Variant report

Variant	rs7998090
Chromosome Location	chr13:48478957-48478958
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-NUDT15-4	chr13:48478857-48479040	NONHSAT033691

Extended variants
information (count: 56 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:52)

rs_ID	r²[population]
rs11617530	0.88[ASN][1000 genomes]
rs11620507	0.81[ASN][1000 genomes]
rs1324801	0.83[ASN][1000 genomes]
rs1324802	0.83[ASN][1000 genomes]
rs1408618	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1555723	0.83[ASN][1000 genomes]
rs1555724	0.83[ASN][1000 genomes]
rs1924811	0.83[ASN][1000 genomes]
rs1974040	0.80[ASN][1000 genomes]
rs2038789	0.85[AMR][1000 genomes];0.97[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2147502	0.86[ASN][1000 genomes]
rs2274189	0.89[ASN][1000 genomes]
rs2406690	1.00[CEU][hapmap];0.87[CHB][hapmap];0.84[CHD][hapmap];1.00[GIH][hapmap];0.91[JPT][hapmap];0.96[MEX][hapmap];1.00[TSI][hapmap];0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs28874956	0.86[ASN][1000 genomes]
rs4142533	0.85[ASN][1000 genomes]
rs4369555	0.95[CHB][hapmap]
rs4508328	0.93[AFR][1000 genomes];0.81[AMR][1000 genomes];0.89[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4558305	0.86[EUR][1000 genomes]
rs4941616	0.97[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4942712	0.95[CHB][hapmap];0.98[CHD][hapmap];0.86[JPT][hapmap];0.88[ASN][1000 genomes]
rs4942713	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4942715	0.95[AMR][1000 genomes];0.93[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs4942717	0.89[ASN][1000 genomes]
rs4942718	0.89[ASN][1000 genomes]
rs61972224	0.89[ASN][1000 genomes]
rs73187725	0.93[ASN][1000 genomes]
rs7321745	0.93[AMR][1000 genomes];0.92[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs7329550	0.82[ASN][1000 genomes]
rs7330169	0.82[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs7337764	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7981303	0.94[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9526406	0.87[ASN][1000 genomes]
rs9526407	1.00[CHB][hapmap];0.98[CHD][hapmap];0.91[JPT][hapmap];0.89[ASN][1000 genomes]
rs9526410	0.97[AFR][1000 genomes];0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs9526411	0.87[ASN][1000 genomes]
rs9526414	0.89[ASN][1000 genomes]
rs9526416	0.90[AMR][1000 genomes];0.84[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs9534851	0.80[ASN][1000 genomes]
rs9534856	1.00[CHB][hapmap];0.98[CHD][hapmap];0.86[JPT][hapmap];0.89[ASN][1000 genomes]
rs9534857	1.00[CHB][hapmap];0.86[JPT][hapmap];0.88[ASN][1000 genomes]
rs9534858	0.89[ASN][1000 genomes]
rs9534859	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9534860	0.89[ASN][1000 genomes]
rs9534861	0.87[ASN][1000 genomes]
rs9534862	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9534863	0.89[ASN][1000 genomes]
rs9534864	0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs9534867	0.93[AFR][1000 genomes];0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9534888	0.95[CHB][hapmap]
rs9534947	0.81[CHB][hapmap]
rs9562775	0.88[AFR][1000 genomes];0.82[AMR][1000 genomes];0.98[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs9567941	0.83[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv3510679	chr13:48236624-48498185	Enhancers Active TSS Weak transcription Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Strong transcription Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
2	esv3510680	chr13:48236624-48498185	Enhancers Weak transcription ZNF genes & repeats Flanking Active TSS Bivalent Enhancer Active TSS Strong transcription Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
3	nsv933980	chr13:48431000-48557419	Weak transcription Enhancers Strong transcription Genic enhancers Flanking Active TSS ZNF genes & repeats Active TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	4 gene(s)	inside rSNPs	diseases
4	esv1803690	chr13:48470681-48508091	Enhancers Active TSS Weak transcription Flanking Active TSS Strong transcription ZNF genes & repeats Bivalent Enhancer Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs7998090	SERP2	cis	cerebellum	SCAN

Chromatin state (count:19 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr13:48451000-48480200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
2	chr13:48465000-48484000	Weak transcription	Primary T cells from cord blood	blood
3	chr13:48468600-48485600	Weak transcription	Gastric	stomach
4	chr13:48468800-48479600	Weak transcription	Sigmoid Colon	Sigmoid Colon
5	chr13:48468800-48482400	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
6	chr13:48472000-48482200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
7	chr13:48472200-48482400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
8	chr13:48472200-48482400	Weak transcription	NHEK	skin
9	chr13:48472200-48491400	Weak transcription	HUES6 Cell Line	embryonic stem cell
10	chr13:48476000-48479800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
11	chr13:48477000-48506400	Weak transcription	Psoas Muscle	Psoas
12	chr13:48478000-48479000	Active TSS	Monocytes-CD14+_RO01746	blood
13	chr13:48478000-48479400	ZNF genes & repeats	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
14	chr13:48478000-48479600	Enhancers	HUVEC	blood vessel
15	chr13:48478200-48482600	Weak transcription	H1 Cell Line	embryonic stem cell
16	chr13:48478600-48490000	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
17	chr13:48478800-48491000	Weak transcription	Adipose Nuclei	Adipose
18	chr13:48478800-48491800	Weak transcription	Left Ventricle	heart
19	chr13:48478800-48492200	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived

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