Variant report

Variant	rs554879
Chromosome Location	chr9:98067809-98067810
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr9:98067681..98069650-chr9:98269294..98272244,2	MCF-7	breast:
2	chr9:98058741..98060444-chr9:98067413..98069103,2	MCF-7	breast:
3	chr9:98066646..98069496-chr9:98077286..98078854,2	K562	blood:
4	chr9:98065148..98068101-chr9:98075705..98077262,2	K562	blood:
5	chr9:98063794..98065314-chr9:98066856..98068521,2	MCF-7	breast:
6	chr9:98064416..98068474-chr9:98070574..98074570,5	K562	blood:

Variant related genes	Relation type
ENSG00000185920	Chromatin interaction

Extended variants
information (count: 17 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:16)

rs_ID	r²[population]
rs10283758	0.86[TSI][hapmap]
rs12337959	0.88[TSI][hapmap]
rs1886992	0.88[TSI][hapmap]
rs2655056	0.89[AFR][1000 genomes];0.91[AMR][1000 genomes];0.90[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs356659	0.92[CEU][hapmap];0.95[MEX][hapmap];0.97[TSI][hapmap];0.81[EUR][1000 genomes]
rs356664	0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs4647404	0.84[TSI][hapmap]
rs4647421	0.82[TSI][hapmap]
rs4647432	0.84[TSI][hapmap]
rs473825	0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs4744453	0.88[TSI][hapmap]
rs640628	0.92[CEU][hapmap];0.95[MEX][hapmap];0.90[TSI][hapmap]
rs646350	0.92[CEU][hapmap]
rs675781	0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs7034538	0.82[CEU][hapmap]
rs7357617	0.88[TSI][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	nsv831657	chr9:97959274-98204769	Enhancers Weak transcription Bivalent/Poised TSS Bivalent Enhancer Flanking Active TSS Strong transcription Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	32 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs554879	LOC57653	cis	cerebellum	SCAN
rs554879	IARS	cis	parietal	SCAN

Chromatin state (count:40 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:98055000-98068600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
2	chr9:98059800-98068000	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
3	chr9:98059800-98068600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
4	chr9:98060400-98075000	Weak transcription	NHEK	skin
5	chr9:98061000-98068800	Weak transcription	Small Intestine	intestine
6	chr9:98063200-98068200	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
7	chr9:98063400-98068200	Weak transcription	Osteobl	bone
8	chr9:98063400-98069800	Weak transcription	Fetal Kidney	kidney
9	chr9:98063600-98068200	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
10	chr9:98064000-98068600	Weak transcription	Ovary	ovary
11	chr9:98064800-98068600	Weak transcription	Sigmoid Colon	Sigmoid Colon
12	chr9:98066000-98068600	Weak transcription	Psoas Muscle	Psoas
13	chr9:98066000-98069000	Enhancers	HUVEC	blood vessel
14	chr9:98066200-98068200	Weak transcription	Fetal Muscle Leg	muscle
15	chr9:98066200-98075200	Weak transcription	Left Ventricle	heart
16	chr9:98066400-98068000	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
17	chr9:98066600-98068600	Weak transcription	Fetal Stomach	stomach
18	chr9:98066800-98074800	Weak transcription	Thymus	Thymus
19	chr9:98067000-98069200	Enhancers	Cortex derived primary cultured neurospheres	brain
20	chr9:98067000-98075200	Weak transcription	Lung	lung
21	chr9:98067200-98069000	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
22	chr9:98067200-98069000	Enhancers	NHLF	lung
23	chr9:98067400-98068200	Enhancers	A549	lung
24	chr9:98067400-98068400	Enhancers	Muscle Satellite Cultured Cells	--
25	chr9:98067400-98068400	Enhancers	HSMM	muscle
26	chr9:98067400-98068400	Enhancers	HSMMtube	muscle
27	chr9:98067400-98068800	Enhancers	iPS-20b Cell Line	embryonic stem cell
28	chr9:98067400-98069000	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
29	chr9:98067400-98069000	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
30	chr9:98067400-98069000	Enhancers	Fetal Lung	lung
31	chr9:98067400-98069200	Enhancers	NHDF-Ad	bronchial
32	chr9:98067400-98070400	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
33	chr9:98067600-98068800	Enhancers	HUES48 Cell Line	embryonic stem cell
34	chr9:98067600-98068800	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
35	chr9:98067600-98068800	Enhancers	NH-A	brain
36	chr9:98067600-98069000	Enhancers	Hela-S3	cervix
37	chr9:98067600-98070400	Enhancers	Duodenum Mucosa	Duodenum
38	chr9:98067800-98068600	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
39	chr9:98067800-98068600	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
40	chr9:98067800-98074200	Weak transcription	GM12878-XiMat	blood

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