Variant report

Variant	rs9289809
Chromosome Location	chr3:150092864-150092865
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr3:150081211..150094856-chr3:150124384..150132921,41	MCF-7	breast:
2	chr3:150081035..150094397-chr3:150122156..150134666,40	MCF-7	breast:
3	chr3:150092338..150094835-chr3:150138440..150140402,2	MCF-7	breast:
4	chr3:150091318..150093525-chr3:150137664..150139823,2	K562	blood:
5	chr3:150083276..150085160-chr3:150092333..150095234,2	K562	blood:
6	chr3:150064599..150068049-chr3:150092339..150097012,5	MCF-7	breast:
7	chr3:150087084..150094553-chr3:150124263..150130094,16	K562	blood:

Variant related genes	Relation type
ENSG00000196428	Chromatin interaction

Extended variants
information (count: 11 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:10)

rs_ID	r²[population]
rs10513374	0.84[CEU][hapmap]
rs10935800	0.84[CEU][hapmap]
rs2122474	0.90[ASN][1000 genomes]
rs34749904	0.81[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs4681618	0.81[CEU][hapmap]
rs9784335	0.81[CEU][hapmap]
rs9826729	0.81[CEU][hapmap]
rs9853316	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9870838	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9882777	0.81[CEU][hapmap]

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	nsv829755	chr3:149992023-150156001	Enhancers Weak transcription Transcr. at gene 5' and 3' Genic enhancers Flanking Active TSS Active TSS Strong transcription ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	49 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs9289809	SLC26A9	trans	cerebellum	SCAN
rs9289809	AADACL2	cis	parietal	SCAN

Chromatin state (count:57 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:150086200-150102200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
2	chr3:150088800-150093800	Weak transcription	iPS-20b Cell Line	embryonic stem cell
3	chr3:150089400-150094200	Weak transcription	Small Intestine	intestine
4	chr3:150089600-150094200	Weak transcription	Placenta	Placenta
5	chr3:150089600-150097400	Weak transcription	iPS-15b Cell Line	embryonic stem cell
6	chr3:150089800-150094000	Weak transcription	H9 Cell Line	embryonic stem cell
7	chr3:150089800-150094000	Weak transcription	Brain Germinal Matrix	brain
8	chr3:150089800-150094000	Weak transcription	Skeletal Muscle Female	skeletal muscle
9	chr3:150089800-150094200	Weak transcription	Left Ventricle	heart
10	chr3:150089800-150094600	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
11	chr3:150090000-150093000	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
12	chr3:150090000-150093800	Weak transcription	Skeletal Muscle Male	skeletal muscle
13	chr3:150090200-150093000	Weak transcription	Fetal Intestine Large	intestine
14	chr3:150090200-150094200	Weak transcription	Duodenum Mucosa	Duodenum
15	chr3:150090200-150124600	Weak transcription	Aorta	Aorta
16	chr3:150090400-150093000	Weak transcription	K562	blood
17	chr3:150090400-150093800	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
18	chr3:150090400-150093800	Weak transcription	Liver	Liver
19	chr3:150090400-150094200	Weak transcription	Rectal Mucosa Donor 31	rectum
20	chr3:150090600-150093000	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
21	chr3:150090600-150093000	Weak transcription	Fetal Intestine Small	intestine
22	chr3:150090600-150093200	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
23	chr3:150090600-150093400	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
24	chr3:150090600-150094200	Weak transcription	HUES48 Cell Line	embryonic stem cell
25	chr3:150090600-150094200	Weak transcription	Pancreatic Islets	Pancreatic Islet
26	chr3:150090800-150093000	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
27	chr3:150090800-150093000	Weak transcription	Placenta Amnion	Placenta Amnion
28	chr3:150090800-150093400	Weak transcription	Adipose Nuclei	Adipose
29	chr3:150090800-150093400	Weak transcription	HepG2	liver
30	chr3:150090800-150093800	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
31	chr3:150090800-150093800	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
32	chr3:150090800-150094000	Weak transcription	Fetal Heart	heart
33	chr3:150090800-150094200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
34	chr3:150090800-150094200	Weak transcription	Psoas Muscle	Psoas
35	chr3:150090800-150094200	Weak transcription	Right Atrium	heart
36	chr3:150090800-150096000	Weak transcription	Gastric	stomach
37	chr3:150090800-150096000	Weak transcription	Stomach Mucosa	stomach
38	chr3:150090800-150096200	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
39	chr3:150090800-150096600	Weak transcription	H1 Cell Line	embryonic stem cell
40	chr3:150090800-150097400	Weak transcription	iPS-18 Cell Line	embryonic stem cell
41	chr3:150090800-150107000	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
42	chr3:150090800-150108600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
43	chr3:150090800-150111000	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
44	chr3:150090800-150111000	Weak transcription	NHEK	skin
45	chr3:150091200-150093200	Weak transcription	Osteobl	bone
46	chr3:150091200-150094000	Weak transcription	HSMM	muscle
47	chr3:150091800-150093400	Weak transcription	Monocytes-CD14+_RO01746	blood
48	chr3:150091800-150101800	Weak transcription	Primary B cells from cord blood	blood
49	chr3:150092000-150093600	Weak transcription	NHLF	lung
50	chr3:150092000-150094200	Weak transcription	HUVEC	blood vessel

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