Variant report

Variant	rs10865953
Chromosome Location	chr3:48759562-48759563
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr3:48751108..48754821-chr3:48757989..48761007,3	K562	blood:
2	chr3:48753321..48755795-chr3:48757352..48760937,4	MCF-7	breast:

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-PRKAR2A-4	chr3:48759515-48759784	expReg_chr3_3635_-

Variant related genes	Relation type
ENSG00000068745	Chromatin interaction

Extended variants
information (count: 26 )
Associated
traits (count: 31 )

rSNPs within LD-proxies of this variant (count:25)

rs_ID	r²[population]
rs12632533	1.00[CEU][hapmap];1.00[GIH][hapmap];0.93[TSI][hapmap]
rs14018	1.00[CEU][hapmap];0.83[TSI][hapmap];0.83[EUR][1000 genomes]
rs4858799	0.98[EUR][1000 genomes]
rs4858800	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.98[MKK][hapmap];1.00[TSI][hapmap];0.92[YRI][hapmap];0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs4858830	1.00[CEU][hapmap];1.00[YRI][hapmap];0.90[AFR][1000 genomes];0.84[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs4974088	1.00[CEU][hapmap];0.80[TSI][hapmap]
rs6442129	0.87[AFR][1000 genomes];0.84[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs6442131	0.84[EUR][1000 genomes]
rs6766238	1.00[CEU][hapmap];0.91[MEX][hapmap];0.86[TSI][hapmap];0.84[EUR][1000 genomes]
rs6796790	1.00[CEU][hapmap];0.82[MEX][hapmap];0.83[TSI][hapmap];0.86[EUR][1000 genomes]
rs6801211	1.00[CEU][hapmap];0.86[EUR][1000 genomes]
rs6806356	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.88[AFR][1000 genomes];0.84[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs7610519	0.94[AFR][1000 genomes];0.88[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs7621226	1.00[CEU][hapmap]
rs7641050	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs9284885	1.00[CEU][hapmap];0.82[MEX][hapmap];0.80[TSI][hapmap]
rs9311431	1.00[CEU][hapmap]
rs9822485	0.81[LWK][hapmap];0.92[YRI][hapmap]
rs9848268	0.81[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs9859473	1.00[CEU][hapmap];0.91[MEX][hapmap];0.86[TSI][hapmap];0.80[EUR][1000 genomes]
rs9873227	0.86[EUR][1000 genomes]
rs9874010	0.92[YRI][hapmap]
rs9879978	1.00[CEU][hapmap]
rs9882443	0.84[ASW][hapmap];1.00[CEU][hapmap];1.00[GIH][hapmap];0.91[MEX][hapmap];0.93[TSI][hapmap];0.85[YRI][hapmap];0.92[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs990211	0.84[ASW][hapmap];0.82[CEU][hapmap];1.00[GIH][hapmap];0.83[LWK][hapmap];0.81[MEX][hapmap];0.88[MKK][hapmap];1.00[YRI][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	nsv590247	chr3:48661985-48801929	Transcr. at gene 5' and 3' Strong transcription Active TSS Genic enhancers Enhancers Flanking Active TSS Weak transcription Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	53 gene(s)	inside rSNPs	diseases

mRNA abundance (count:31)

SNP	Gene	Cis/trans	Tissue	Source
rs10865953	WDR6	cis	parietal	SCAN
rs10865953	TLR9	cis	parietal	SCAN
rs10865953	WDR6	cis	Muscle Skeletal	GTEx
rs10865953	DALRD3	cis	parietal	SCAN
rs10865953	ZNF589	cis	parietal	SCAN
rs10865953	AMT	cis	parietal	SCAN
rs10865953	LEPR	trans	lymphoblastoid	RTeQTL
rs10865953	WDR6	cis	cerebellum	SCAN
rs10865953	NCKIPSD	cis	Esophagus Muscularis	GTEx
rs10865953	QRICH1	cis	cerebellum	SCAN
rs10865953	AMT	cis	Thyroid	GTEx
rs10865953	PHF7	cis	parietal	SCAN
rs10865953	P4HTM	cis	parietal	SCAN
rs10865953	PH-4	Cis_1M	lymphoblastoid	RTeQTL
rs10865953	NICN1	cis	cerebellum	SCAN
rs10865953	CDC25A	cis	cerebellum	SCAN
rs10865953	AMT	cis	lung	GTEx
rs10865953	NCKIPSD	cis	Nerve Tibial	GTEx
rs10865953	NICN1	cis	Thyroid	GTEx
rs10865953	ARIH2	Cis_1M	lymphoblastoid	RTeQTL
rs10865953	NICN1-AS1	cis	Thyroid	GTEx
rs10865953	NCKIPSD	cis	cerebellum	SCAN
rs10865953	NCKIPSD	cis	Muscle Skeletal	GTEx
rs10865953	AMT	cis	Adipose Subcutaneous	GTEx
rs10865953	NICN1	cis	parietal	SCAN
rs10865953	AMT	cis	cerebellum	SCAN
rs10865953	QARS	cis	parietal	SCAN
rs10865953	DALRD3	cis	cerebellum	SCAN
rs10865953	AMT	cis	Artery Tibial	GTEx
rs10865953	P4HTM	cis	lung	GTEx
rs10865953	IQCF1	cis	cerebellum	SCAN

Chromatin state (count:12 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:48755200-48760000	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
2	chr3:48755200-48760200	Weak transcription	Small Intestine	intestine
3	chr3:48755400-48760200	Weak transcription	Colonic Mucosa	Colon
4	chr3:48755400-48760200	Weak transcription	A549	lung
5	chr3:48755400-48760400	Weak transcription	Duodenum Mucosa	Duodenum
6	chr3:48755600-48760200	Weak transcription	K562	blood
7	chr3:48757000-48760000	Enhancers	Rectal Mucosa Donor 31	rectum
8	chr3:48758000-48759600	Enhancers	Stomach Mucosa	stomach
9	chr3:48758200-48760200	Weak transcription	Fetal Intestine Small	intestine
10	chr3:48758800-48760400	Enhancers	Rectal Mucosa Donor 29	rectum
11	chr3:48759000-48760600	Enhancers	Sigmoid Colon	Sigmoid Colon
12	chr3:48759400-48761200	Weak transcription	Gastric	stomach

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