Variant report

Variant	rs587777
Chromosome Location	chr6:5127615-5127616
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	chr6:5120935..5125341-chr6:5126554..5131441,5	K562	blood:
2	chr6:5119211..5120955-chr6:5124804..5127728,2	K562	blood:

Extended variants
information (count: 43 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:28)

rs_ID	r²[population]
rs127124	0.87[AMR][1000 genomes];0.90[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs127125	0.87[AMR][1000 genomes];0.90[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs200863	0.88[ASN][1000 genomes]
rs364886	0.87[AMR][1000 genomes];0.90[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs376334	0.80[ASN][1000 genomes]
rs385315	0.95[ASN][1000 genomes]
rs402541	0.84[ASN][1000 genomes]
rs412628	0.87[AMR][1000 genomes];0.90[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs423801	0.87[AMR][1000 genomes];0.90[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs435175	0.85[ASN][1000 genomes]
rs438298	0.83[ASN][1000 genomes]
rs445204	0.88[ASN][1000 genomes]
rs449200	0.80[ASN][1000 genomes]
rs454984	0.87[AMR][1000 genomes];0.90[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs455803	0.87[AMR][1000 genomes];0.89[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs457846	0.92[AFR][1000 genomes];0.89[AMR][1000 genomes];0.90[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs458395	0.81[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs461144	0.81[ASN][1000 genomes]
rs461698	0.87[ASN][1000 genomes]
rs462749	0.86[AMR][1000 genomes];0.86[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs464606	0.87[AMR][1000 genomes];0.90[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs464681	0.87[ASN][1000 genomes]
rs464863	0.87[AMR][1000 genomes];0.90[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs466837	0.89[ASN][1000 genomes]
rs585970	0.83[ASN][1000 genomes]
rs683261	0.92[ASN][1000 genomes]
rs85204	0.87[AMR][1000 genomes];0.90[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9606	0.87[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	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
13	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
14	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
15	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

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs587777	LYRM4	cis	multi-tissue	Pritchard

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:5099000-5130000	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
2	chr6:5101800-5132200	Weak transcription	iPS-15b Cell Line	embryonic stem cell
3	chr6:5103200-5132800	Weak transcription	Primary hematopoietic stem cells	blood
4	chr6:5105200-5131400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
5	chr6:5105800-5128200	Weak transcription	Primary B cells from cord blood	blood
6	chr6:5107800-5132000	Weak transcription	Pancreas	Pancrea
7	chr6:5109200-5130200	Weak transcription	Cortex derived primary cultured neurospheres	brain
8	chr6:5112200-5128600	Weak transcription	Primary T cells from cord blood	blood
9	chr6:5112800-5132600	Weak transcription	Primary hematopoietic stem cells short term culture	blood
10	chr6:5113000-5130400	Weak transcription	Gastric	stomach
11	chr6:5113200-5130400	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
12	chr6:5113400-5132400	Weak transcription	Stomach Smooth Muscle	stomach
13	chr6:5116000-5129000	Weak transcription	Fetal Intestine Small	intestine
14	chr6:5122400-5129000	Weak transcription	Fetal Stomach	stomach
15	chr6:5123000-5128400	Weak transcription	Primary neutrophils fromperipheralblood	blood
16	chr6:5123200-5130400	Weak transcription	Left Ventricle	heart
17	chr6:5123400-5132200	Weak transcription	Skeletal Muscle Male	skeletal muscle
18	chr6:5123600-5129200	Weak transcription	Lung	lung
19	chr6:5124600-5128200	Weak transcription	Fetal Thymus	thymus
20	chr6:5124800-5127800	Enhancers	HepG2	liver
21	chr6:5124800-5133200	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
22	chr6:5125000-5130600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
23	chr6:5125000-5133200	Weak transcription	Right Ventricle	heart
24	chr6:5125600-5130200	Weak transcription	Fetal Muscle Leg	muscle
25	chr6:5125800-5128400	Weak transcription	Adipose Nuclei	Adipose
26	chr6:5125800-5128600	Weak transcription	Spleen	Spleen
27	chr6:5126400-5131800	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
28	chr6:5126600-5128600	Weak transcription	K562	blood
29	chr6:5126600-5130200	Weak transcription	iPS-18 Cell Line	embryonic stem cell
30	chr6:5126600-5130400	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
31	chr6:5126600-5130400	Weak transcription	Right Atrium	heart
32	chr6:5126600-5133200	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
33	chr6:5126600-5134000	Weak transcription	NHEK	skin
34	chr6:5126800-5128600	Weak transcription	Placenta	Placenta
35	chr6:5126800-5130000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
36	chr6:5126800-5130000	Weak transcription	Fetal Heart	heart
37	chr6:5126800-5130400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
38	chr6:5126800-5131600	Weak transcription	H9 Cell Line	embryonic stem cell
39	chr6:5126800-5132000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
40	chr6:5126800-5132000	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
41	chr6:5126800-5132200	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
42	chr6:5126800-5132200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
43	chr6:5126800-5132200	Weak transcription	Ovary	ovary
44	chr6:5126800-5132800	Weak transcription	Breast Myoepithelial Primary Cells	Breast
45	chr6:5127000-5130600	Weak transcription	HUES48 Cell Line	embryonic stem cell
46	chr6:5127000-5131400	Weak transcription	iPS-20b Cell Line	embryonic stem cell
47	chr6:5127000-5132200	Weak transcription	NHDF-Ad	bronchial
48	chr6:5127200-5132600	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
49	chr6:5127600-5129000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
50	chr6:5127600-5130400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived

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