Variant report

Variant	rs13301669
Chromosome Location	chr9:116652898-116652899
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr9:116646398..116649591-chr9:116652096..116654192,3	K562	blood:
2	chr9:116651215..116653821-chr9:116654616..116657370,3	MCF-7	breast:

Extended variants
information (count: 13 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:12)

rs_ID	r²[population]
rs12551599	0.98[EUR][1000 genomes]
rs13285566	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17200294	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.97[TSI][hapmap];0.89[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17200714	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[AFR][1000 genomes];0.90[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs34488026	0.85[AFR][1000 genomes];0.85[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs34727401	0.87[AMR][1000 genomes];0.97[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs4979289	1.00[CEU][hapmap]
rs4979290	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.87[GIH][hapmap];1.00[JPT][hapmap];0.88[MEX][hapmap];1.00[TSI][hapmap];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4979306	0.81[EUR][1000 genomes]
rs6478041	1.00[YRI][hapmap]
rs7040810	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7041034	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]

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

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv430093	chr9:116330446-117325446	Weak transcription Enhancers Strong transcription Flanking Active TSS Bivalent/Poised TSS Active TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	165 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs13301669	SLC46A2	cis	parietal	SCAN
rs13301669	ZNF618	cis	cerebellum	SCAN
rs13301669	C9orf84	cis	parietal	SCAN

Chromatin state (count:54 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:116639200-116663400	Weak transcription	Gastric	stomach
2	chr9:116649000-116653000	Weak transcription	Brain Anterior Caudate	brain
3	chr9:116649200-116658000	Weak transcription	Muscle Satellite Cultured Cells	--
4	chr9:116649600-116660000	Weak transcription	Small Intestine	intestine
5	chr9:116649800-116655000	Weak transcription	Stomach Mucosa	stomach
6	chr9:116649800-116663800	Weak transcription	HSMMtube	muscle
7	chr9:116649800-116668600	Weak transcription	H9 Cell Line	embryonic stem cell
8	chr9:116650000-116653800	Weak transcription	Osteobl	bone
9	chr9:116650200-116657600	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
10	chr9:116650200-116657800	Weak transcription	HUVEC	blood vessel
11	chr9:116650400-116653200	ZNF genes & repeats	H9 Derived Neuron Cultured Cells	ES cell derived
12	chr9:116650600-116662800	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
13	chr9:116651000-116654200	Weak transcription	Liver	Liver
14	chr9:116651000-116654800	ZNF genes & repeats	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
15	chr9:116651000-116662600	Weak transcription	Fetal Intestine Small	intestine
16	chr9:116651000-116662800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
17	chr9:116651000-116668000	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
18	chr9:116651200-116653200	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
19	chr9:116651200-116663200	Weak transcription	Fetal Stomach	stomach
20	chr9:116651200-116675000	Weak transcription	Colon Smooth Muscle	Colon
21	chr9:116651600-116653000	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
22	chr9:116651600-116655400	ZNF genes & repeats	Primary hematopoietic stem cells G-CSF-mobilized Male	--
23	chr9:116651800-116653200	ZNF genes & repeats	HUES6 Cell Line	embryonic stem cell
24	chr9:116651800-116654200	ZNF genes & repeats	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
25	chr9:116651800-116654600	ZNF genes & repeats	Primary hematopoietic stem cells G-CSF-mobilized Female	--
26	chr9:116651800-116654600	Strong transcription	HSMM	muscle
27	chr9:116651800-116655400	ZNF genes & repeats	Primary hematopoietic stem cells	blood
28	chr9:116652000-116653200	ZNF genes & repeats	Fetal Kidney	kidney
29	chr9:116652000-116653800	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
30	chr9:116652000-116655200	Weak transcription	Pancreas	Pancrea
31	chr9:116652200-116655200	Weak transcription	Ovary	ovary
32	chr9:116652200-116668400	Weak transcription	NH-A	brain
33	chr9:116652400-116653200	ZNF genes & repeats	HUES48 Cell Line	embryonic stem cell
34	chr9:116652600-116653000	ZNF genes & repeats	HUES64 Cell Line	embryonic stem cell
35	chr9:116652600-116653200	ZNF genes & repeats	iPS-20b Cell Line	embryonic stem cell
36	chr9:116652600-116653200	ZNF genes & repeats	Fetal Brain Female	brain
37	chr9:116652800-116653000	ZNF genes & repeats	ES-I3 Cell Line	embryonic stem cell
38	chr9:116652800-116653000	ZNF genes & repeats	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
39	chr9:116652800-116653000	ZNF genes & repeats	Fetal Lung	lung
40	chr9:116652800-116653000	ZNF genes & repeats	Fetal Muscle Trunk	muscle
41	chr9:116652800-116653000	ZNF genes & repeats	K562	blood
42	chr9:116652800-116653000	ZNF genes & repeats	NHDF-Ad	bronchial
43	chr9:116652800-116653200	ZNF genes & repeats	IMR90 fetal lung fibroblasts Cell Line	lung
44	chr9:116652800-116653200	ZNF genes & repeats	iPS-18 Cell Line	embryonic stem cell
45	chr9:116652800-116653200	ZNF genes & repeats	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
46	chr9:116652800-116653200	ZNF genes & repeats	Duodenum Smooth Muscle	Duodenum
47	chr9:116652800-116653200	ZNF genes & repeats	Fetal Muscle Leg	muscle
48	chr9:116652800-116653200	ZNF genes & repeats	A549	lung
49	chr9:116652800-116653200	ZNF genes & repeats	NHLF	lung
50	chr9:116652800-116653400	ZNF genes & repeats	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived

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