Variant report

Variant	rs1323772
Chromosome Location	chr9:85833752-85833753
allele	A/G
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	MXI1	chr9:85833644-85836224	SK-N-SH	brain:	n/a	chr9:85834186-85834201 chr9:85834188-85834203

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr9:85813794..85816602-chr9:85833659..85835490,2	MCF-7	breast:
2	chr9:85832727..85836639-chr9:86319596..86323973,3	MCF-7	breast:

Variant related genes	Relation type
ENSG00000229109	TF binding region
ENSG00000135018	Chromatin interaction
ENSG00000254473	Chromatin interaction
ENSG00000251776	Chromatin interaction

Extended variants
information (count: 17 )
Associated
traits (count: 1 )

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

rs_ID	r²[population]
rs10867954	0.81[CHB][hapmap];0.84[CHD][hapmap]
rs11139954	0.89[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs11139955	0.84[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs11139959	1.00[CEU][hapmap];0.88[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs11139963	1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[AMR][1000 genomes];0.81[ASN][1000 genomes]
rs11139965	0.92[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs11139971	0.95[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs11139973	0.91[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs11139975	1.00[CEU][hapmap];0.81[CHB][hapmap];0.83[CHD][hapmap];0.97[GIH][hapmap];0.82[MKK][hapmap];1.00[TSI][hapmap];0.92[AMR][1000 genomes];0.90[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs11139976	0.90[CHB][hapmap];0.96[CHD][hapmap];0.94[GIH][hapmap];1.00[JPT][hapmap];0.85[MEX][hapmap];0.90[ASN][1000 genomes]
rs11139978	0.81[CHB][hapmap];0.84[CHD][hapmap]
rs11139983	0.81[CHB][hapmap];0.84[CHD][hapmap]
rs11139995	0.84[CHB][hapmap]
rs17400361	1.00[CEU][hapmap];0.88[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs4877745	0.81[CHB][hapmap]
rs58862231	0.91[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs7848774	0.94[CEU][hapmap];1.00[MEX][hapmap];0.96[TSI][hapmap];0.89[AMR][1000 genomes];0.91[EUR][1000 genomes]

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs1323772	ISCA1	cis	parietal	SCAN

Chromatin state (count:39 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:85824200-85834200	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
2	chr9:85827800-85833800	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
3	chr9:85832000-85834200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
4	chr9:85832000-85834200	Weak transcription	Gastric	stomach
5	chr9:85833200-85834000	Enhancers	Placenta Amnion	Placenta Amnion
6	chr9:85833400-85833800	Enhancers	Esophagus	oesophagus
7	chr9:85833400-85834000	Enhancers	Breast Myoepithelial Primary Cells	Breast
8	chr9:85833400-85834000	Enhancers	Fetal Adrenal Gland	Adrenal Gland
9	chr9:85833400-85834000	Enhancers	HMEC	breast
10	chr9:85833400-85834200	Enhancers	Placenta	Placenta
11	chr9:85833600-85833800	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
12	chr9:85833600-85833800	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
13	chr9:85833600-85833800	Active TSS	Fetal Kidney	kidney
14	chr9:85833600-85833800	Flanking Active TSS	Lung	lung
15	chr9:85833600-85833800	Flanking Active TSS	Pancreas	Pancrea
16	chr9:85833600-85833800	Enhancers	Skeletal Muscle Male	skeletal muscle
17	chr9:85833600-85833800	Enhancers	Stomach Smooth Muscle	stomach
18	chr9:85833600-85833800	Active TSS	Hela-S3	cervix
19	chr9:85833600-85833800	Enhancers	HUVEC	blood vessel
20	chr9:85833600-85834000	Enhancers	iPS-18 Cell Line	embryonic stem cell
21	chr9:85833600-85834000	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
22	chr9:85833600-85834000	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
23	chr9:85833600-85834000	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
24	chr9:85833600-85834000	Enhancers	Adipose Nuclei	Adipose
25	chr9:85833600-85834000	Enhancers	Brain Anterior Caudate	brain
26	chr9:85833600-85834000	Enhancers	Brain Cingulate Gyrus	brain
27	chr9:85833600-85834000	Enhancers	Brain Germinal Matrix	brain
28	chr9:85833600-85834000	Enhancers	Fetal Intestine Small	intestine
29	chr9:85833600-85834000	Bivalent Enhancer	Fetal Muscle Leg	muscle
30	chr9:85833600-85834000	Enhancers	Fetal Stomach	stomach
31	chr9:85833600-85834000	Enhancers	Ovary	ovary
32	chr9:85833600-85834000	Enhancers	Right Atrium	heart
33	chr9:85833600-85834000	Enhancers	Right Ventricle	heart
34	chr9:85833600-85834000	Flanking Active TSS	HepG2	liver
35	chr9:85833600-85834200	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
36	chr9:85833600-85834200	Enhancers	Fetal Brain Male	brain
37	chr9:85833600-85834800	Active TSS	A549	lung
38	chr9:85833600-85835000	Active TSS	Duodenum Smooth Muscle	Duodenum
39	chr9:85833600-85835600	Active TSS	Pancreatic Islets	Pancreatic Islet

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