Variant report

Variant	rs732531
Chromosome Location	chr5:178337215-178337216
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr5:178322017..178324460-chr5:178337015..178339677,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000198939	Chromatin interaction

Extended variants
information (count: 17 )
Associated
traits (count: 5 )

rSNPs within LD-proxies of this variant (count:14)

rs_ID	r²[population]
rs1046724	1.00[ASW][hapmap];0.95[CEU][hapmap];1.00[GIH][hapmap];0.86[LWK][hapmap];1.00[MEX][hapmap];0.93[MKK][hapmap];0.90[TSI][hapmap]
rs11249600	0.95[CEU][hapmap];0.91[CHB][hapmap];0.84[JPT][hapmap];1.00[YRI][hapmap]
rs11744810	0.95[CEU][hapmap]
rs11748636	0.95[CEU][hapmap]
rs11952817	0.91[CHB][hapmap];0.84[JPT][hapmap]
rs12516516	1.00[CEU][hapmap]
rs13166562	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap]
rs13171869	1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];0.96[TSI][hapmap]
rs1496948	1.00[CEU][hapmap]
rs1566105	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs1845939	1.00[CEU][hapmap]
rs7448421	1.00[ASW][hapmap];0.95[CEU][hapmap];0.91[CHB][hapmap];0.92[CHD][hapmap];0.96[GIH][hapmap];0.84[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.98[MKK][hapmap];0.90[TSI][hapmap];1.00[YRI][hapmap]
rs7448445	0.95[CEU][hapmap];0.91[CHB][hapmap];0.82[JPT][hapmap];1.00[YRI][hapmap]
rs7722159	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv883218	chr5:178219855-178349391	Strong transcription Weak transcription ZNF genes & repeats Enhancers Flanking Active TSS Active TSS Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
2	esv3470830	chr5:178334452-178339256	Weak transcription ZNF genes & repeats Strong transcription	TF binding region CpG island Chromatin interactive region	2 gene(s)	inside rSNPs	diseases
3	esv3470831	chr5:178334452-178339256	Weak transcription ZNF genes & repeats Strong transcription	TF binding region CpG island Chromatin interactive region	2 gene(s)	inside rSNPs	diseases

mRNA abundance (count:5)

SNP	Gene	Cis/trans	Tissue	Source
rs732531	BTNL9	cis	cerebellum	SCAN
rs732531	TMED9	cis	parietal	SCAN
rs732531	TRIM52	cis	parietal	SCAN
rs732531	B4GALT7	cis	parietal	SCAN
rs732531	EIF4E1B	cis	cerebellum	SCAN

Chromatin state (count:24 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:178335600-178340600	ZNF genes & repeats	Brain Substantia Nigra	brain
2	chr5:178335600-178349000	ZNF genes & repeats	Liver	Liver
3	chr5:178335800-178337800	ZNF genes & repeats	Gastric	stomach
4	chr5:178335800-178337800	ZNF genes & repeats	Skeletal Muscle Male	skeletal muscle
5	chr5:178335800-178342200	ZNF genes & repeats	Duodenum Smooth Muscle	Duodenum
6	chr5:178335800-178367000	ZNF genes & repeats	Breast Myoepithelial Primary Cells	Breast
7	chr5:178336000-178337800	ZNF genes & repeats	Brain Hippocampus Middle	brain
8	chr5:178336000-178338000	ZNF genes & repeats	Ovary	ovary
9	chr5:178336000-178340400	ZNF genes & repeats	Adipose Nuclei	Adipose
10	chr5:178336200-178337800	ZNF genes & repeats	ES-UCSF4 Cell Line	embryonic stem cell
11	chr5:178336200-178337800	ZNF genes & repeats	Duodenum Mucosa	Duodenum
12	chr5:178336200-178337800	ZNF genes & repeats	Fetal Lung	lung
13	chr5:178336200-178338000	ZNF genes & repeats	Brain Cingulate Gyrus	brain
14	chr5:178336200-178338000	ZNF genes & repeats	Brain Dorsolateral Prefrontal Cortex	brain
15	chr5:178336400-178337600	ZNF genes & repeats	Stomach Smooth Muscle	stomach
16	chr5:178336400-178337800	ZNF genes & repeats	Aorta	Aorta
17	chr5:178336400-178337800	ZNF genes & repeats	Spleen	Spleen
18	chr5:178336600-178337800	ZNF genes & repeats	Pancreatic Islets	Pancreatic Islet
19	chr5:178336800-178337800	ZNF genes & repeats	Fetal Stomach	stomach
20	chr5:178336800-178338000	ZNF genes & repeats	Esophagus	oesophagus
21	chr5:178336800-178340000	Weak transcription	Fetal Kidney	kidney
22	chr5:178337000-178338000	ZNF genes & repeats	Brain Germinal Matrix	brain
23	chr5:178337000-178340600	ZNF genes & repeats	Primary hematopoietic stem cells G-CSF-mobilized Male	--
24	chr5:178337200-178337400	ZNF genes & repeats	Ganglion Eminence derived primary cultured neurospheres	brain

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