Variant report

Variant	rs464606
Chromosome Location	chr6:5130429-5130430
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	chr6:5120295..5122743-chr6:5128225..5130886,2	K562	blood:
2	chr6:5120935..5125341-chr6:5126554..5131441,5	K562	blood:

Extended variants
information (count: 49 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:36)

rs_ID	r²[population]
rs11242992	0.81[CEU][hapmap]
rs127124	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs127125	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs200863	1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[ASN][1000 genomes]
rs364886	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs373696	1.00[MEX][hapmap]
rs385315	1.00[CHB][hapmap];0.95[CHD][hapmap];1.00[JPT][hapmap];0.96[ASN][1000 genomes]
rs402541	0.88[CHB][hapmap];0.85[CHD][hapmap];0.83[ASN][1000 genomes]
rs412628	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs423801	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs435175	0.84[ASN][1000 genomes]
rs438298	0.82[ASN][1000 genomes]
rs438934	0.81[MEX][hapmap]
rs445204	0.89[ASN][1000 genomes]
rs454984	0.94[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs455803	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs457453	0.88[CHB][hapmap];0.92[JPT][hapmap]
rs457846	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs458395	0.85[CEU][hapmap];0.89[JPT][hapmap]
rs460416	0.96[MEX][hapmap]
rs461698	0.86[ASN][1000 genomes]
rs462749	0.92[CEU][hapmap];0.94[CHB][hapmap];0.84[CHD][hapmap];0.98[GIH][hapmap];1.00[MEX][hapmap];0.97[TSI][hapmap];0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs464681	0.94[CHB][hapmap];0.85[CHD][hapmap];0.86[ASN][1000 genomes]
rs464863	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs466837	0.90[ASN][1000 genomes]
rs4959328	0.81[CEU][hapmap]
rs4960067	0.81[CEU][hapmap]
rs585956	0.81[AFR][1000 genomes];0.81[ASN][1000 genomes]
rs585970	0.81[AMR][1000 genomes];0.82[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs587777	0.87[AMR][1000 genomes];0.90[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs683261	1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[ASN][1000 genomes]
rs6914985	0.81[CEU][hapmap]
rs73717674	0.93[AFR][1000 genomes]
rs85204	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];0.99[MKK][hapmap];1.00[TSI][hapmap];0.96[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9504338	0.81[CEU][hapmap]
rs9606	0.88[CHB][hapmap];0.85[CHD][hapmap];0.86[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:13 , 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

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs464606	LYRM4	cis	cerebellum	SCAN

Chromatin state (count:58 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:5101800-5132200	Weak transcription	iPS-15b Cell Line	embryonic stem cell
2	chr6:5103200-5132800	Weak transcription	Primary hematopoietic stem cells	blood
3	chr6:5105200-5131400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
4	chr6:5107800-5132000	Weak transcription	Pancreas	Pancrea
5	chr6:5112800-5132600	Weak transcription	Primary hematopoietic stem cells short term culture	blood
6	chr6:5113400-5132400	Weak transcription	Stomach Smooth Muscle	stomach
7	chr6:5123400-5132200	Weak transcription	Skeletal Muscle Male	skeletal muscle
8	chr6:5124800-5133200	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
9	chr6:5125000-5130600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
10	chr6:5125000-5133200	Weak transcription	Right Ventricle	heart
11	chr6:5126400-5131800	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
12	chr6:5126600-5133200	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
13	chr6:5126600-5134000	Weak transcription	NHEK	skin
14	chr6:5126800-5131600	Weak transcription	H9 Cell Line	embryonic stem cell
15	chr6:5126800-5132000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
16	chr6:5126800-5132000	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
17	chr6:5126800-5132200	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
18	chr6:5126800-5132200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
19	chr6:5126800-5132200	Weak transcription	Ovary	ovary
20	chr6:5126800-5132800	Weak transcription	Breast Myoepithelial Primary Cells	Breast
21	chr6:5127000-5130600	Weak transcription	HUES48 Cell Line	embryonic stem cell
22	chr6:5127000-5131400	Weak transcription	iPS-20b Cell Line	embryonic stem cell
23	chr6:5127000-5132200	Weak transcription	NHDF-Ad	bronchial
24	chr6:5127200-5132600	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
25	chr6:5128600-5131000	Enhancers	Spleen	Spleen
26	chr6:5128600-5132400	Weak transcription	Primary B cells from cord blood	blood
27	chr6:5128800-5130600	Weak transcription	Placenta	Placenta
28	chr6:5128800-5132400	Weak transcription	H1 Cell Line	embryonic stem cell
29	chr6:5128800-5136200	Weak transcription	Primary neutrophils fromperipheralblood	blood
30	chr6:5129000-5130800	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
31	chr6:5129000-5130800	Strong transcription	Fetal Intestine Small	intestine
32	chr6:5129000-5136800	Weak transcription	Primary T cells from cord blood	blood
33	chr6:5129000-5162000	Weak transcription	K562	blood
34	chr6:5129200-5130600	Enhancers	Lung	lung
35	chr6:5129200-5132600	Weak transcription	Primary monocytes fromperipheralblood	blood
36	chr6:5129800-5131800	Weak transcription	Primary B cells from peripheral blood	blood
37	chr6:5129800-5138000	Weak transcription	HepG2	liver
38	chr6:5130000-5130800	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
39	chr6:5130000-5131000	Enhancers	Fetal Heart	heart
40	chr6:5130000-5132600	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
41	chr6:5130200-5130600	Weak transcription	Brain Anterior Caudate	brain
42	chr6:5130200-5130800	Flanking Active TSS	Adipose Nuclei	Adipose
43	chr6:5130200-5130800	Enhancers	Fetal Muscle Leg	muscle
44	chr6:5130200-5132000	Enhancers	Cortex derived primary cultured neurospheres	brain
45	chr6:5130200-5132400	Enhancers	iPS-18 Cell Line	embryonic stem cell
46	chr6:5130400-5130600	Enhancers	Brain Inferior Temporal Lobe	brain
47	chr6:5130400-5130600	Enhancers	Brain Dorsolateral Prefrontal Cortex	brain
48	chr6:5130400-5130600	Enhancers	Brain Substantia Nigra	brain
49	chr6:5130400-5130600	ZNF genes & repeats	Gastric	stomach
50	chr6:5130400-5130800	Active TSS	H1 Derived Mesenchymal Stem Cells	ES cell derived

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