Variant report

Variant	rs10494303
Chromosome Location	chr1:153893023-153893024
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:12)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:12 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr1:153878654..153880951-chr1:153891156..153893030,2	K562	blood:
2	chr1:153642898..153644985-chr1:153891363..153894144,2	K562	blood:
3	chr1:153890509..153893105-chr1:153967139..153969855,2	K562	blood:
4	chr1:153774428..153778178-chr1:153892159..153894443,3	MCF-7	breast:
5	chr1:153813066..153815919-chr1:153892208..153893963,2	MCF-7	breast:
6	chr1:153883515..153885221-chr1:153892964..153894776,3	MCF-7	breast:
7	chr1:153858652..153861331-chr1:153892093..153894371,2	MCF-7	breast:
8	chr1:153890756..153897034-chr1:153961597..153964863,14	K562	blood:
9	chr1:153892664..153896587-chr1:153948190..153951187,6	K562	blood:
10	chr1:153892719..153895039-chr1:153953793..153956278,2	K562	blood:
11	chr1:153769425..153770358-chr1:153892435..153893347,3	MCF-7	breast:
12	chr1:149820075..149822620-chr1:153892093..153893716,2	MCF-7	breast:

No data

Variant related genes	Relation type
ENSG00000203819	Chromatin interaction
ENSG00000231416	Chromatin interaction
ENSG00000143621	Chromatin interaction
ENSG00000143543	Chromatin interaction
ENSG00000177954	Chromatin interaction
ENSG00000272654	Chromatin interaction
ENSG00000261716	Chromatin interaction

Extended variants
information (count: 19 )
Associated
traits (count: 5 )

rSNPs within LD-proxies of this variant (count:13)

rs_ID	r²[population]
rs10127484	0.81[CEU][hapmap];0.82[EUR][1000 genomes]
rs10908512	0.91[AFR][1000 genomes];0.93[AMR][1000 genomes];0.89[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs10908525	0.85[EUR][1000 genomes]
rs10908526	0.85[EUR][1000 genomes]
rs11264573	0.81[CEU][hapmap]
rs11264621	0.82[EUR][1000 genomes]
rs12142733	0.88[CEU][hapmap];0.83[TSI][hapmap];0.80[EUR][1000 genomes]
rs2252508	0.88[CEU][hapmap];0.81[TSI][hapmap];0.84[EUR][1000 genomes]
rs2841102	0.83[JPT][hapmap]
rs3791186	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];1.00[MKK][hapmap];0.95[TSI][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];0.98[AMR][1000 genomes];0.89[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7414227	0.81[CEU][hapmap]
rs7522030	0.81[CEU][hapmap]
rs7549032	0.83[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	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
2	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
3	nsv531892	chr1:153671910-153954090	Flanking Active TSS Weak transcription Strong transcription Genic enhancers Transcr. at gene 5' and 3' Enhancers Active TSS ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	136 gene(s)	inside rSNPs	diseases
4	nsv532551	chr1:153732039-154192279	Enhancers Weak transcription Genic enhancers Flanking Active TSS Strong transcription Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	233 gene(s)	inside rSNPs	diseases
5	esv1830240	chr1:153885261-154370938	Enhancers Flanking Active TSS Weak transcription Genic enhancers Active TSS Transcr. at gene 5' and 3' Strong transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	239 gene(s)	inside rSNPs	diseases
6	nsv872450	chr1:153889042-153937513	Genic enhancers Strong transcription Enhancers Active TSS Flanking Active TSS Weak transcription Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	61 gene(s)	inside rSNPs	diseases

mRNA abundance (count:5)

SNP	Gene	Cis/trans	Tissue	Source
rs10494303	FLG	cis	parietal	SCAN
rs10494303	HAX1	cis	cerebellum	SCAN
rs10494303	SLC27A3	cis	cerebellum	SCAN
rs10494303	CREB3L4	cis	parietal	SCAN
rs10494303	PSMD4	cis	parietal	SCAN

Chromatin state (count:126 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:153846200-153894200	Weak transcription	Esophagus	oesophagus
2	chr1:153853800-153893400	Weak transcription	Placenta Amnion	Placenta Amnion
3	chr1:153866400-153894000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
4	chr1:153878600-153894000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
5	chr1:153890400-153893200	Enhancers	Primary T helper naive cells from peripheral blood	blood
6	chr1:153890400-153893200	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
7	chr1:153890400-153893400	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
8	chr1:153890400-153893600	Enhancers	Skeletal Muscle Male	skeletal muscle
9	chr1:153891200-153893200	Enhancers	Primary T cells fromperipheralblood	blood
10	chr1:153891400-153894000	Enhancers	Colon Smooth Muscle	Colon
11	chr1:153891600-153893400	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
12	chr1:153891600-153893400	Enhancers	Brain Hippocampus Middle	brain
13	chr1:153891600-153893600	Enhancers	Liver	Liver
14	chr1:153891600-153894800	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
15	chr1:153891800-153893200	Enhancers	Adipose Nuclei	Adipose
16	chr1:153891800-153893200	Enhancers	Fetal Heart	heart
17	chr1:153891800-153893200	Genic enhancers	Fetal Thymus	thymus
18	chr1:153891800-153893400	Enhancers	Duodenum Smooth Muscle	Duodenum
19	chr1:153891800-153893400	Enhancers	Fetal Muscle Leg	muscle
20	chr1:153891800-153893400	Transcr. at gene 5' and 3'	K562	blood
21	chr1:153891800-153893600	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
22	chr1:153891800-153893800	Enhancers	HSMMtube	muscle
23	chr1:153891800-153894000	Enhancers	Primary T cells effector/memory enriched fromperipheralblood	blood
24	chr1:153891800-153894000	Enhancers	Primary mononuclear cells fromperipheralblood	Blood
25	chr1:153891800-153894000	Enhancers	Stomach Mucosa	stomach
26	chr1:153891800-153894400	Flanking Active TSS	Fetal Brain Female	brain
27	chr1:153892000-153893600	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
28	chr1:153892200-153893400	Enhancers	Foreskin Melanocyte Primary Cells skin01	Skin
29	chr1:153892200-153893600	Enhancers	Brain Substantia Nigra	brain
30	chr1:153892200-153893800	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
31	chr1:153892200-153894000	Enhancers	Pancreas	Pancrea
32	chr1:153892200-153894000	Enhancers	Psoas Muscle	Psoas
33	chr1:153892200-153894600	Flanking Active TSS	Primary hematopoietic stem cells	blood
34	chr1:153892400-153893200	Flanking Active TSS	iPS-15b Cell Line	embryonic stem cell
35	chr1:153892400-153893200	Enhancers	Aorta	Aorta
36	chr1:153892400-153893600	Enhancers	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
37	chr1:153892400-153893800	Flanking Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
38	chr1:153892400-153894000	Enhancers	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
39	chr1:153892400-153894000	Flanking Active TSS	Breast Myoepithelial Primary Cells	Breast
40	chr1:153892400-153894000	Enhancers	Primary monocytes fromperipheralblood	blood
41	chr1:153892400-153894000	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
42	chr1:153892400-153894000	Enhancers	Fetal Adrenal Gland	Adrenal Gland
43	chr1:153892400-153894000	Enhancers	Gastric	stomach
44	chr1:153892400-153894200	Enhancers	Placenta	Placenta
45	chr1:153892400-153894200	Enhancers	Sigmoid Colon	Sigmoid Colon
46	chr1:153892400-153894400	Flanking Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
47	chr1:153892400-153894400	Flanking Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
48	chr1:153892400-153894400	Flanking Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
49	chr1:153892400-153894400	Flanking Active TSS	Brain Angular Gyrus	brain
50	chr1:153892400-153894400	Flanking Active TSS	Brain Germinal Matrix	brain

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