Variant report

Variant	rs9535674
Chromosome Location	chr13:52034830-52034831
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-WDFY2-2	chr13:52034808-52034832	NONHSAT033915

Extended variants
information (count: 39 )
Associated
traits (count: 5 )

rSNPs within LD-proxies of this variant (count:38)

rs_ID	r²[population]
rs17075688	0.83[AFR][1000 genomes];0.81[AMR][1000 genomes];0.81[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2274061	0.86[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.96[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.88[MKK][hapmap];0.86[TSI][hapmap];1.00[YRI][hapmap];0.86[AMR][1000 genomes];0.87[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2274929	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.88[AMR][1000 genomes];0.87[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs3825524	0.87[ASW][hapmap];1.00[CEU][hapmap];0.93[CHB][hapmap];0.96[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap];0.86[MKK][hapmap];0.86[TSI][hapmap];1.00[YRI][hapmap];0.89[AMR][1000 genomes];0.87[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6561634	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73197821	0.80[EUR][1000 genomes]
rs7321642	0.82[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs7333661	0.96[AMR][1000 genomes];0.88[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7335141	0.95[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs7989674	0.80[EUR][1000 genomes]
rs7989850	0.82[CEU][hapmap];0.83[TSI][hapmap];0.80[EUR][1000 genomes]
rs7996243	1.00[CEU][hapmap];0.81[CHD][hapmap];0.95[GIH][hapmap];0.93[JPT][hapmap];0.91[MEX][hapmap];0.83[EUR][1000 genomes]
rs7998084	0.82[CEU][hapmap];0.92[CHB][hapmap];0.93[CHD][hapmap];0.81[GIH][hapmap]
rs8001311	0.81[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs9316537	0.81[ASW][hapmap];0.95[YRI][hapmap]
rs9316539	0.89[AMR][1000 genomes];0.87[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9316545	0.82[CEU][hapmap]
rs9526752	0.87[ASW][hapmap];1.00[CEU][hapmap];0.93[CHB][hapmap];0.96[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap];0.90[MKK][hapmap];0.86[TSI][hapmap];1.00[YRI][hapmap];0.84[AMR][1000 genomes];0.87[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs9526754	0.87[ASW][hapmap];0.95[CEU][hapmap];0.86[CHB][hapmap];0.96[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];0.92[MKK][hapmap];0.86[TSI][hapmap];0.95[YRI][hapmap];0.89[AMR][1000 genomes];0.86[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9526757	0.85[CHB][hapmap];1.00[JPT][hapmap];0.81[ASN][1000 genomes]
rs9526764	0.81[CEU][hapmap];0.80[EUR][1000 genomes]
rs9526765	0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs9535645	1.00[CEU][hapmap];0.87[CHD][hapmap];0.95[GIH][hapmap];0.93[JPT][hapmap];0.91[MEX][hapmap];0.83[EUR][1000 genomes]
rs9535653	1.00[CEU][hapmap];0.92[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.84[AMR][1000 genomes];0.87[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9535669	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9535670	0.82[CEU][hapmap];0.83[TSI][hapmap];0.80[EUR][1000 genomes]
rs9535671	0.80[EUR][1000 genomes]
rs9535672	0.81[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs9535673	0.85[ASN][1000 genomes]
rs9535677	0.81[AMR][1000 genomes];0.81[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs9535679	0.81[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs9535683	0.80[EUR][1000 genomes]
rs9535692	0.88[AMR][1000 genomes];0.95[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs9535696	0.81[CEU][hapmap];0.92[CHB][hapmap]
rs9535697	0.81[CEU][hapmap]
rs9568600	0.85[CEU][hapmap];0.92[CHB][hapmap];0.96[CHD][hapmap];0.89[GIH][hapmap];0.93[JPT][hapmap];0.92[TSI][hapmap];0.81[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs9568603	0.81[ASW][hapmap];0.82[CEU][hapmap];0.92[CHB][hapmap];0.93[CHD][hapmap];0.85[GIH][hapmap];0.93[JPT][hapmap];0.92[LWK][hapmap];0.82[MEX][hapmap];0.84[MKK][hapmap];0.83[TSI][hapmap];1.00[YRI][hapmap];0.92[AFR][1000 genomes];0.81[AMR][1000 genomes];0.81[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs9568612	0.82[CEU][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	nsv977240	chr13:52033195-52035408	Weak transcription Strong transcription Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases

mRNA abundance (count:5)

SNP	Gene	Cis/trans	Tissue	Source
rs9535674	DDX26	cis	multi-tissue	Pritchard
rs9535674	WDFY2	cis	parietal	SCAN
rs9535674	HNRNPA1L2	cis	cerebellum	SCAN
rs9535674	CKAP2	cis	parietal	SCAN
rs9535674	INTS6	cis	lymphoblastoid	seeQTL

Chromatin state (count:30 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr13:52028600-52036000	Weak transcription	HSMMtube	muscle
2	chr13:52030400-52035200	Weak transcription	HSMM	muscle
3	chr13:52030600-52035800	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
4	chr13:52030600-52036000	Weak transcription	iPS-18 Cell Line	embryonic stem cell
5	chr13:52030600-52038800	Weak transcription	HepG2	liver
6	chr13:52030800-52035400	Weak transcription	Primary T helper cells PMA-I stimulated	--
7	chr13:52030800-52035400	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
8	chr13:52030800-52036000	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
9	chr13:52030800-52036000	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
10	chr13:52030800-52036200	Weak transcription	Primary hematopoietic stem cells	blood
11	chr13:52030800-52036200	Weak transcription	Duodenum Mucosa	Duodenum
12	chr13:52031000-52036000	Weak transcription	Esophagus	oesophagus
13	chr13:52031000-52039800	Weak transcription	A549	lung
14	chr13:52031000-52044800	Weak transcription	Liver	Liver
15	chr13:52031200-52035800	Weak transcription	Primary T cells from cord blood	blood
16	chr13:52031200-52036200	Weak transcription	Gastric	stomach
17	chr13:52031200-52041400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
18	chr13:52031400-52035800	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
19	chr13:52031400-52036200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
20	chr13:52031400-52036200	Weak transcription	Stomach Smooth Muscle	stomach
21	chr13:52031400-52036600	Weak transcription	Skeletal Muscle Female	skeletal muscle
22	chr13:52031400-52036800	Weak transcription	Fetal Stomach	stomach
23	chr13:52031400-52037000	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
24	chr13:52031600-52035800	Weak transcription	Fetal Muscle Trunk	muscle
25	chr13:52031600-52036400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
26	chr13:52031600-52041600	Weak transcription	Pancreas	Pancrea
27	chr13:52031800-52035800	Weak transcription	Fetal Muscle Leg	muscle
28	chr13:52031800-52045400	Weak transcription	Primary B cells from cord blood	blood
29	chr13:52032000-52035400	Weak transcription	Spleen	Spleen
30	chr13:52034800-52036600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast

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