Variant report

Variant	rs4845564
Chromosome Location	chr1:153642012-153642013
allele	C/T
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:14)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:14 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr1:153641625..153644878-chr1:153937648..153941391,3	K562	blood:
2	chr1:153640832..153646304-chr1:153937039..153940655,5	MCF-7	breast:
3	chr1:153585070..153587943-chr1:153641105..153643486,2	MCF-7	breast:
4	chr1:153640859..153647825-chr1:153650423..153657512,10	K562	blood:
5	chr1:153604920..153606894-chr1:153640638..153643940,3	K562	blood:
6	chr1:153641137..153644859-chr1:153962268..153964805,3	MCF-7	breast:
7	chr1:153638812..153642214-chr1:153649454..153652124,3	MCF-7	breast:
8	chr1:153641911..153645780-chr1:153697153..153701509,4	MCF-7	breast:
9	chr1:153641515..153644992-chr1:153698475..153702164,4	MCF-7	breast:
10	chr1:153505342..153508148-chr1:153641864..153643367,2	MCF-7	breast:
11	chr1:153641872..153644049-chr1:153747164..153750461,3	MCF-7	breast:
12	chr1:153607039..153609365-chr1:153641782..153643312,2	K562	blood:
13	chr1:153641478..153645789-chr1:153651108..153654010,4	K562	blood:
14	chr1:153581285..153583404-chr1:153640253..153643290,3	MCF-7	breast:

No data

Variant related genes	Relation type
ENSG00000143578	Chromatin interaction
ENSG00000160679	Chromatin interaction
ENSG00000238279	Chromatin interaction
ENSG00000199565	Chromatin interaction
ENSG00000273026	Chromatin interaction
ENSG00000143554	Chromatin interaction
ENSG00000189171	Chromatin interaction
ENSG00000169418	Chromatin interaction
ENSG00000188643	Chromatin interaction
ENSG00000143624	Chromatin interaction
ENSG00000143570	Chromatin interaction
ENSG00000272030	Chromatin interaction
ENSG00000177954	Chromatin interaction
ENSG00000271853	Chromatin interaction

Extended variants
information (count: 48 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:31)

rs_ID	r²[population]
rs10797096	0.84[AFR][1000 genomes];0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10908848	0.97[AFR][1000 genomes];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11265625	0.99[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11265633	0.90[ASN][1000 genomes]
rs11548102	0.83[EUR][1000 genomes]
rs11588347	0.84[AFR][1000 genomes];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12139953	0.93[AFR][1000 genomes];0.89[AMR][1000 genomes];0.94[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs12730186	0.81[AMR][1000 genomes];0.94[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs12755890	0.87[AFR][1000 genomes];0.80[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs28518786	0.94[EUR][1000 genomes]
rs28754733	0.83[EUR][1000 genomes]
rs3795396	0.82[ASN][1000 genomes]
rs3806233	0.85[EUR][1000 genomes]
rs3806234	0.87[ASN][1000 genomes]
rs3862047	0.82[AFR][1000 genomes];0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs4072425	0.83[EUR][1000 genomes]
rs4310476	0.82[AMR][1000 genomes]
rs4351684	0.86[ASN][1000 genomes]
rs4845563	0.87[AMR][1000 genomes];0.97[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs55772653	0.96[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6427640	0.84[ASN][1000 genomes]
rs66721814	0.87[AMR][1000 genomes];0.97[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs6674929	0.83[AFR][1000 genomes];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7345	0.85[ASN][1000 genomes]
rs9330298	0.85[EUR][1000 genomes]
rs9661993	0.87[ASN][1000 genomes]
rs9662664	0.90[AFR][1000 genomes];0.90[AMR][1000 genomes];0.92[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs9700928	0.81[EUR][1000 genomes]
rs9726753	0.84[EUR][1000 genomes]
rs9792963	0.83[EUR][1000 genomes]
rs9792967	0.83[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:17 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1010488	chr1:152901263-153670972	Genic enhancers Active TSS Strong transcription Bivalent/Poised TSS Weak transcription Flanking Active TSS Enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	236 gene(s)	inside rSNPs	diseases
2	nsv535171	chr1:152901263-153670972	Enhancers Flanking Active TSS Weak transcription Genic enhancers Bivalent Enhancer Strong transcription Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	236 gene(s)	inside rSNPs	diseases
3	nsv547928	chr1:153612133-153714252	Weak transcription Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Strong transcription Genic enhancers Flanking Active TSS Enhancers Active TSS Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	47 gene(s)	inside rSNPs	diseases
4	esv2830411	chr1:153613393-153725007	Flanking Bivalent TSS/Enh Strong transcription Flanking Active TSS Enhancers Bivalent Enhancer Genic enhancers Active TSS Weak transcription Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	48 gene(s)	inside rSNPs	diseases
5	nsv1067771	chr1:153613593-153724866	Flanking Active TSS Bivalent Enhancer Strong transcription Weak transcription Genic enhancers Enhancers Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	48 gene(s)	inside rSNPs	diseases
6	nsv530052	chr1:153613593-153724866	Active TSS Flanking Bivalent TSS/Enh Flanking Active TSS Weak transcription Genic enhancers Enhancers Strong transcription Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	48 gene(s)	inside rSNPs	diseases
7	nsv1005818	chr1:153613597-153724980	Weak transcription Flanking Active TSS Bivalent/Poised TSS Enhancers Genic enhancers Flanking Bivalent TSS/Enh Strong transcription Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	48 gene(s)	inside rSNPs	diseases
8	nsv535173	chr1:153613597-153724980	Strong transcription Weak transcription Flanking Active TSS Enhancers Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	48 gene(s)	inside rSNPs	diseases
9	nsv1007835	chr1:153613597-153729959	Genic enhancers Bivalent/Poised TSS Flanking Active TSS Weak transcription Strong transcription Enhancers Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	48 gene(s)	inside rSNPs	diseases
10	nsv535174	chr1:153613597-153729959	Active TSS Enhancers Strong transcription Flanking Active TSS Weak transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	48 gene(s)	inside rSNPs	diseases
11	nsv1011897	chr1:153613597-153836703	Active TSS Genic enhancers Weak transcription Enhancers Strong transcription Bivalent Enhancer Flanking Active TSS ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	70 gene(s)	inside rSNPs	diseases
12	nsv464028	chr1:153622220-153723037	Flanking Bivalent TSS/Enh Flanking Active TSS Strong transcription Active TSS Weak transcription Bivalent Enhancer Enhancers Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	47 gene(s)	inside rSNPs	diseases
13	nsv547929	chr1:153622220-153723037	Active TSS ZNF genes & repeats Flanking Active TSS Flanking Bivalent TSS/Enh Strong transcription Weak transcription Enhancers Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	47 gene(s)	inside rSNPs	diseases
14	nsv999364	chr1:153622634-154419436	Strong transcription Genic enhancers Flanking Active TSS Active TSS Weak transcription Transcr. at gene 5' and 3' Enhancers Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	286 gene(s)	inside rSNPs	diseases
15	nsv535175	chr1:153622634-154419436	Enhancers Weak transcription Active TSS Transcr. at gene 5' and 3' Flanking Active TSS Genic enhancers Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	286 gene(s)	inside rSNPs	diseases
16	nsv1001312	chr1:153622834-153724867	Enhancers Transcr. at gene 5' and 3' Genic enhancers Active TSS Flanking Active TSS Bivalent/Poised TSS Weak transcription Strong transcription Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	47 gene(s)	inside rSNPs	diseases
17	nsv535176	chr1:153622834-153724867	Active TSS Weak transcription Bivalent Enhancer Enhancers Genic enhancers Flanking Active TSS Strong transcription Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	47 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs4845564	RP1-178F15.4	cis	Muscle Skeletal	GTEx
rs4845564	RP1-178F15.4	cis	Adipose Subcutaneous	GTEx
rs4845564	S100A13	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:127 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:153632000-153642200	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
2	chr1:153632000-153642800	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
3	chr1:153632400-153642400	Weak transcription	Right Atrium	heart
4	chr1:153632600-153642200	Strong transcription	Primary monocytes fromperipheralblood	blood
5	chr1:153632600-153642200	Strong transcription	Fetal Stomach	stomach
6	chr1:153633400-153642200	Strong transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
7	chr1:153633400-153642200	Strong transcription	Brain Anterior Caudate	brain
8	chr1:153633600-153642200	Strong transcription	ES-I3 Cell Line	embryonic stem cell
9	chr1:153633600-153642200	Strong transcription	iPS-15b Cell Line	embryonic stem cell
10	chr1:153634200-153642400	Strong transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
11	chr1:153634800-153642400	Strong transcription	iPS DF 6.9 Cell Line	embryonic stem cell
12	chr1:153637200-153642200	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
13	chr1:153640000-153642200	Weak transcription	Pancreatic Islets	Pancreatic Islet
14	chr1:153640000-153642600	Weak transcription	Aorta	Aorta
15	chr1:153640400-153642200	Genic enhancers	Primary T helper naive cells from peripheral blood	blood
16	chr1:153640400-153642200	Genic enhancers	Primary T helper cells fromperipheralblood	blood
17	chr1:153640600-153642200	Genic enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
18	chr1:153640600-153642200	Genic enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
19	chr1:153640600-153642400	Transcr. at gene 5' and 3'	Breast Myoepithelial Primary Cells	Breast
20	chr1:153640800-153642200	Genic enhancers	Skeletal Muscle Female	skeletal muscle
21	chr1:153640800-153642200	Genic enhancers	Thymus	Thymus
22	chr1:153640800-153642400	Weak transcription	Primary neutrophils fromperipheralblood	blood
23	chr1:153640800-153642400	Genic enhancers	Primary T regulatory cells fromperipheralblood	blood
24	chr1:153640800-153642400	Genic enhancers	Fetal Muscle Leg	muscle
25	chr1:153641200-153642200	Genic enhancers	Placenta	Placenta
26	chr1:153641200-153642200	Genic enhancers	Fetal Thymus	thymus
27	chr1:153641200-153642400	Genic enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
28	chr1:153641200-153642400	Genic enhancers	Primary T cells fromperipheralblood	blood
29	chr1:153641200-153642400	Enhancers	Primary T killer naive cells fromperipheralblood	blood
30	chr1:153641200-153642400	Enhancers	Primary T killer memory cells from peripheral blood	blood
31	chr1:153641200-153642400	Genic enhancers	Fetal Muscle Trunk	muscle
32	chr1:153641200-153642400	Enhancers	Pancreas	Pancrea
33	chr1:153641200-153643200	Transcr. at gene 5' and 3'	Dnd41	blood
34	chr1:153641400-153642400	Transcr. at gene 5' and 3'	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
35	chr1:153641400-153642400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
36	chr1:153641400-153642400	Weak transcription	Left Ventricle	heart
37	chr1:153641600-153642200	Genic enhancers	Cortex derived primary cultured neurospheres	brain
38	chr1:153641600-153642200	Genic enhancers	Adipose Nuclei	Adipose
39	chr1:153641600-153642200	Enhancers	Liver	Liver
40	chr1:153641600-153642200	Weak transcription	Brain Inferior Temporal Lobe	brain
41	chr1:153641600-153642200	Genic enhancers	Fetal Adrenal Gland	Adrenal Gland
42	chr1:153641600-153642200	Weak transcription	Right Ventricle	heart
43	chr1:153641600-153642200	Weak transcription	Sigmoid Colon	Sigmoid Colon
44	chr1:153641600-153642200	Active TSS	GM12878-XiMat	blood
45	chr1:153641600-153642200	Transcr. at gene 5' and 3'	Hela-S3	cervix
46	chr1:153641600-153642400	Enhancers	Primary B cells from cord blood	blood
47	chr1:153641600-153642400	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
48	chr1:153641600-153642400	Transcr. at gene 5' and 3'	Brain Germinal Matrix	brain
49	chr1:153641600-153642400	Weak transcription	Gastric	stomach
50	chr1:153641600-153642400	Weak transcription	Spleen	Spleen

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