Variant report

Variant	rs28613361
Chromosome Location	chr1:153610017-153610018
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr1:153609968-153610093	H1-hESC	embryonic stem cell:	n/a	n/a
2	POLR2A	chr1:153609930-153610577	GM12878	blood:	n/a	n/a
3	POLR2A	chr1:153609875-153610176	HepG2	liver:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr1:153535304..153546939-chr1:153598248..153612195,40	MCF-7	breast:

Variant related genes	Relation type
S100A13	TF binding region
ENSG00000272030	TF binding region
ENSG00000271853	TF binding region
CHTOP	TF binding region
ENSG00000196754	Chromatin interaction

Extended variants
information (count: 37 )
Associated
traits (count: 10 )

rSNPs within LD-proxies of this variant (count:35)

rs_ID	r²[population]
rs1046381	0.92[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs10797056	0.97[AFR][1000 genomes];0.88[AMR][1000 genomes];0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs10797090	0.81[AMR][1000 genomes];0.90[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs10908746	0.84[AFR][1000 genomes];0.86[AMR][1000 genomes];0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs11265633	0.85[EUR][1000 genomes]
rs1128894	0.82[AMR][1000 genomes];0.91[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs11580122	0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12564925	0.82[AFR][1000 genomes];0.86[AMR][1000 genomes];0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12730186	0.82[ASN][1000 genomes]
rs1810836	0.85[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs1888115	0.85[AMR][1000 genomes];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2274739	0.84[AFR][1000 genomes];0.86[AMR][1000 genomes];0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2274740	0.84[AFR][1000 genomes];0.86[AMR][1000 genomes];0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs28379831	0.84[AFR][1000 genomes];0.86[AMR][1000 genomes];0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs28380060	0.88[AMR][1000 genomes];0.93[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs28510471	0.99[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28518786	0.86[ASN][1000 genomes]
rs28580554	0.88[AMR][1000 genomes];0.93[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs28700217	0.85[AMR][1000 genomes];0.93[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs3790411	0.83[ASN][1000 genomes]
rs3790412	0.81[AFR][1000 genomes];0.86[AMR][1000 genomes];0.93[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs3795396	0.81[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs3818632	0.82[AMR][1000 genomes];0.92[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs3828031	0.81[AFR][1000 genomes];0.86[AMR][1000 genomes];0.93[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4351684	0.89[EUR][1000 genomes]
rs4845557	0.97[AFR][1000 genomes];0.88[AMR][1000 genomes];0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4845558	0.87[AMR][1000 genomes];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4845560	0.82[EUR][1000 genomes]
rs6427640	0.89[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs6694006	0.84[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs7345	0.81[AMR][1000 genomes];0.89[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs7934	0.94[AFR][1000 genomes];0.88[AMR][1000 genomes];0.93[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs913860	0.86[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs913861	0.86[AMR][1000 genomes];0.93[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs9661993	0.82[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 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

mRNA abundance (count:10)

SNP	Gene	Cis/trans	Tissue	Source
rs28613361	RP1-178F15.5	cis	Adipose Subcutaneous	GTEx
rs28613361	S100A13	cis	Adipose Subcutaneous	GTEx
rs28613361	RP1-178F15.4	cis	Artery Aorta	GTEx
rs28613361	RP1-178F15.4	cis	lung	GTEx
rs28613361	S100A13	Cis_1M	lymphoblastoid	RTeQTL
rs28613361	RP1-178F15.4	cis	Heart Left Ventricle	GTEx
rs28613361	RP1-178F15.4	cis	Muscle Skeletal	GTEx
rs28613361	CHTOP	cis	Muscle Skeletal	GTEx
rs28613361	RP1-178F15.4	cis	Adipose Subcutaneous	GTEx
rs28613361	RP1-178F15.4	cis	Skin Sun Exposed Lower leg	GTEx

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:153607200-153610200	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
2	chr1:153608000-153611200	Genic enhancers	Fetal Adrenal Gland	Adrenal Gland
3	chr1:153608000-153611600	Genic enhancers	Fetal Muscle Trunk	muscle
4	chr1:153608200-153610200	Genic enhancers	Fetal Muscle Leg	muscle
5	chr1:153608200-153610800	Genic enhancers	Adipose Nuclei	Adipose
6	chr1:153608200-153611000	Genic enhancers	Primary T killer memory cells from peripheral blood	blood
7	chr1:153608200-153611000	Genic enhancers	Fetal Intestine Small	intestine
8	chr1:153608200-153611000	Enhancers	Stomach Mucosa	stomach
9	chr1:153608200-153611800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
10	chr1:153608200-153613200	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
11	chr1:153608200-153618600	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
12	chr1:153608200-153618800	Strong transcription	HUES6 Cell Line	embryonic stem cell
13	chr1:153608200-153619600	Strong transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
14	chr1:153608400-153610600	Genic enhancers	Brain Anterior Caudate	brain
15	chr1:153608400-153616400	Genic enhancers	Primary T helper cells fromperipheralblood	blood
16	chr1:153608400-153618600	Strong transcription	Primary neutrophils fromperipheralblood	blood
17	chr1:153608400-153618800	Strong transcription	H9 Cell Line	embryonic stem cell
18	chr1:153608400-153618800	Strong transcription	iPS-20b Cell Line	embryonic stem cell
19	chr1:153608400-153619200	Strong transcription	HUES48 Cell Line	embryonic stem cell
20	chr1:153608400-153619200	Strong transcription	iPS-18 Cell Line	embryonic stem cell
21	chr1:153608400-153619800	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
22	chr1:153608600-153610400	Genic enhancers	Breast Myoepithelial Primary Cells	Breast
23	chr1:153608600-153611000	Genic enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
24	chr1:153608600-153611200	Genic enhancers	Primary T helper memory cells from peripheral blood 2	blood
25	chr1:153608600-153611200	Genic enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
26	chr1:153608600-153615600	Strong transcription	Fetal Intestine Large	intestine
27	chr1:153608600-153618600	Strong transcription	Primary hematopoietic stem cells short term culture	blood
28	chr1:153608600-153618800	Strong transcription	HUVEC	blood vessel
29	chr1:153608600-153619400	Strong transcription	H1 Cell Line	embryonic stem cell
30	chr1:153608600-153619400	Strong transcription	Osteobl	bone
31	chr1:153608600-153619600	Strong transcription	Primary hematopoietic stem cells	blood
32	chr1:153608600-153619600	Strong transcription	Cortex derived primary cultured neurospheres	brain
33	chr1:153608600-153619600	Strong transcription	HMEC	breast
34	chr1:153608600-153620200	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
35	chr1:153608600-153620200	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
36	chr1:153608800-153610600	Genic enhancers	Duodenum Smooth Muscle	Duodenum
37	chr1:153608800-153610600	Genic enhancers	A549	lung
38	chr1:153608800-153611000	Genic enhancers	Primary T helper naive cells from peripheral blood	blood
39	chr1:153608800-153611000	Genic enhancers	Primary T helper cells PMA-I stimulated	--
40	chr1:153608800-153611000	Genic enhancers	Brain Dorsolateral Prefrontal Cortex	brain
41	chr1:153608800-153611000	Genic enhancers	Brain Substantia Nigra	brain
42	chr1:153608800-153611000	Genic enhancers	Skeletal Muscle Female	skeletal muscle
43	chr1:153608800-153611200	Genic enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
44	chr1:153608800-153611200	Genic enhancers	Brain Hippocampus Middle	brain
45	chr1:153608800-153611600	Genic enhancers	Left Ventricle	heart
46	chr1:153608800-153612200	Genic enhancers	Primary T helper naive cells fromperipheralblood	blood
47	chr1:153608800-153618400	Strong transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
48	chr1:153608800-153618800	Strong transcription	iPS-15b Cell Line	embryonic stem cell
49	chr1:153608800-153619400	Strong transcription	HUES64 Cell Line	embryonic stem cell
50	chr1:153608800-153619800	Strong transcription	Rectal Mucosa Donor 31	rectum

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