Variant report

Variant	rs2409627
Chromosome Location	chr5:58444322-58444323
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 21 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:19)

rs_ID	r²[population]
rs11955845	0.92[EUR][1000 genomes]
rs13160617	0.87[CEU][hapmap];1.00[CHB][hapmap];0.85[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.85[LWK][hapmap];0.82[MKK][hapmap];1.00[TSI][hapmap];0.92[YRI][hapmap];0.84[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs13164981	0.94[CEU][hapmap];0.85[JPT][hapmap];0.84[EUR][1000 genomes]
rs13178514	0.85[EUR][1000 genomes]
rs13180599	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs13185063	0.94[CEU][hapmap];0.88[JPT][hapmap];0.84[EUR][1000 genomes]
rs13185828	0.94[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.91[TSI][hapmap];0.91[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs13185996	0.84[EUR][1000 genomes]
rs13186000	0.84[EUR][1000 genomes]
rs13186012	0.94[CEU][hapmap];0.88[JPT][hapmap];0.91[TSI][hapmap];0.85[EUR][1000 genomes]
rs13186015	0.85[EUR][1000 genomes]
rs16877155	0.94[CEU][hapmap];0.88[JPT][hapmap];0.81[TSI][hapmap];0.85[EUR][1000 genomes]
rs2059191	0.94[CEU][hapmap];0.88[JPT][hapmap];0.90[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs33950471	0.93[CEU][hapmap];1.00[TSI][hapmap];0.89[EUR][1000 genomes]
rs34235034	0.91[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs35406293	0.87[AMR][1000 genomes]
rs56273963	0.85[EUR][1000 genomes]
rs889229	0.87[CEU][hapmap]
rs9647533	0.80[AFR][1000 genomes];0.87[AMR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv2830363	chr5:57893949-58555491	Weak transcription Active TSS Enhancers Flanking Active TSS Transcr. at gene 5' and 3' Strong transcription Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	8 gene(s)	inside rSNPs	diseases
2	nsv881702	chr5:58432413-58474854	Enhancers Weak transcription Strong transcription Flanking Active TSS Genic enhancers Active TSS ZNF genes & repeats Transcr. at gene 5' and 3'	Chromatin interactive region	n/a	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs2409627	SLC38A9	cis	parietal	SCAN
rs2409627	CCNO	cis	parietal	SCAN
rs2409627	LRRC70	cis	cerebellum	SCAN

Chromatin state (count:26 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:58424000-58447000	Weak transcription	Sigmoid Colon	Sigmoid Colon
2	chr5:58424200-58446200	Weak transcription	Fetal Intestine Large	intestine
3	chr5:58424200-58446600	Weak transcription	Rectal Mucosa Donor 31	rectum
4	chr5:58427200-58454000	Weak transcription	Primary neutrophils fromperipheralblood	blood
5	chr5:58429800-58447200	Weak transcription	Left Ventricle	heart
6	chr5:58433000-58451600	Weak transcription	Fetal Muscle Leg	muscle
7	chr5:58437400-58454000	Weak transcription	Rectal Smooth Muscle	rectum
8	chr5:58437800-58444800	Weak transcription	Psoas Muscle	Psoas
9	chr5:58438000-58445200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
10	chr5:58439000-58484000	Weak transcription	Fetal Kidney	kidney
11	chr5:58440000-58447000	Weak transcription	Stomach Mucosa	stomach
12	chr5:58440200-58444600	Weak transcription	Colon Smooth Muscle	Colon
13	chr5:58440200-58448600	Weak transcription	Brain Anterior Caudate	brain
14	chr5:58440600-58444800	Weak transcription	Skeletal Muscle Female	skeletal muscle
15	chr5:58440600-58447000	Weak transcription	Skeletal Muscle Male	skeletal muscle
16	chr5:58441200-58446600	Weak transcription	Fetal Heart	heart
17	chr5:58442400-58448600	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
18	chr5:58443000-58447000	Weak transcription	Primary T cells from cord blood	blood
19	chr5:58443000-58447400	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
20	chr5:58443000-58447600	Weak transcription	Primary T helper cells fromperipheralblood	blood
21	chr5:58443200-58445800	Weak transcription	Hela-S3	cervix
22	chr5:58443200-58447000	Weak transcription	Primary T helper cells PMA-I stimulated	--
23	chr5:58443200-58447000	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
24	chr5:58443800-58446400	Enhancers	Pancreatic Islets	Pancreatic Islet
25	chr5:58444000-58449800	Genic enhancers	A549	lung
26	chr5:58444200-58445600	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived

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