Variant report

Variant	rs3021500
Chromosome Location	chr8:11023997-11023998
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-AF131215.4.1-3	chr8:11023544-11024685	ucscGeneNc_uc010lrw_1

Extended variants
information (count: 65 )
Associated
traits (count: 7 )

rSNPs within LD-proxies of this variant (count:58)

rs_ID	r²[population]
rs10087081	1.00[JPT][hapmap];0.80[ASN][1000 genomes]
rs10105377	0.80[ASN][1000 genomes]
rs10106207	0.96[CEU][hapmap];0.82[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.87[AFR][1000 genomes];0.91[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs10108618	0.81[CEU][hapmap]
rs10503415	1.00[JPT][hapmap]
rs11250117	1.00[JPT][hapmap];1.00[YRI][hapmap]
rs11250119	0.82[JPT][hapmap]
rs11773990	0.82[CEU][hapmap]
rs13281566	0.81[ASN][1000 genomes]
rs17724467	0.89[CEU][hapmap];1.00[JPT][hapmap];0.81[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs2001329	0.85[CEU][hapmap];0.83[EUR][1000 genomes]
rs2001433	0.81[CEU][hapmap]
rs2409689	0.81[CEU][hapmap]
rs2409691	0.81[CEU][hapmap]
rs2409710	0.89[CEU][hapmap];1.00[JPT][hapmap];0.83[AMR][1000 genomes];0.85[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs2409713	0.82[CHB][hapmap];1.00[JPT][hapmap];0.89[ASN][1000 genomes]
rs2409714	0.82[CHB][hapmap];1.00[JPT][hapmap];0.89[ASN][1000 genomes]
rs2409715	0.82[CHB][hapmap];1.00[JPT][hapmap];0.89[ASN][1000 genomes]
rs2409716	0.82[CHB][hapmap];1.00[JPT][hapmap];0.89[ASN][1000 genomes]
rs2409717	0.89[ASN][1000 genomes]
rs2409718	0.96[CEU][hapmap];0.82[CHB][hapmap];1.00[JPT][hapmap];0.87[AFR][1000 genomes];0.87[AMR][1000 genomes];0.94[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs28417109	0.80[ASN][1000 genomes]
rs28630509	0.86[ASN][1000 genomes]
rs2898257	0.85[CEU][hapmap]
rs2898260	0.82[CEU][hapmap]
rs3021494	0.89[CEU][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap]
rs34208825	0.88[EUR][1000 genomes]
rs34772085	0.80[ASN][1000 genomes]
rs4333549	0.89[CEU][hapmap];1.00[JPT][hapmap];0.83[AMR][1000 genomes];0.85[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs4523214	0.85[JPT][hapmap]
rs4840542	0.85[CEU][hapmap]
rs4840549	0.82[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.89[ASN][1000 genomes]
rs4840550	0.88[EUR][1000 genomes]
rs4840551	0.83[CEU][hapmap];1.00[YRI][hapmap];0.84[AFR][1000 genomes];0.91[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs4841489	0.82[CEU][hapmap]
rs4841490	0.81[CEU][hapmap]
rs4841495	0.82[CEU][hapmap];0.82[JPT][hapmap];0.84[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs4841498	0.81[CEU][hapmap];0.83[EUR][1000 genomes]
rs4841501	0.82[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.89[ASN][1000 genomes]
rs4841503	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4841504	0.93[CEU][hapmap];0.90[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs6601560	0.87[CEU][hapmap]
rs6601562	0.81[CEU][hapmap]
rs6601564	0.89[CEU][hapmap];1.00[JPT][hapmap];0.82[AMR][1000 genomes];0.84[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs6601565	0.81[EUR][1000 genomes]
rs6601570	0.80[EUR][1000 genomes]
rs6980856	0.81[CEU][hapmap]
rs6986032	0.81[EUR][1000 genomes]
rs6996846	0.81[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs7004825	0.85[JPT][hapmap];1.00[YRI][hapmap];0.87[AFR][1000 genomes]
rs7005680	0.81[EUR][1000 genomes]
rs7011756	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];0.98[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7460507	1.00[JPT][hapmap]
rs7820860	0.81[CEU][hapmap]
rs7823349	0.82[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.89[ASN][1000 genomes]
rs7829396	0.82[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.86[ASN][1000 genomes]
rs7835318	0.81[CEU][hapmap]
rs9657519	0.85[CEU][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	nsv519941	chr8:11016889-11039816	Enhancers Weak transcription Strong transcription ZNF genes & repeats Flanking Active TSS Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases

mRNA abundance (count:7)

SNP	Gene	Cis/trans	Tissue	Source
rs3021500	AF131215.2	cis	Stomach	GTEx
rs3021500	AF131215.9	cis	Nerve Tibial	GTEx
rs3021500	BLK	Cis_1M	lymphoblastoid	RTeQTL
rs3021500	C8orf5	Cis_1M	lymphoblastoid	RTeQTL
rs3021500	C8orf5	cis	normal skin	skin_eQTL
rs3021500	AF131215.2	cis	Nerve Tibial	GTEx
rs3021500	C8orf5	cis	uninvolved skin	skin_eQTL

Chromatin state (count:23 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr8:10966400-11026200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
2	chr8:11006800-11026200	Weak transcription	HSMM	muscle
3	chr8:11009200-11024800	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
4	chr8:11013400-11026400	Weak transcription	Esophagus	oesophagus
5	chr8:11013600-11028800	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
6	chr8:11016600-11032200	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
7	chr8:11017400-11025400	Weak transcription	HSMMtube	muscle
8	chr8:11021800-11024800	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
9	chr8:11021800-11025000	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
10	chr8:11021800-11026200	Weak transcription	Pancreas	Pancrea
11	chr8:11021800-11026400	Weak transcription	Gastric	stomach
12	chr8:11022000-11025600	Weak transcription	Primary T helper cells fromperipheralblood	blood
13	chr8:11022000-11026000	Weak transcription	Primary T helper naive cells from peripheral blood	blood
14	chr8:11022000-11026400	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
15	chr8:11022200-11024400	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
16	chr8:11022400-11025400	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
17	chr8:11022600-11024400	Weak transcription	Primary T killer memory cells from peripheral blood	blood
18	chr8:11022600-11026000	Weak transcription	Primary T helper cells PMA-I stimulated	--
19	chr8:11022600-11035000	Weak transcription	H1 Cell Line	embryonic stem cell
20	chr8:11023000-11024400	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
21	chr8:11023000-11024800	Weak transcription	HUES64 Cell Line	embryonic stem cell
22	chr8:11023000-11026000	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
23	chr8:11023400-11024600	Weak transcription	Primary T killer naive cells fromperipheralblood	blood

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