Variant report

Variant	rs6559643
Chromosome Location	chr9:72196579-72196580
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr1:150207954..150208537-chr9:72196079..72196874,2	MCF-7	breast:
2	chr9:72195299..72197073-chr9:72236850..72239797,2	MCF-7	breast:
3	chr9:72192844..72194505-chr9:72195601..72198020,2	K562	blood:

Variant related genes	Relation type
ENSG00000143401	Chromatin interaction

Extended variants
information (count: 35 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:34)

rs_ID	r²[population]
rs10123008	0.89[CEU][hapmap];0.90[CHB][hapmap];0.81[EUR][1000 genomes]
rs10780527	0.92[CHB][hapmap];0.92[CHD][hapmap];1.00[JPT][hapmap];0.99[ASN][1000 genomes]
rs10780528	0.92[CHB][hapmap];0.92[CHD][hapmap];1.00[JPT][hapmap];0.99[ASN][1000 genomes]
rs10780539	0.85[CHB][hapmap];0.85[JPT][hapmap]
rs10867825	0.86[JPT][hapmap];0.90[ASN][1000 genomes]
rs10867828	0.85[JPT][hapmap]
rs10867830	0.84[CHB][hapmap]
rs11139338	0.93[ASW][hapmap];0.95[CEU][hapmap];0.92[CHB][hapmap];0.96[CHD][hapmap];0.91[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.88[MEX][hapmap];1.00[MKK][hapmap];0.91[TSI][hapmap];1.00[YRI][hapmap];0.91[AFR][1000 genomes];0.95[AMR][1000 genomes];0.91[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11139361	0.95[CEU][hapmap];0.85[CHB][hapmap];0.96[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];0.88[MEX][hapmap];0.93[TSI][hapmap];0.84[AMR][1000 genomes];0.90[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1330334	0.91[CEU][hapmap];0.92[CHB][hapmap];0.84[CHD][hapmap];0.85[GIH][hapmap];0.93[JPT][hapmap];0.82[MEX][hapmap];0.81[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1411440	0.92[JPT][hapmap];0.81[EUR][1000 genomes]
rs1556211	0.83[CEU][hapmap];0.92[CHB][hapmap];1.00[JPT][hapmap];0.95[ASN][1000 genomes]
rs1854702	1.00[CEU][hapmap];0.85[CHB][hapmap];0.93[JPT][hapmap];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1854703	0.83[CEU][hapmap];0.92[CHB][hapmap];0.93[JPT][hapmap];0.94[ASN][1000 genomes]
rs1967880	0.92[CHB][hapmap];0.96[CHD][hapmap];1.00[JPT][hapmap];0.99[ASN][1000 genomes]
rs1970017	0.92[CHB][hapmap];0.96[CHD][hapmap];1.00[JPT][hapmap];0.99[ASN][1000 genomes]
rs2026150	0.85[JPT][hapmap]
rs2309515	0.85[JPT][hapmap]
rs4744913	0.92[CHB][hapmap];1.00[JPT][hapmap];0.99[ASN][1000 genomes]
rs4744914	0.98[ASN][1000 genomes]
rs4744917	1.00[CEU][hapmap];0.85[CHB][hapmap];0.93[JPT][hapmap];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4744918	0.94[ASN][1000 genomes]
rs4744919	1.00[CEU][hapmap];0.89[CHB][hapmap];1.00[JPT][hapmap];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7030393	0.95[CEU][hapmap];0.85[CHB][hapmap];0.93[JPT][hapmap];0.84[AMR][1000 genomes];0.91[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7031694	0.93[ASW][hapmap];0.82[CEU][hapmap];0.85[JPT][hapmap]
rs7033141	0.85[ASW][hapmap];0.85[LWK][hapmap];0.94[YRI][hapmap]
rs72719029	0.86[AFR][1000 genomes];0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7350265	0.83[AMR][1000 genomes];0.92[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7850006	0.90[ASN][1000 genomes]
rs7853783	0.92[CHB][hapmap];1.00[JPT][hapmap];0.99[ASN][1000 genomes]
rs7864173	0.88[ASN][1000 genomes]
rs7871895	0.91[CEU][hapmap];0.86[CHB][hapmap];1.00[JPT][hapmap];0.94[YRI][hapmap];0.85[AFR][1000 genomes];0.95[AMR][1000 genomes];0.93[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs986352	0.81[CEU][hapmap];0.84[JPT][hapmap]
rs987653	0.85[CHB][hapmap];0.85[JPT][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	nsv893437	chr9:72118962-72223176	Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Strong transcription Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Active TSS Transcr. at gene 5' and 3'	Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs6559643	GDA	cis	parietal	SCAN

Chromatin state (count:32 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:72180400-72208400	Weak transcription	Gastric	stomach
2	chr9:72186200-72200800	Weak transcription	HSMMtube	muscle
3	chr9:72187400-72204800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
4	chr9:72187800-72198600	Weak transcription	NHDF-Ad	bronchial
5	chr9:72188800-72198800	Weak transcription	Cortex derived primary cultured neurospheres	brain
6	chr9:72189400-72197400	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
7	chr9:72189400-72199200	Weak transcription	NH-A	brain
8	chr9:72192800-72197200	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
9	chr9:72193200-72204400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
10	chr9:72193400-72196600	Weak transcription	Adipose Nuclei	Adipose
11	chr9:72193400-72200200	Weak transcription	Right Ventricle	heart
12	chr9:72193800-72197200	Weak transcription	Brain Angular Gyrus	brain
13	chr9:72194000-72197200	Enhancers	HepG2	liver
14	chr9:72195000-72197000	Enhancers	Fetal Adrenal Gland	Adrenal Gland
15	chr9:72195000-72198800	Enhancers	Left Ventricle	heart
16	chr9:72195200-72197600	Weak transcription	Small Intestine	intestine
17	chr9:72195200-72198000	Weak transcription	Stomach Mucosa	stomach
18	chr9:72195400-72198400	Enhancers	Liver	Liver
19	chr9:72195400-72200400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
20	chr9:72195400-72200600	Weak transcription	Sigmoid Colon	Sigmoid Colon
21	chr9:72195800-72208200	Weak transcription	Fetal Lung	lung
22	chr9:72196000-72197200	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
23	chr9:72196000-72197200	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
24	chr9:72196000-72197200	Weak transcription	Duodenum Mucosa	Duodenum
25	chr9:72196000-72197400	Weak transcription	Right Atrium	heart
26	chr9:72196000-72198000	Weak transcription	Brain Germinal Matrix	brain
27	chr9:72196000-72204800	Weak transcription	Fetal Brain Male	brain
28	chr9:72196200-72204800	Weak transcription	Brain Inferior Temporal Lobe	brain
29	chr9:72196400-72196600	Bivalent Enhancer	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
30	chr9:72196400-72197000	Enhancers	Fetal Muscle Leg	muscle
31	chr9:72196400-72199400	Enhancers	Fetal Heart	heart
32	chr9:72196400-72201000	Enhancers	HUVEC	blood vessel

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