13 gene(s)	inside rSNPs	diseases
12	nsv600873	chr6:5089278-5400658	Enhancers Active TSS Flanking Active TSS Strong transcription Weak transcription ZNF genes & repeats Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA	12 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs200849	LYRM4	Cis_1M	lymphoblastoid	RTeQTL
rs200849	LYRM4	cis	multi-tissue	Pritchard

Chromatin state (count:28 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:5091000-5108200	Weak transcription	Spleen	Spleen
2	chr6:5091000-5108800	Weak transcription	Right Atrium	heart
3	chr6:5091000-5109000	Weak transcription	Lung	lung
4	chr6:5093000-5097000	Enhancers	Fetal Heart	heart
5	chr6:5093600-5095800	Enhancers	NHDF-Ad	bronchial
6	chr6:5093600-5095800	Enhancers	NHLF	lung
7	chr6:5093600-5096000	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
8	chr6:5094000-5095800	Enhancers	Hela-S3	cervix
9	chr6:5094000-5096000	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
10	chr6:5094000-5096000	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
11	chr6:5094000-5096000	Enhancers	Osteobl	bone
12	chr6:5094400-5097600	Enhancers	Primary B cells from peripheral blood	blood
13	chr6:5094400-5098800	Weak transcription	Aorta	Aorta
14	chr6:5094800-5095800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
15	chr6:5094800-5095800	Weak transcription	Left Ventricle	heart
16	chr6:5094800-5096000	Enhancers	Muscle Satellite Cultured Cells	--
17	chr6:5094800-5096000	Enhancers	HSMMtube	muscle
18	chr6:5094800-5096600	Weak transcription	K562	blood
19	chr6:5094800-5097400	Weak transcription	Right Ventricle	heart
20	chr6:5095000-5096000	Flanking Active TSS	GM12878-XiMat	blood
21	chr6:5095000-5096000	Enhancers	HSMM	muscle
22	chr6:5095400-5095800	Weak transcription	HepG2	liver
23	chr6:5095400-5096000	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
24	chr6:5095400-5096200	Enhancers	Primary B cells from cord blood	blood
25	chr6:5095400-5106800	Weak transcription	Fetal Stomach	stomach
26	chr6:5095600-5095800	Weak transcription	Primary monocytes fromperipheralblood	blood
27	chr6:5095600-5095800	Enhancers	Sigmoid Colon	Sigmoid Colon
28	chr6:5095600-5095800	Flanking Active TSS	NH-A	brain

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