Variant report

Variant	rs540714
Chromosome Location	chr19:21472444-21472445
allele	A/C/G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-ZNF708-4	chr19:21472356-21472800	NONHSAT063695

Extended variants
information (count: 92 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:79)

rs_ID	r²[population]
rs1114305	0.93[CHB][hapmap];0.85[EUR][1000 genomes]
rs2086319	1.00[CHB][hapmap];0.94[JPT][hapmap];1.00[YRI][hapmap];0.92[EUR][1000 genomes]
rs2434996	0.80[EUR][1000 genomes]
rs2562402	0.93[CHB][hapmap];0.92[CHD][hapmap];1.00[GIH][hapmap];0.87[MEX][hapmap];1.00[TSI][hapmap];0.85[EUR][1000 genomes]
rs2562409	0.85[EUR][1000 genomes]
rs2562415	0.85[EUR][1000 genomes]
rs2562435	1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];0.89[JPT][hapmap];0.87[LWK][hapmap];0.93[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap]
rs2562438	0.92[EUR][1000 genomes]
rs2562456	0.89[CHD][hapmap]
rs2650797	0.85[EUR][1000 genomes]
rs2650798	1.00[CHB][hapmap];0.89[JPT][hapmap];0.85[EUR][1000 genomes]
rs2650842	0.92[EUR][1000 genomes]
rs2650849	0.85[EUR][1000 genomes]
rs2650851	0.85[EUR][1000 genomes]
rs279804	0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs279805	0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs279810	0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs279811	0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs279812	0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs279814	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs279815	0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs279816	0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs279817	0.84[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs279818	0.91[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs279819	0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs279820	0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2914626	0.93[CHB][hapmap];0.85[EUR][1000 genomes]
rs2914627	0.85[EUR][1000 genomes]
rs2914645	1.00[CHB][hapmap];0.89[JPT][hapmap];1.00[YRI][hapmap];0.85[EUR][1000 genomes]
rs2928188	0.86[EUR][1000 genomes]
rs2928209	0.92[EUR][1000 genomes]
rs2928216	0.92[EUR][1000 genomes]
rs2928218	0.90[CHB][hapmap];1.00[JPT][hapmap];0.92[EUR][1000 genomes]
rs2937157	0.85[EUR][1000 genomes]
rs2937174	1.00[CHB][hapmap];0.89[JPT][hapmap];0.85[EUR][1000 genomes]
rs2968022	0.88[JPT][hapmap];1.00[YRI][hapmap];0.92[EUR][1000 genomes]
rs2968023	0.92[EUR][1000 genomes]
rs2968024	0.92[EUR][1000 genomes]
rs2968041	0.85[EUR][1000 genomes]
rs2968045	1.00[CHB][hapmap];0.89[JPT][hapmap];0.85[EUR][1000 genomes]
rs2968046	0.93[CHB][hapmap];0.94[CHD][hapmap];1.00[GIH][hapmap];0.84[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];0.85[EUR][1000 genomes]
rs2968066	0.94[AMR][1000 genomes];0.92[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2968082	0.93[CHB][hapmap];0.85[EUR][1000 genomes]
rs2968086	0.92[EUR][1000 genomes]
rs472472	1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];0.94[JPT][hapmap];1.00[LWK][hapmap];0.88[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.85[AFR][1000 genomes];0.88[AMR][1000 genomes];0.92[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs475162	0.92[EUR][1000 genomes]
rs476376	0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs478046	0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs487991	0.97[AMR][1000 genomes];0.92[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs489613	0.82[AMR][1000 genomes]
rs489845	1.00[CHB][hapmap];0.94[JPT][hapmap];1.00[YRI][hapmap];0.85[AFR][1000 genomes];1.00[AMR][1000 genomes];0.92[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs492271	0.82[AMR][1000 genomes];0.92[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs499445	1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];0.94[JPT][hapmap];0.88[LWK][hapmap];0.83[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.82[AMR][1000 genomes];0.92[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs501563	1.00[CHB][hapmap];0.93[JPT][hapmap];1.00[YRI][hapmap];0.88[AMR][1000 genomes];0.92[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs504026	0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs508656	0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs511469	0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs516519	0.82[ASN][1000 genomes]
rs527060	0.92[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs537114	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs540637	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs541639	1.00[CHB][hapmap];0.94[CHD][hapmap];0.94[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs547516	0.94[JPT][hapmap];1.00[YRI][hapmap];0.88[AMR][1000 genomes];0.92[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs555596	0.82[AMR][1000 genomes];0.92[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs571937	0.90[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs57740	0.86[CHD][hapmap]
rs583680	0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs586144	0.80[AMR][1000 genomes];0.86[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs598959	1.00[CHB][hapmap];0.94[JPT][hapmap];1.00[AMR][1000 genomes];0.92[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs600186	1.00[CHB][hapmap];0.94[JPT][hapmap];0.88[AMR][1000 genomes];0.86[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs609806	0.82[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs612877	0.92[EUR][1000 genomes]
rs627522	0.93[CHB][hapmap];0.97[CHD][hapmap]
rs631436	0.82[AMR][1000 genomes];0.86[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs651454	0.88[AMR][1000 genomes];0.92[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs661453	0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs8102235	0.85[EUR][1000 genomes]
rs8112775	1.00[CHB][hapmap];0.97[CHD][hapmap];0.94[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.97[AMR][1000 genomes];0.92[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs924485	0.93[CHB][hapmap];0.89[JPT][hapmap];1.00[YRI][hapmap];0.85[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:13 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv3385528	chr19:21030777-21495566	Active TSS Weak transcription Strong transcription ZNF genes & repeats Flanking Active TSS Genic enhancers Enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	32 gene(s)	inside rSNPs	diseases
2	esv3518033	chr19:21278465-21747567	Strong transcription Weak transcription ZNF genes & repeats Active TSS Enhancers Flanking Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	41 gene(s)	inside rSNPs	diseases
3	esv3518034	chr19:21278465-21747567	ZNF genes & repeats Weak transcription Genic enhancers Active TSS Enhancers Flanking Active TSS Strong transcription Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	41 gene(s)	inside rSNPs	diseases
4	esv3414204	chr19:21301761-21839451	ZNF genes & repeats Weak transcription Flanking Active TSS Transcr. at gene 5' and 3' Enhancers Strong transcription Flanking Bivalent TSS/Enh Active TSS Bivalent Enhancer Genic enhancers Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	44 gene(s)	inside rSNPs	diseases
5	nsv578950	chr19:21388995-21477431	Strong transcription ZNF genes & repeats Weak transcription Enhancers Active TSS Flanking Active TSS Bivalent Enhancer Genic enhancers	TF binding region Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
6	nsv911415	chr19:21388995-21487170	ZNF genes & repeats Weak transcription Strong transcription Enhancers Active TSS Bivalent Enhancer Flanking Active TSS Genic enhancers	TF binding region Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
7	nsv911416	chr19:21388995-21548211	Flanking Active TSS Weak transcription Strong transcription ZNF genes & repeats Active TSS Enhancers Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases
8	nsv911417	chr19:21388995-21564001	Weak transcription Strong transcription Active TSS ZNF genes & repeats Enhancers Genic enhancers Flanking Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases
9	nsv911419	chr19:21391844-21487170	Strong transcription Weak transcription ZNF genes & repeats Enhancers Bivalent Enhancer Active TSS Flanking Active TSS Genic enhancers	TF binding region Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
10	esv3325271	chr19:21445407-21792817	Weak transcription ZNF genes & repeats Active TSS Flanking Active TSS Strong transcription Genic enhancers Enhancers Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	35 gene(s)	inside rSNPs	diseases
11	nsv911420	chr19:21454672-21613397	ZNF genes & repeats Strong transcription Active TSS Weak transcription Enhancers Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	15 gene(s)	inside rSNPs	diseases
12	esv2762027	chr19:21465718-21474111	ZNF genes & repeats Weak transcription Strong transcription	TF binding region Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
13	esv2751783	chr19:21465822-21726337	Strong transcription ZNF genes & repeats Enhancers Weak transcription Flanking Active TSS Genic enhancers Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	31 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:26 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr19:21465000-21496000	ZNF genes & repeats	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
2	chr19:21465400-21484600	ZNF genes & repeats	Liver	Liver
3	chr19:21467000-21472800	ZNF genes & repeats	Monocytes-CD14+_RO01746	blood
4	chr19:21467200-21489600	ZNF genes & repeats	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
5	chr19:21468000-21474200	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
6	chr19:21468600-21472800	Weak transcription	Left Ventricle	heart
7	chr19:21469400-21474400	Weak transcription	Brain Inferior Temporal Lobe	brain
8	chr19:21470000-21472800	Weak transcription	Cortex derived primary cultured neurospheres	brain
9	chr19:21470000-21474400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
10	chr19:21470000-21474400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
11	chr19:21470600-21484200	ZNF genes & repeats	Primary T helper cells fromperipheralblood	blood
12	chr19:21471200-21474200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
13	chr19:21471200-21474400	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
14	chr19:21471200-21479800	ZNF genes & repeats	iPS-20b Cell Line	embryonic stem cell
15	chr19:21471400-21473600	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
16	chr19:21471600-21472600	ZNF genes & repeats	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
17	chr19:21471600-21474800	Weak transcription	Brain Germinal Matrix	brain
18	chr19:21471600-21479800	ZNF genes & repeats	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
19	chr19:21472000-21476400	Weak transcription	Osteobl	bone
20	chr19:21472000-21481800	ZNF genes & repeats	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
21	chr19:21472200-21474400	Weak transcription	NH-A	brain
22	chr19:21472200-21487600	ZNF genes & repeats	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
23	chr19:21472200-21490400	ZNF genes & repeats	Primary hematopoietic stem cells G-CSF-mobilized Male	--
24	chr19:21472400-21472600	ZNF genes & repeats	HSMMtube	muscle
25	chr19:21472400-21472800	ZNF genes & repeats	HSMM	muscle
26	chr19:21472400-21475200	ZNF genes & repeats	H1 Derived Mesenchymal Stem Cells	ES cell derived

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