Variant report

Variant	rs10429558
Chromosome Location	chr9:96336790-96336791
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:3)
CpG islands
(count:0)
Chromatin interactive
region (count:3)
LncRNA
region (count:1)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:3 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr9:96336453-96336994	K562	blood:	n/a	n/a
2	POLR2A	chr9:96336738-96336996	HepG2	liver:	n/a	n/a
3	POLR2A	chr9:96336738-96337162	MCF10A-Er-Src	breast:	n/a	n/a

No data

(count:3 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr9:96211672..96218862-chr9:96335264..96341672,16	MCF-7	breast:
2	chr9:96207153..96210037-chr9:96334442..96336797,2	MCF-7	breast:
3	chr9:96300899..96303747-chr9:96334511..96337154,2	MCF-7	breast:

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

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-FAM120AOS-5	chr9:96336376-96337293	NONHSAT133277

No data

Variant related genes	Relation type
PHF2	TF binding region
ENSG00000188938	Chromatin interaction
ENSG00000048828	Chromatin interaction

Extended variants
information (count: 30 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:28)

rs_ID	r²[population]
rs10046907	0.81[YRI][hapmap]
rs10761236	0.82[ASN][1000 genomes]
rs10761237	0.81[YRI][hapmap]
rs11975	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12341488	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.93[AFR][1000 genomes];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12554020	0.83[CHB][hapmap];0.83[JPT][hapmap];0.81[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs3815563	0.91[CHB][hapmap];1.00[JPT][hapmap]
rs4552973	0.81[CHB][hapmap];0.83[JPT][hapmap];0.82[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs59483310	0.82[AMR][1000 genomes];0.88[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs59582399	0.84[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs60076242	0.95[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6479482	0.84[EUR][1000 genomes]
rs6479483	0.85[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs6479494	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6479495	0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7020459	0.85[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs7025805	0.86[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs7028729	0.84[EUR][1000 genomes]
rs7035657	0.90[CHB][hapmap];1.00[JPT][hapmap]
rs7036984	0.90[CHB][hapmap];1.00[JPT][hapmap];0.84[EUR][1000 genomes]
rs7048853	0.81[AMR][1000 genomes];0.81[ASN][1000 genomes]
rs7850322	0.82[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs7853605	0.90[CHB][hapmap];1.00[JPT][hapmap]
rs7857183	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.91[AFR][1000 genomes];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7859267	0.88[CHB][hapmap]
rs7860098	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7862998	0.84[EUR][1000 genomes]
rs7870210	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[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	nsv1041803	chr9:96299639-96342013	Flanking Active TSS Weak transcription Strong transcription Active TSS Enhancers Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	15 gene(s)	inside rSNPs	diseases
2	nsv824984	chr9:96310933-96375022	Flanking Active TSS Weak transcription Enhancers Strong transcription Genic enhancers Active TSS ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	18 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs10429558	RP11-165J3.6	cis	Esophagus Muscularis	GTEx
rs10429558	RP11-165J3.6	cis	Thyroid	GTEx
rs10429558	RP11-165J3.6	cis	Skin Sun Exposed Lower leg	GTEx

Chromatin state (count:80 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:96330000-96337200	Weak transcription	NHLF	lung
2	chr9:96330000-96337400	Weak transcription	Hela-S3	cervix
3	chr9:96330000-96337400	Weak transcription	HSMM	muscle
4	chr9:96330200-96336800	Weak transcription	Colon Smooth Muscle	Colon
5	chr9:96330200-96336800	Weak transcription	Fetal Lung	lung
6	chr9:96330200-96337000	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
7	chr9:96330200-96337000	Weak transcription	Fetal Intestine Small	intestine
8	chr9:96330200-96337000	Weak transcription	Stomach Smooth Muscle	stomach
9	chr9:96330200-96337200	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
10	chr9:96330200-96337200	Weak transcription	Aorta	Aorta
11	chr9:96330200-96337200	Weak transcription	Brain Inferior Temporal Lobe	brain
12	chr9:96330200-96337200	Weak transcription	Colonic Mucosa	Colon
13	chr9:96330200-96337200	Weak transcription	Skeletal Muscle Male	skeletal muscle
14	chr9:96330200-96337200	Weak transcription	Osteobl	bone
15	chr9:96330200-96337400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
16	chr9:96330200-96337400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
17	chr9:96330200-96337400	Weak transcription	Placenta Amnion	Placenta Amnion
18	chr9:96330200-96337400	Weak transcription	Psoas Muscle	Psoas
19	chr9:96330200-96337400	Weak transcription	NHEK	skin
20	chr9:96330200-96337600	Weak transcription	Right Atrium	heart
21	chr9:96330400-96337000	Weak transcription	Fetal Heart	heart
22	chr9:96330800-96337200	Weak transcription	Pancreas	Pancrea
23	chr9:96331000-96336800	Weak transcription	H1 Cell Line	embryonic stem cell
24	chr9:96331000-96336800	Weak transcription	Gastric	stomach
25	chr9:96331000-96336800	Weak transcription	Skeletal Muscle Female	skeletal muscle
26	chr9:96331000-96337000	Weak transcription	Fetal Stomach	stomach
27	chr9:96332400-96337400	Weak transcription	Primary B cells from cord blood	blood
28	chr9:96332400-96337400	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
29	chr9:96332600-96336800	Weak transcription	Primary B cells from peripheral blood	blood
30	chr9:96332600-96337400	Weak transcription	Primary neutrophils fromperipheralblood	blood
31	chr9:96333400-96336800	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
32	chr9:96333400-96337200	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
33	chr9:96333400-96337200	Weak transcription	Duodenum Smooth Muscle	Duodenum
34	chr9:96333600-96337600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
35	chr9:96333800-96337200	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
36	chr9:96333800-96337200	Weak transcription	Fetal Brain Female	brain
37	chr9:96333800-96337400	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
38	chr9:96333800-96337400	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
39	chr9:96333800-96337600	Weak transcription	Primary hematopoietic stem cells	blood
40	chr9:96334000-96337200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
41	chr9:96334000-96337400	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
42	chr9:96334800-96337600	Enhancers	Fetal Thymus	thymus
43	chr9:96335400-96337000	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
44	chr9:96335600-96336800	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
45	chr9:96335600-96337400	Weak transcription	Left Ventricle	heart
46	chr9:96335800-96337000	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
47	chr9:96335800-96337200	Enhancers	Placenta	Placenta
48	chr9:96336000-96337200	Weak transcription	Thymus	Thymus
49	chr9:96336400-96336800	Enhancers	Fetal Muscle Trunk	muscle
50	chr9:96336400-96337000	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain

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