Variant report

Variant	rs10458182
Chromosome Location	chr6:5143410-5143411
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr6:5143322..5144392-chr6:5398327..5399283,4	MCF-7	breast:

Extended variants
information (count: 54 )
Associated
traits (count: 2 )

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

rs_ID	r²[population]
rs10484846	1.00[CHB][hapmap];0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11242990	1.00[CHB][hapmap];0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11242991	0.83[AMR][1000 genomes];0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11242993	0.85[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs12110634	1.00[CHB][hapmap];0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12111219	1.00[CHB][hapmap];0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12191255	1.00[CHB][hapmap];0.89[AMR][1000 genomes];0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12192863	1.00[CHB][hapmap];0.91[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12193229	1.00[ASN][1000 genomes]
rs12195956	1.00[CHB][hapmap];0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12202160	1.00[CHB][hapmap];0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12202384	0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12203248	1.00[ASN][1000 genomes]
rs12204382	1.00[CHB][hapmap];1.00[YRI][hapmap];0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12204490	1.00[CHB][hapmap];0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12206931	1.00[CHB][hapmap];0.89[AMR][1000 genomes];0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12213584	1.00[ASN][1000 genomes]
rs17139439	1.00[CHB][hapmap];0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35400671	0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs373696	0.92[YRI][hapmap]
rs425930	0.87[EUR][1000 genomes]
rs434350	0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs460111	0.87[EUR][1000 genomes]
rs460416	1.00[YRI][hapmap];0.91[AFR][1000 genomes]
rs467373	0.87[EUR][1000 genomes]
rs4959330	0.82[AFR][1000 genomes];0.91[AMR][1000 genomes];0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4959331	0.82[AFR][1000 genomes];0.91[AMR][1000 genomes];0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4960066	0.91[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs4960068	1.00[CHB][hapmap];1.00[YRI][hapmap];0.83[AFR][1000 genomes];0.93[AMR][1000 genomes];0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6597114	1.00[CHB][hapmap];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6597115	1.00[CHB][hapmap];1.00[YRI][hapmap];0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6911123	0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72811642	0.96[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72811643	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs761365	1.00[CHB][hapmap];0.93[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7757651	0.91[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9405800	1.00[CHB][hapmap];0.91[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9405801	0.91[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs9504354	1.00[CHB][hapmap];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:15 , 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	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
8	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
9	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
10	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
11	nsv1017821	chr6:5114609-5213200	Enhancers Weak transcription Flanking Active TSS Genic enhancers Active TSS Strong transcription ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region miRNA	5 gene(s)	inside rSNPs	diseases
12	nsv538114	chr6:5114609-5213200	Weak transcription Enhancers Active TSS Strong transcription Flanking Active TSS Genic enhancers ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region miRNA	5 gene(s)	inside rSNPs	diseases
13	nsv5179	chr6:5121824-5167027	Enhancers Weak transcription Active TSS Bivalent Enhancer Genic enhancers Flanking Active TSS ZNF genes & repeats Strong transcription	TF binding region CpG island Chromatin interactive region miRNA	3 gene(s)	inside rSNPs	diseases
14	nsv1030254	chr6:5132261-5431585	Enhancers Weak transcription Active TSS Strong transcription Flanking Active TSS ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA	10 gene(s)	inside rSNPs	diseases
15	nsv1034463	chr6:5137959-5345678	Enhancers Flanking Active TSS Active TSS ZNF genes & repeats Weak transcription Strong transcription Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	10 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs10458182	LYRM4	Cis_1M	lymphoblastoid	RTeQTL
rs10458182	RP11-428J1.5	cis	Esophagus Mucosa	GTEx

Chromatin state (count:40 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:5129000-5162000	Weak transcription	K562	blood
2	chr6:5130600-5172200	Weak transcription	Lung	lung
3	chr6:5133400-5143800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
4	chr6:5133400-5144000	Weak transcription	Fetal Brain Male	brain
5	chr6:5133400-5146000	Weak transcription	Psoas Muscle	Psoas
6	chr6:5133400-5151600	Weak transcription	Breast Myoepithelial Primary Cells	Breast
7	chr6:5133600-5143800	Weak transcription	Fetal Stomach	stomach
8	chr6:5133800-5143600	Weak transcription	Brain Inferior Temporal Lobe	brain
9	chr6:5133800-5153400	Weak transcription	Right Ventricle	heart
10	chr6:5134200-5144200	Weak transcription	Primary hematopoietic stem cells short term culture	blood
11	chr6:5135000-5151000	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
12	chr6:5135200-5151800	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
13	chr6:5136400-5151000	Weak transcription	NHEK	skin
14	chr6:5136400-5151600	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
15	chr6:5137000-5166600	Weak transcription	Primary T cells from cord blood	blood
16	chr6:5139800-5144200	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
17	chr6:5140000-5143800	Weak transcription	Fetal Kidney	kidney
18	chr6:5140000-5144200	Weak transcription	Fetal Lung	lung
19	chr6:5140000-5148600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
20	chr6:5141000-5149200	Weak transcription	Primary B cells from cord blood	blood
21	chr6:5141600-5143600	Weak transcription	HepG2	liver
22	chr6:5141600-5144000	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
23	chr6:5141800-5143800	Weak transcription	Primary B cells from peripheral blood	blood
24	chr6:5143000-5144600	Enhancers	Fetal Muscle Leg	muscle
25	chr6:5143200-5143600	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
26	chr6:5143200-5143600	Enhancers	Fetal Muscle Trunk	muscle
27	chr6:5143200-5143800	Weak transcription	Spleen	Spleen
28	chr6:5143200-5144000	Enhancers	NHLF	lung
29	chr6:5143200-5144400	Enhancers	Foreskin Melanocyte Primary Cells skin01	Skin
30	chr6:5143200-5144400	Enhancers	Fetal Adrenal Gland	Adrenal Gland
31	chr6:5143200-5144600	Enhancers	Skeletal Muscle Male	skeletal muscle
32	chr6:5143200-5144600	Enhancers	Skeletal Muscle Female	skeletal muscle
33	chr6:5143400-5143600	ZNF genes & repeats	iPS DF 19.11 Cell Line	embryonic stem cell
34	chr6:5143400-5143800	Enhancers	NHDF-Ad	bronchial
35	chr6:5143400-5144000	Enhancers	Left Ventricle	heart
36	chr6:5143400-5144400	Enhancers	Cortex derived primary cultured neurospheres	brain
37	chr6:5143400-5144400	Weak transcription	Fetal Intestine Small	intestine
38	chr6:5143400-5144400	Enhancers	Stomach Smooth Muscle	stomach
39	chr6:5143400-5144600	Enhancers	Fetal Thymus	thymus
40	chr6:5143400-5146200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived

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