Variant report

Variant	rs7049168
Chromosome Location	chr9:94910815-94910816
allele	G/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	POLR2A	chr9:94909030-94910844	IMR90	lung:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr9:94900325..94903739-chr9:94909399..94912070,4	MCF-7	breast:
2	chr9:94909662..94911780-chr9:94913646..94915674,2	K562	blood:
3	chr9:94909200..94911052-chr9:95430848..95432803,2	K562	blood:

Variant related genes	Relation type
LINC00475	TF binding region
ENSG00000238996	TF binding region
ENSG00000225511	Chromatin interaction
ENSG00000127080	Chromatin interaction

Extended variants
information (count: 13 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:5)

rs_ID	r²[population]
rs10761144	0.90[ASN][1000 genomes]
rs12345394	0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1537412	0.99[ASN][1000 genomes]
rs7035248	0.80[CHD][hapmap];0.83[MEX][hapmap]
rs7848948	1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap];0.98[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:8 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv949008	chr9:94500776-95182133	Enhancers ZNF genes & repeats Weak transcription Bivalent Enhancer Strong transcription Flanking Active TSS Bivalent/Poised TSS Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	55 gene(s)	inside rSNPs	diseases
2	nsv1050845	chr9:94687959-95312406	Weak transcription Enhancers Strong transcription Flanking Active TSS Active TSS Genic enhancers Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	58 gene(s)	inside rSNPs	diseases
3	nsv1046733	chr9:94690622-95138564	Genic enhancers Weak transcription Flanking Active TSS Strong transcription Enhancers Active TSS Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	49 gene(s)	inside rSNPs	diseases
4	nsv530947	chr9:94697309-95093377	Weak transcription Bivalent Enhancer Strong transcription Enhancers Active TSS Bivalent/Poised TSS Flanking Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	49 gene(s)	inside rSNPs	diseases
5	nsv917089	chr9:94857047-95099848	Weak transcription Flanking Bivalent TSS/Enh Enhancers Strong transcription Genic enhancers Bivalent/Poised TSS Flanking Active TSS Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	45 gene(s)	inside rSNPs	diseases
6	nsv969760	chr9:94877924-94966209	Flanking Bivalent TSS/Enh Weak transcription Flanking Active TSS Enhancers Active TSS Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS Strong transcription Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	26 gene(s)	inside rSNPs	diseases
7	nsv893572	chr9:94891778-94944778	Enhancers Bivalent Enhancer Weak transcription Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	diseases
8	nsv972779	chr9:94910607-94920083	Enhancers Weak transcription Flanking Active TSS Bivalent Enhancer Genic enhancers Strong transcription	TF binding region Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs7049168	CDK20	cis	parietal	SCAN
rs7049168	ANKRD19	cis	parietal	SCAN
rs7049168	FAM120AOS	cis	parietal	SCAN
rs7049168	C9orf3	cis	parietal	SCAN

Chromatin state (count:47 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:94906800-94911200	Genic enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
2	chr9:94908400-94911000	Enhancers	Fetal Muscle Trunk	muscle
3	chr9:94908800-94911000	Enhancers	Placenta	Placenta
4	chr9:94909800-94914400	Weak transcription	Cortex derived primary cultured neurospheres	brain
5	chr9:94910000-94911000	Enhancers	Esophagus	oesophagus
6	chr9:94910000-94911200	Genic enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
7	chr9:94910000-94913000	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
8	chr9:94910000-94914000	Weak transcription	Brain Hippocampus Middle	brain
9	chr9:94910000-94914000	Weak transcription	Colon Smooth Muscle	Colon
10	chr9:94910200-94913000	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
11	chr9:94910200-94913800	Weak transcription	Rectal Smooth Muscle	rectum
12	chr9:94910200-94914000	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
13	chr9:94910200-94914200	Weak transcription	Duodenum Smooth Muscle	Duodenum
14	chr9:94910200-94914200	Weak transcription	Pancreas	Pancrea
15	chr9:94910200-94914600	Weak transcription	Fetal Lung	lung
16	chr9:94910200-94923800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
17	chr9:94910400-94911000	Enhancers	HSMMtube	muscle
18	chr9:94910400-94911200	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
19	chr9:94910400-94912400	Weak transcription	Muscle Satellite Cultured Cells	--
20	chr9:94910400-94912400	Weak transcription	HSMM	muscle
21	chr9:94910400-94913400	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
22	chr9:94910400-94913400	Weak transcription	NH-A	brain
23	chr9:94910400-94913400	Weak transcription	NHDF-Ad	bronchial
24	chr9:94910400-94913400	Weak transcription	Osteobl	bone
25	chr9:94910400-94913800	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
26	chr9:94910400-94913800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
27	chr9:94910400-94913800	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
28	chr9:94910400-94913800	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
29	chr9:94910400-94913800	Weak transcription	Fetal Muscle Leg	muscle
30	chr9:94910400-94913800	Weak transcription	Ovary	ovary
31	chr9:94910400-94913800	Weak transcription	Placenta Amnion	Placenta Amnion
32	chr9:94910400-94913800	Weak transcription	HMEC	breast
33	chr9:94910400-94913800	Weak transcription	NHLF	lung
34	chr9:94910400-94914000	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
35	chr9:94910400-94914000	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
36	chr9:94910400-94914000	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
37	chr9:94910400-94914000	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
38	chr9:94910400-94914000	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
39	chr9:94910400-94914000	Weak transcription	Stomach Smooth Muscle	stomach
40	chr9:94910400-94914000	Weak transcription	A549	lung
41	chr9:94910400-94914000	Weak transcription	HUVEC	blood vessel
42	chr9:94910400-94914000	Weak transcription	NHEK	skin
43	chr9:94910400-94914200	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
44	chr9:94910400-94914200	Weak transcription	K562	blood
45	chr9:94910400-94914400	Weak transcription	Left Ventricle	heart
46	chr9:94910600-94911000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
47	chr9:94910800-94911000	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived

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