Variant report

Variant	rs6601562
Chromosome Location	chr8:10962929-10962930
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-AF131215.2.1-1	chr8:10962201-10964214	ENSG00000269918.1
2	lnc-AF131215.2.1-1	chr8:10962658-10964223	NONHSAT125034

Extended variants
information (count: 58 )
Associated
traits (count: 7 )

rSNPs within LD-proxies of this variant (count:51)

rs_ID	r²[population]
rs10105315	0.96[CEU][hapmap];1.00[CHB][hapmap]
rs10108618	0.92[CEU][hapmap];1.00[CHB][hapmap];0.83[AMR][1000 genomes]
rs10113808	0.96[CEU][hapmap];1.00[CHB][hapmap]
rs1057625	1.00[ASN][1000 genomes]
rs1057626	0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11773990	0.85[CEU][hapmap];1.00[CHB][hapmap]
rs11777887	1.00[CHB][hapmap]
rs11777918	1.00[CHB][hapmap]
rs11778398	1.00[CHB][hapmap]
rs11991118	0.96[CEU][hapmap];1.00[CHB][hapmap]
rs11991716	1.00[CHB][hapmap]
rs13256092	1.00[CHB][hapmap]
rs17724226	1.00[CHB][hapmap]
rs17724467	0.92[CEU][hapmap];0.88[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs17780806	1.00[CHB][hapmap];0.89[ASN][1000 genomes]
rs2001329	0.80[CEU][hapmap]
rs2001433	0.85[CEU][hapmap];1.00[CHB][hapmap]
rs2409689	0.84[CEU][hapmap];1.00[CHB][hapmap]
rs2409691	0.92[CEU][hapmap]
rs2409692	1.00[CHB][hapmap]
rs2409694	1.00[CHB][hapmap]
rs2409698	0.87[EUR][1000 genomes]
rs2409701	0.89[EUR][1000 genomes]
rs2409710	0.85[CEU][hapmap];0.81[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs2409720	1.00[CHB][hapmap]
rs2898257	0.89[CEU][hapmap];1.00[CHB][hapmap]
rs2898260	1.00[CEU][hapmap];1.00[CHB][hapmap]
rs3021494	0.84[CEU][hapmap]
rs3021500	0.81[CEU][hapmap]
rs34069332	0.85[EUR][1000 genomes]
rs4333549	0.85[CEU][hapmap];0.81[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs4523214	0.93[CEU][hapmap];0.84[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs4840542	0.80[CEU][hapmap];1.00[CHB][hapmap];0.81[AMR][1000 genomes]
rs4840544	0.86[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs4840551	1.00[CHB][hapmap]
rs4841489	0.85[CEU][hapmap];1.00[CHB][hapmap]
rs4841490	0.88[CEU][hapmap];1.00[CHB][hapmap]
rs4841495	0.93[CEU][hapmap];0.86[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs6601560	0.96[CEU][hapmap];1.00[CHB][hapmap];0.81[AMR][1000 genomes]
rs6601561	0.85[EUR][1000 genomes]
rs6601564	0.84[CEU][hapmap];0.82[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs6980856	0.84[CEU][hapmap];1.00[CHB][hapmap]
rs6981201	0.85[ASN][1000 genomes]
rs6991930	0.96[CEU][hapmap];1.00[CHB][hapmap];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6996846	0.88[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs7005680	0.82[EUR][1000 genomes]
rs7011756	0.81[CEU][hapmap]
rs7820860	0.92[CEU][hapmap];1.00[CHB][hapmap];0.80[AMR][1000 genomes]
rs7825690	1.00[CHB][hapmap]
rs7835318	0.92[CEU][hapmap];0.83[AMR][1000 genomes]
rs9657519	0.80[CEU][hapmap];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	nsv1027845	chr8:10959666-10995565	Enhancers Weak transcription Flanking Active TSS Active TSS Strong transcription ZNF genes & repeats Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
7	esv3328426	chr8:10962741-10963093	Weak transcription Enhancers Strong transcription	lncRNA	n/a	inside rSNPs	diseases

mRNA abundance (count:7)

SNP	Gene	Cis/trans	Tissue	Source
rs6601562	AF131215.2	cis	Nerve Tibial	GTEx
rs6601562	AF131215.9	cis	Nerve Tibial	GTEx
rs6601562	AF131215.9	cis	Esophagus Mucosa	GTEx
rs6601562	C8orf5	Cis_1M	lymphoblastoid	RTeQTL
rs6601562	BLK	Cis_1M	lymphoblastoid	RTeQTL
rs6601562	AF131215.9	cis	Skin Sun Exposed Lower leg	GTEx
rs6601562	NEIL2	cis	Nerve Tibial	GTEx

Chromatin state (count:35 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr8:10950600-10965000	Weak transcription	Gastric	stomach
2	chr8:10955200-10968000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
3	chr8:10956800-10964800	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
4	chr8:10957200-10964800	Weak transcription	Primary B cells from peripheral blood	blood
5	chr8:10958200-10965000	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
6	chr8:10958200-10967200	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
7	chr8:10958200-10970200	Weak transcription	H9 Cell Line	embryonic stem cell
8	chr8:10958400-10965200	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
9	chr8:10958400-10974800	Weak transcription	Primary T helper naive cells from peripheral blood	blood
10	chr8:10958600-10964800	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
11	chr8:10958600-10965000	Weak transcription	Primary T helper cells fromperipheralblood	blood
12	chr8:10958600-10971200	Weak transcription	Primary T helper cells PMA-I stimulated	--
13	chr8:10958600-10971200	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
14	chr8:10958800-10967400	Weak transcription	Primary T cells fromperipheralblood	blood
15	chr8:10959600-10964800	Weak transcription	Pancreas	Pancrea
16	chr8:10960400-10963800	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
17	chr8:10960400-10967000	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
18	chr8:10960400-10968400	Weak transcription	Spleen	Spleen
19	chr8:10960800-10965200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
20	chr8:10960800-10970800	Weak transcription	HSMM	muscle
21	chr8:10961200-10964600	Weak transcription	Fetal Intestine Small	intestine
22	chr8:10961200-10964800	Weak transcription	Fetal Stomach	stomach
23	chr8:10961200-10975400	Weak transcription	iPS-20b Cell Line	embryonic stem cell
24	chr8:10961600-10970600	Weak transcription	Fetal Intestine Large	intestine
25	chr8:10961800-10963600	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
26	chr8:10961800-10968800	Weak transcription	Sigmoid Colon	Sigmoid Colon
27	chr8:10961800-10971400	Weak transcription	H1 Cell Line	embryonic stem cell
28	chr8:10962000-10968000	Weak transcription	GM12878-XiMat	blood
29	chr8:10962200-10964400	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
30	chr8:10962400-10964800	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
31	chr8:10962400-10964800	Weak transcription	HMEC	breast
32	chr8:10962400-10967600	Weak transcription	Stomach Smooth Muscle	stomach
33	chr8:10962400-10969600	Weak transcription	NH-A	brain
34	chr8:10962600-10964000	Enhancers	Breast Myoepithelial Primary Cells	Breast
35	chr8:10962800-10965000	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived

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