Variant report

Variant	rs3021497
Chromosome Location	chr8:10996089-10996090
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-AF131215.4.1-1	chr8:10994408-10996117	ENSG00000254556.1

Extended variants
information (count: 82 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:75)

rs_ID	r²[population]
rs10087767	1.00[CHB][hapmap]
rs10088853	0.96[CEU][hapmap];1.00[CHB][hapmap];0.90[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs10089518	1.00[CHB][hapmap]
rs10095003	1.00[ASN][1000 genomes]
rs10100660	1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs10101329	0.96[CEU][hapmap];1.00[CHB][hapmap];0.92[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10110684	1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs10503415	0.92[CEU][hapmap];0.81[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs10503417	1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs10903337	1.00[CHB][hapmap]
rs11775489	1.00[ASN][1000 genomes]
rs11776603	0.92[CEU][hapmap];1.00[CHB][hapmap];0.83[YRI][hapmap];0.85[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11777355	1.00[ASN][1000 genomes]
rs11777887	1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs11777918	1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs11778121	1.00[CHB][hapmap]
rs11783045	1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs11783890	1.00[ASN][1000 genomes]
rs11785237	1.00[ASN][1000 genomes]
rs11785392	1.00[CHB][hapmap]
rs11989369	1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs13248014	1.00[CHB][hapmap];0.83[YRI][hapmap];1.00[ASN][1000 genomes]
rs13248264	1.00[CHB][hapmap]
rs13248300	1.00[CHB][hapmap]
rs13249916	1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs13251528	1.00[CHB][hapmap]
rs13256743	1.00[CHB][hapmap];0.83[YRI][hapmap];1.00[ASN][1000 genomes]
rs13265553	1.00[CHB][hapmap];0.89[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13266785	0.82[CEU][hapmap];0.90[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13273857	1.00[CHB][hapmap]
rs13276708	0.95[CEU][hapmap];1.00[CHB][hapmap];0.90[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13276836	1.00[CHB][hapmap]
rs13281566	0.81[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs17152841	1.00[CHB][hapmap]
rs17725480	1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs17725534	1.00[CHB][hapmap];0.91[YRI][hapmap];1.00[ASN][1000 genomes]
rs17726209	0.87[CEU][hapmap];1.00[CHB][hapmap];0.84[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17779791	1.00[CHB][hapmap]
rs17782536	0.85[CEU][hapmap];1.00[CHB][hapmap];0.90[YRI][hapmap];0.84[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17782554	0.87[CEU][hapmap];1.00[CHB][hapmap];0.83[YRI][hapmap];0.84[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1987190	1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs2409691	1.00[CHB][hapmap]
rs2409692	1.00[CHB][hapmap]
rs2409693	1.00[CHB][hapmap]
rs2409695	1.00[CHB][hapmap]
rs2409719	0.83[CEU][hapmap];1.00[CHB][hapmap];1.00[YRI][hapmap];0.85[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2409720	1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs2409725	1.00[ASN][1000 genomes]
rs2409726	1.00[ASN][1000 genomes]
rs2409729	1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs3021495	0.96[CEU][hapmap];1.00[CHB][hapmap];0.91[YRI][hapmap];0.94[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3021498	0.85[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3021501	0.85[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34309263	0.90[AFR][1000 genomes];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34367737	0.88[AFR][1000 genomes];0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35211404	1.00[ASN][1000 genomes]
rs4291231	0.96[CEU][hapmap];1.00[CHB][hapmap];0.90[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4412337	1.00[ASN][1000 genomes]
rs4451268	1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs4618656	1.00[CHB][hapmap]
rs4642600	0.92[CEU][hapmap];1.00[CHB][hapmap];0.80[YRI][hapmap];0.88[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4840548	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[YRI][hapmap];0.83[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4841486	1.00[CHB][hapmap]
rs4841497	0.96[CEU][hapmap];1.00[CHB][hapmap];0.88[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4841499	0.94[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6601561	1.00[CHB][hapmap]
rs6601563	1.00[CHB][hapmap]
rs67418928	1.00[ASN][1000 genomes]
rs67559300	1.00[ASN][1000 genomes]
rs71518512	0.81[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs73198943	0.85[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs7830569	0.83[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs7832722	1.00[CHB][hapmap]
rs9329238	1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs9657544	1.00[CHB][hapmap]

Variant overlapped rSNPs/rCNVs (count:7 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1035072	chr8:10819444-11480692	Bivalent Enhancer Enhancers Flanking Bivalent TSS/Enh Weak transcription Strong transcription Flanking Active TSS Bivalent/Poised TSS Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	50 gene(s)	inside rSNPs	diseases
2	nsv539473	chr8:10819444-11480692	Weak transcription Flanking Active TSS Active TSS Enhancers Bivalent Enhancer Bivalent/Poised TSS Strong transcription Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	50 gene(s)	inside rSNPs	diseases
3	esv1815171	chr8:10940039-11128712	Enhancers Flanking Active TSS Weak transcription Bivalent/Poised TSS Active TSS Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Strong transcription Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	15 gene(s)	inside rSNPs	diseases
4	nsv1025426	chr8:10942929-11037903	Weak transcription Enhancers Flanking Active TSS Active TSS Strong transcription ZNF genes & repeats Bivalent Enhancer Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
5	nsv1026331	chr8:10955941-11046394	Enhancers Strong transcription Weak transcription Flanking Active TSS Active TSS Bivalent Enhancer Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
6	nsv529399	chr8:10970091-11805960	Enhancers Strong transcription Weak transcription Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh Flanking Active TSS Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	54 gene(s)	inside rSNPs	diseases
7	nsv1019796	chr8:10979442-11010826	Weak transcription Enhancers Active TSS Flanking Active TSS ZNF genes & repeats Genic enhancers Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs3021497	AF131215.2	cis	Nerve Tibial	GTEx
rs3021497	C8orf5	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:20 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr8:10966200-10999000	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
2	chr8:10966400-11026200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
3	chr8:10982800-11003400	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
4	chr8:10983000-11002000	Weak transcription	Primary T cells fromperipheralblood	blood
5	chr8:10983000-11003200	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
6	chr8:10983200-10997000	Weak transcription	H1 Cell Line	embryonic stem cell
7	chr8:10983200-11001800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
8	chr8:10984400-11000000	Weak transcription	Rectal Smooth Muscle	rectum
9	chr8:10986400-11002000	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
10	chr8:10987200-10997000	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
11	chr8:10989600-11014200	Weak transcription	Pancreas	Pancrea
12	chr8:10991800-10996800	Weak transcription	Spleen	Spleen
13	chr8:10991800-10998800	Weak transcription	Gastric	stomach
14	chr8:10991800-11011800	Weak transcription	Left Ventricle	heart
15	chr8:10992800-11002000	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
16	chr8:10994400-10997000	Weak transcription	H9 Cell Line	embryonic stem cell
17	chr8:10994800-10997000	Weak transcription	Breast Myoepithelial Primary Cells	Breast
18	chr8:10995600-10996800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
19	chr8:10995600-10997000	Weak transcription	HUES64 Cell Line	embryonic stem cell
20	chr8:10995600-10999000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell

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