Variant report

Variant	rs12730186
Chromosome Location	chr1:153623136-153623137
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr1:153542770..153546215-chr1:153620036..153623245,5	MCF-7	breast:
2	chr1:153622142..153624263-chr1:153962051..153964552,2	MCF-7	breast:
3	chr1:153621962..153623668-chr6:15660534..15662735,2	MCF-7	breast:
4	chr1:153621742..153623509-chr1:153747385..153749734,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000177954	Chromatin interaction
ENSG00000143554	Chromatin interaction

Extended variants
information (count: 68 )
Associated
traits (count: 5 )

rSNPs within LD-proxies of this variant (count:51)

rs_ID	r²[population]
rs1046381	0.88[ASN][1000 genomes]
rs10797056	0.88[ASN][1000 genomes]
rs10797090	0.92[ASN][1000 genomes]
rs10797096	0.84[AMR][1000 genomes];0.95[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs10908746	0.88[ASN][1000 genomes]
rs10908848	0.86[AMR][1000 genomes];0.93[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs11265625	0.86[AMR][1000 genomes];0.95[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs1128894	0.84[ASN][1000 genomes]
rs11548102	0.86[EUR][1000 genomes]
rs11580122	0.84[ASN][1000 genomes]
rs11588347	0.84[AMR][1000 genomes];0.94[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs12139953	0.88[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12564925	0.88[ASN][1000 genomes]
rs1810836	0.81[ASN][1000 genomes]
rs1888115	0.86[ASN][1000 genomes]
rs2274739	0.88[ASN][1000 genomes]
rs2274740	0.88[ASN][1000 genomes]
rs28379831	0.88[ASN][1000 genomes]
rs28380060	0.88[ASN][1000 genomes]
rs28510471	0.82[ASN][1000 genomes]
rs28518786	0.89[AMR][1000 genomes];0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs28580554	0.88[ASN][1000 genomes]
rs28613361	0.82[ASN][1000 genomes]
rs28700217	0.88[ASN][1000 genomes]
rs28754733	0.85[EUR][1000 genomes]
rs3790412	0.90[ASN][1000 genomes]
rs3795396	0.80[ASN][1000 genomes]
rs3806233	0.86[EUR][1000 genomes]
rs3806234	0.93[ASN][1000 genomes]
rs3818632	0.86[ASN][1000 genomes]
rs3828031	0.90[ASN][1000 genomes]
rs3862047	0.86[AMR][1000 genomes];0.96[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4072425	0.80[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs4351684	0.85[ASN][1000 genomes]
rs4845557	0.88[ASN][1000 genomes]
rs4845563	0.86[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4845564	0.81[AMR][1000 genomes];0.94[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs55772653	0.86[AMR][1000 genomes];0.96[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs6427640	0.87[ASN][1000 genomes]
rs66721814	0.86[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6674929	0.84[AMR][1000 genomes];0.93[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs7345	0.86[ASN][1000 genomes]
rs7934	0.91[ASN][1000 genomes]
rs913860	0.81[ASN][1000 genomes]
rs913861	0.91[ASN][1000 genomes]
rs9330298	0.82[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs9662664	0.80[AMR][1000 genomes];0.88[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs9700928	0.83[EUR][1000 genomes]
rs9726753	0.81[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs9792963	0.80[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs9792967	0.80[AMR][1000 genomes];0.86[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:5)

SNP	Gene	Cis/trans	Tissue	Source
rs12730186	S100A13	Cis_1M	lymphoblastoid	RTeQTL
rs12730186	RP1-178F15.4	cis	Adipose Subcutaneous	GTEx
rs12730186	RP1-178F15.4	cis	Muscle Skeletal	GTEx
rs12730186	CHTOP	cis	Muscle Skeletal	GTEx
rs12730186	S100A14	cis	Esophagus Mucosa	GTEx

Chromatin state (count:78 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:153618400-153625400	Weak transcription	Small Intestine	intestine
2	chr1:153618400-153630800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
3	chr1:153618400-153631200	Weak transcription	Aorta	Aorta
4	chr1:153618600-153631000	Weak transcription	Pancreatic Islets	Pancreatic Islet
5	chr1:153618600-153631000	Weak transcription	Placenta Amnion	Placenta Amnion
6	chr1:153618800-153625000	Weak transcription	Hela-S3	cervix
7	chr1:153618800-153625000	Weak transcription	HUVEC	blood vessel
8	chr1:153618800-153625200	Weak transcription	NHDF-Ad	bronchial
9	chr1:153618800-153625400	Weak transcription	NH-A	brain
10	chr1:153618800-153626400	Weak transcription	HepG2	liver
11	chr1:153618800-153630800	Weak transcription	iPS-20b Cell Line	embryonic stem cell
12	chr1:153619000-153625000	Weak transcription	Colonic Mucosa	Colon
13	chr1:153619200-153623400	Weak transcription	iPS-18 Cell Line	embryonic stem cell
14	chr1:153619200-153630800	Weak transcription	Fetal Kidney	kidney
15	chr1:153619400-153625000	Weak transcription	Sigmoid Colon	Sigmoid Colon
16	chr1:153619400-153625200	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
17	chr1:153619600-153624400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
18	chr1:153619600-153625000	Weak transcription	HMEC	breast
19	chr1:153619600-153625000	Weak transcription	Osteobl	bone
20	chr1:153619600-153625400	Weak transcription	Primary hematopoietic stem cells	blood
21	chr1:153619600-153630800	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
22	chr1:153619800-153625200	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
23	chr1:153619800-153625200	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
24	chr1:153619800-153625200	Weak transcription	Duodenum Smooth Muscle	Duodenum
25	chr1:153620000-153625000	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
26	chr1:153620000-153625000	Weak transcription	NHEK	skin
27	chr1:153620000-153625200	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
28	chr1:153620000-153625200	Weak transcription	Rectal Mucosa Donor 29	rectum
29	chr1:153620000-153630400	Weak transcription	Dnd41	blood
30	chr1:153620000-153630400	Weak transcription	GM12878-XiMat	blood
31	chr1:153620200-153623600	Enhancers	Pancreas	Pancrea
32	chr1:153620200-153624200	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
33	chr1:153620200-153625000	Weak transcription	Primary neutrophils fromperipheralblood	blood
34	chr1:153620200-153625000	Weak transcription	Muscle Satellite Cultured Cells	--
35	chr1:153620200-153625000	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
36	chr1:153620200-153625200	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
37	chr1:153620200-153625200	Weak transcription	A549	lung
38	chr1:153620200-153625200	Weak transcription	NHLF	lung
39	chr1:153620200-153630400	Weak transcription	Primary B cells from peripheral blood	blood
40	chr1:153620200-153630400	Weak transcription	Duodenum Mucosa	Duodenum
41	chr1:153620200-153630600	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
42	chr1:153620200-153630600	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
43	chr1:153620200-153630600	Weak transcription	Primary B cells from cord blood	blood
44	chr1:153620200-153631000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
45	chr1:153620200-153631000	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
46	chr1:153620800-153624400	Weak transcription	H1 Cell Line	embryonic stem cell
47	chr1:153620800-153624400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
48	chr1:153620800-153624400	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
49	chr1:153620800-153625000	Weak transcription	Primary monocytes fromperipheralblood	blood
50	chr1:153620800-153625000	Weak transcription	Monocytes-CD14+_RO01746	blood

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