Variant report

Variant	rs9590039
Chromosome Location	chr13:95238154-95238155
allele	C/T
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	STAT3	chr13:95237893-95238192	MCF10A-Er-Src	breast:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr13:95236767..95238765-chr13:95240414..95242453,2	MCF-7	breast:

Variant related genes	Relation type
TGDS	TF binding region

Extended variants
information (count: 21 )
Associated
traits (count: 6 )

rSNPs within LD-proxies of this variant (count:17)

rs_ID	r²[population]
rs16949940	1.00[CEU][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2226078	0.80[CEU][hapmap];1.00[CHD][hapmap]
rs4417425	0.80[CEU][hapmap]
rs61965607	0.80[EUR][1000 genomes]
rs6492722	0.80[CEU][hapmap];1.00[CHD][hapmap]
rs7322453	1.00[CEU][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs7330899	0.87[EUR][1000 genomes]
rs7984105	0.80[CEU][hapmap];1.00[CHD][hapmap]
rs7997429	0.90[CEU][hapmap];0.88[EUR][1000 genomes]
rs8001569	0.93[CEU][hapmap];0.84[EUR][1000 genomes]
rs9301978	0.89[CEU][hapmap];0.88[EUR][1000 genomes]
rs9516436	0.82[ASW][hapmap];1.00[CEU][hapmap];1.00[CHD][hapmap];0.96[GIH][hapmap];1.00[MEX][hapmap];0.81[MKK][hapmap];1.00[TSI][hapmap];0.82[YRI][hapmap];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs9516439	0.80[EUR][1000 genomes]
rs9524552	0.83[EUR][1000 genomes]
rs9524564	0.80[CEU][hapmap]
rs9590036	0.88[EUR][1000 genomes]
rs9590043	0.80[CEU][hapmap];0.81[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv34004	chr13:94906537-95392644	Enhancers Flanking Active TSS Bivalent Enhancer Strong transcription Weak transcription Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	27 gene(s)	inside rSNPs	diseases
2	nsv562756	chr13:95178317-95238154	Enhancers Weak transcription Active TSS Strong transcription Flanking Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	7 gene(s)	inside rSNPs	diseases
3	nsv832685	chr13:95179676-95279966	Active TSS Flanking Active TSS Weak transcription Strong transcription Enhancers Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	15 gene(s)	inside rSNPs	diseases
4	nsv832686	chr13:95206742-95400992	Enhancers Weak transcription Active TSS Bivalent Enhancer Strong transcription Bivalent/Poised TSS Flanking Active TSS Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	20 gene(s)	inside rSNPs	diseases

mRNA abundance (count:6)

SNP	Gene	Cis/trans	Tissue	Source
rs9590039	TGDS	cis	Liver	GTEx
rs9590039	GPR180	cis	Muscle Skeletal	GTEx
rs9590039	GPR180	cis	parietal	SCAN
rs9590039	GPR180	cis	cerebellum	SCAN
rs9590039	TGDS	cis	multi-tissue	Pritchard
rs9590039	GPR180	cis	Skin Sun Exposed Lower leg	GTEx

Chromatin state (count:125 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr13:95219200-95238200	Strong transcription	Primary T cells from cord blood	blood
2	chr13:95219600-95245600	Strong transcription	Primary hematopoietic stem cells short term culture	blood
3	chr13:95221000-95240000	Strong transcription	Fetal Thymus	thymus
4	chr13:95221000-95241000	Strong transcription	Dnd41	blood
5	chr13:95221200-95239200	Weak transcription	Brain Germinal Matrix	brain
6	chr13:95221400-95242800	Strong transcription	Primary T helper cells fromperipheralblood	blood
7	chr13:95221400-95245800	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
8	chr13:95221600-95240000	Strong transcription	Breast Myoepithelial Primary Cells	Breast
9	chr13:95221800-95239800	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
10	chr13:95221800-95241200	Strong transcription	Primary T helper cells PMA-I stimulated	--
11	chr13:95222000-95238200	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
12	chr13:95222000-95240000	Strong transcription	Primary B cells from peripheral blood	blood
13	chr13:95222000-95245000	Strong transcription	Monocytes-CD14+_RO01746	blood
14	chr13:95222000-95247200	Weak transcription	Fetal Brain Male	brain
15	chr13:95222200-95239200	Strong transcription	Primary T cells fromperipheralblood	blood
16	chr13:95222200-95245000	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
17	chr13:95222200-95245200	Strong transcription	Primary monocytes fromperipheralblood	blood
18	chr13:95222400-95239800	Strong transcription	HUES6 Cell Line	embryonic stem cell
19	chr13:95222600-95240000	Strong transcription	iPS-18 Cell Line	embryonic stem cell
20	chr13:95222800-95239600	Strong transcription	HUES64 Cell Line	embryonic stem cell
21	chr13:95223000-95245800	Strong transcription	iPS-20b Cell Line	embryonic stem cell
22	chr13:95224200-95246400	Weak transcription	Fetal Heart	heart
23	chr13:95224200-95246400	Weak transcription	Stomach Mucosa	stomach
24	chr13:95224400-95242800	Weak transcription	iPS-15b Cell Line	embryonic stem cell
25	chr13:95225000-95247400	Weak transcription	Fetal Brain Female	brain
26	chr13:95225200-95242800	Weak transcription	Small Intestine	intestine
27	chr13:95226000-95245800	Weak transcription	Pancreatic Islets	Pancreatic Islet
28	chr13:95226200-95245400	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
29	chr13:95226800-95246800	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
30	chr13:95230400-95238200	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
31	chr13:95233000-95246600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
32	chr13:95233200-95242800	Weak transcription	NHEK	skin
33	chr13:95233200-95246600	Weak transcription	Placenta Amnion	Placenta Amnion
34	chr13:95233200-95247000	Weak transcription	Brain Cingulate Gyrus	brain
35	chr13:95233400-95247600	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
36	chr13:95233800-95242800	Weak transcription	Brain Substantia Nigra	brain
37	chr13:95234200-95244600	Weak transcription	Esophagus	oesophagus
38	chr13:95234400-95246800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
39	chr13:95234400-95246800	Weak transcription	Brain Inferior Temporal Lobe	brain
40	chr13:95234400-95247000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
41	chr13:95234600-95247200	Weak transcription	Lung	lung
42	chr13:95234800-95246400	Weak transcription	Colon Smooth Muscle	Colon
43	chr13:95235000-95246800	Weak transcription	Spleen	Spleen
44	chr13:95235200-95243600	Weak transcription	Skeletal Muscle Male	skeletal muscle
45	chr13:95235200-95246400	Weak transcription	Brain Anterior Caudate	brain
46	chr13:95235200-95246600	Weak transcription	Psoas Muscle	Psoas
47	chr13:95235200-95246800	Weak transcription	Right Ventricle	heart
48	chr13:95235200-95247000	Weak transcription	Ovary	ovary
49	chr13:95235200-95247400	Weak transcription	Gastric	stomach
50	chr13:95235400-95241400	Strong transcription	Hela-S3	cervix

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