Variant report

Variant	rs11548104
Chromosome Location	chr1:153587308-153587309
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:8)
CpG islands
(count:0)
Chromatin interactive
region (count:7)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:8 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	CTCF	chr1:153587160-153587310	HPF	lung:	n/a	n/a
2	CTCF	chr1:153587220-153587370	HAc	cerebellar:	n/a	n/a
3	CTCF	chr1:153587240-153587390	NHEK	skin:	n/a	n/a
4	ZNF263	chr1:153586588-153587386	HEK293-T-REx	kidney:	n/a	chr1:153586857-153586878
5	CTCF	chr1:153587180-153587330	Hela-S3	cervix:	n/a	n/a
6	CTCF	chr1:153587220-153587370	HMEC	breast:	n/a	n/a
7	CTCF	chr1:153587160-153587310	NHDF-neo	bronchial:	n/a	n/a
8	POLR2A	chr1:153587067-153587419	HCT-116	colon:	n/a	n/a

No data

(count:7 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr1:153533881..153554060-chr1:153575339..153590405,58	MCF-7	breast:
2	chr1:153519212..153523090-chr1:153584863..153588698,4	MCF-7	breast:
3	chr1:153586138..153590435-chr1:153962533..153966036,4	K562	blood:
4	chr1:153585070..153587943-chr1:153641105..153643486,2	MCF-7	breast:
5	chr1:153358652..153360555-chr1:153585881..153587585,2	MCF-7	breast:
6	chr1:153536449..153542914-chr1:153579157..153590800,34	MCF-7	breast:
7	chr1:153505490..153510008-chr1:153584041..153589482,7	MCF-7	breast:

No data

Variant related genes	Relation type
S100A16	TF binding region
ENSG00000197956	Chromatin interaction
ENSG00000196154	Chromatin interaction
ENSG00000196754	Chromatin interaction
ENSG00000177954	Chromatin interaction
ENSG00000238279	Chromatin interaction
ENSG00000188015	Chromatin interaction
ENSG00000143621	Chromatin interaction

Extended variants
information (count: 51 )
Associated
traits (count: 14 )

rSNPs within LD-proxies of this variant (count:49)

rs_ID	r²[population]
rs1046381	0.83[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs10797056	0.82[TSI][hapmap];0.82[EUR][1000 genomes]
rs10908746	0.82[EUR][1000 genomes]
rs1128894	0.82[EUR][1000 genomes]
rs11497739	1.00[CEU][hapmap];0.95[CHB][hapmap];0.96[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.80[MEX][hapmap];0.81[MKK][hapmap];0.95[TSI][hapmap];0.86[AMR][1000 genomes];0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11548102	0.81[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11548103	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12564925	0.82[TSI][hapmap];0.82[EUR][1000 genomes]
rs1411273	0.93[EUR][1000 genomes]
rs1810836	0.82[EUR][1000 genomes]
rs1888115	0.82[TSI][hapmap];0.82[EUR][1000 genomes]
rs2274739	0.82[TSI][hapmap];0.82[EUR][1000 genomes]
rs2274740	0.82[TSI][hapmap];0.82[EUR][1000 genomes]
rs28379831	0.82[EUR][1000 genomes]
rs28380060	0.82[TSI][hapmap];0.82[EUR][1000 genomes]
rs28416529	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];0.86[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs28580554	0.82[TSI][hapmap];0.82[EUR][1000 genomes]
rs28700217	0.82[EUR][1000 genomes]
rs28754733	1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[JPT][hapmap];0.96[ASN][1000 genomes]
rs35760493	0.95[ASN][1000 genomes]
rs3790411	0.96[CEU][hapmap];0.93[TSI][hapmap];0.91[EUR][1000 genomes]
rs3790412	0.82[TSI][hapmap];0.82[EUR][1000 genomes]
rs3795396	0.82[TSI][hapmap]
rs3806233	1.00[CHB][hapmap];0.86[CHD][hapmap];0.94[JPT][hapmap];0.90[ASN][1000 genomes]
rs3818632	0.82[TSI][hapmap];0.83[EUR][1000 genomes]
rs3828031	0.82[TSI][hapmap];0.82[EUR][1000 genomes]
rs3862047	0.80[CHD][hapmap]
rs4072425	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.81[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4845557	0.82[EUR][1000 genomes]
rs7345	0.82[TSI][hapmap]
rs7934	0.82[TSI][hapmap];0.82[EUR][1000 genomes]
rs913860	0.82[TSI][hapmap];0.82[EUR][1000 genomes]
rs913861	0.82[TSI][hapmap];0.83[EUR][1000 genomes]
rs9330298	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.98[ASN][1000 genomes]
rs9330299	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];0.90[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9330300	0.85[AFR][1000 genomes];0.91[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9330301	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];0.90[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9660679	0.91[AMR][1000 genomes];0.93[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9699949	0.95[ASN][1000 genomes]
rs9700179	0.95[CHB][hapmap];0.87[CHD][hapmap];1.00[JPT][hapmap];0.94[ASN][1000 genomes]
rs9700928	0.95[CHB][hapmap];0.96[CHD][hapmap];1.00[JPT][hapmap];0.98[ASN][1000 genomes]
rs9726753	0.80[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9729773	0.82[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs9792913	0.98[ASN][1000 genomes]
rs9792963	0.81[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9792967	0.81[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9793310	0.94[AFR][1000 genomes];0.88[AMR][1000 genomes];0.92[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs985242	0.93[EUR][1000 genomes]
rs999418	0.96[AFR][1000 genomes];0.97[AMR][1000 genomes];0.93[EUR][1000 genomes];0.98[ASN][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:14)

SNP	Gene	Cis/trans	Tissue	Source
rs11548104	S100A16	cis	parietal	SCAN
rs11548104	S100A16	cis	cerebellum	SCAN
rs11548104	S100A13	cis	multi-tissue	Pritchard
rs11548104	S100A13	cis	parietal	SCAN
rs11548104	RP1-178F15.4	cis	Skin Sun Exposed Lower leg	GTEx
rs11548104	RP1-178F15.4	cis	Adipose Subcutaneous	GTEx
rs11548104	CTSS	cis	parietal	SCAN
rs11548104	S100A14	cis	Thyroid	GTEx
rs11548104	S100A10	cis	cerebellum	SCAN
rs11548104	S100A13	Cis_1M	lymphoblastoid	RTeQTL
rs11548104	SLC27A3	cis	cerebellum	SCAN
rs11548104	CHTOP	cis	Muscle Skeletal	GTEx
rs11548104	S100A13	cis	lymphoblastoid	seeQTL
rs11548104	RP1-178F15.4	cis	Muscle Skeletal	GTEx

Chromatin state (count:96 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:153582800-153591200	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
2	chr1:153583000-153589000	Active TSS	Esophagus	oesophagus
3	chr1:153583600-153590000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
4	chr1:153584000-153588600	Weak transcription	K562	blood
5	chr1:153584200-153588600	Weak transcription	Primary monocytes fromperipheralblood	blood
6	chr1:153584200-153588800	Weak transcription	Monocytes-CD14+_RO01746	blood
7	chr1:153584600-153587600	Enhancers	Placenta	Placenta
8	chr1:153585000-153589200	Weak transcription	Brain Angular Gyrus	brain
9	chr1:153585400-153589000	Weak transcription	Brain Inferior Temporal Lobe	brain
10	chr1:153585400-153589800	Weak transcription	Brain Substantia Nigra	brain
11	chr1:153585600-153587400	Enhancers	Colonic Mucosa	Colon
12	chr1:153585600-153587400	Weak transcription	Fetal Thymus	thymus
13	chr1:153585600-153589400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
14	chr1:153585600-153590400	Enhancers	Lung	lung
15	chr1:153585600-153590600	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
16	chr1:153585600-153591000	Weak transcription	iPS-20b Cell Line	embryonic stem cell
17	chr1:153585600-153591200	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
18	chr1:153585600-153591400	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
19	chr1:153585600-153592200	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
20	chr1:153585600-153596400	Weak transcription	Brain Hippocampus Middle	brain
21	chr1:153585600-153597600	Weak transcription	H9 Cell Line	embryonic stem cell
22	chr1:153585600-153598800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
23	chr1:153585600-153599000	Weak transcription	Aorta	Aorta
24	chr1:153585800-153587600	Enhancers	Fetal Muscle Leg	muscle
25	chr1:153585800-153587800	Enhancers	Fetal Stomach	stomach
26	chr1:153585800-153588000	Enhancers	Fetal Muscle Trunk	muscle
27	chr1:153585800-153588600	Transcr. at gene 5' and 3'	NHEK	skin
28	chr1:153585800-153599200	Weak transcription	Fetal Brain Male	brain
29	chr1:153586000-153587400	Flanking Active TSS	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
30	chr1:153586000-153587400	Weak transcription	Gastric	stomach
31	chr1:153586000-153587600	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
32	chr1:153586000-153588200	Weak transcription	iPS-15b Cell Line	embryonic stem cell
33	chr1:153586000-153588600	Weak transcription	HUES6 Cell Line	embryonic stem cell
34	chr1:153586000-153588600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
35	chr1:153586000-153588600	Weak transcription	Adipose Nuclei	Adipose
36	chr1:153586000-153588600	Weak transcription	Left Ventricle	heart
37	chr1:153586000-153589000	Weak transcription	Ovary	ovary
38	chr1:153586000-153589400	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
39	chr1:153586000-153589600	Weak transcription	Brain Cingulate Gyrus	brain
40	chr1:153586000-153589800	Weak transcription	Brain Anterior Caudate	brain
41	chr1:153586000-153590000	Weak transcription	HUVEC	blood vessel
42	chr1:153586000-153591000	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
43	chr1:153586000-153591000	Weak transcription	HUES64 Cell Line	embryonic stem cell
44	chr1:153586000-153591000	Weak transcription	Cortex derived primary cultured neurospheres	brain
45	chr1:153586000-153595600	Weak transcription	HUES48 Cell Line	embryonic stem cell
46	chr1:153586000-153596200	Weak transcription	Fetal Kidney	kidney
47	chr1:153586000-153598800	Weak transcription	Psoas Muscle	Psoas
48	chr1:153586200-153587400	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
49	chr1:153586200-153587400	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
50	chr1:153586200-153587400	Enhancers	A549	lung

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