Variant report

Variant	rs2562431
Chromosome Location	chr19:21639351-21639352
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr19:21637958..21640581-chr19:21645162..21647289,2	K562	blood:

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-ZNF708-2	chr19:21639263-21639390	ENSG00000268119.1
2	lnc-ZNF708-2	chr19:21639263-21639390	ENSG00000268119.1
3	lnc-ZNF708-2	chr19:21639263-21639390	ENSG00000268119.1
4	lnc-ZNF708-2	chr19:21639263-21639390	ENSG00000268119.1

Variant related genes	Relation type
ENSG00000268119	Chromatin interaction

Extended variants
information (count: 63 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:54)

rs_ID	r²[population]
rs1027585	0.82[AFR][1000 genomes]
rs1027586	0.82[AFR][1000 genomes]
rs1027587	0.82[AFR][1000 genomes]
rs10403785	0.86[AFR][1000 genomes]
rs10412107	0.81[AFR][1000 genomes]
rs10414463	0.88[AFR][1000 genomes]
rs10420451	1.00[AFR][1000 genomes]
rs10426240	0.83[AFR][1000 genomes]
rs10426636	0.89[AFR][1000 genomes]
rs1500399	0.83[AFR][1000 genomes]
rs1963611	0.80[AFR][1000 genomes]
rs1983017	0.93[AFR][1000 genomes]
rs1983018	0.93[AFR][1000 genomes]
rs1983019	0.93[AFR][1000 genomes]
rs2009347	0.88[AFR][1000 genomes]
rs2013529	0.81[YRI][hapmap];0.83[AFR][1000 genomes]
rs2088760	0.88[AFR][1000 genomes]
rs2173725	0.83[AFR][1000 genomes]
rs2255010	0.86[AFR][1000 genomes]
rs2255100	0.88[AFR][1000 genomes]
rs2562418	0.82[AFR][1000 genomes]
rs2562437	0.96[AFR][1000 genomes]
rs2562463	0.83[AFR][1000 genomes]
rs2562475	0.93[AFR][1000 genomes]
rs2562476	0.93[AFR][1000 genomes]
rs2562477	0.93[AFR][1000 genomes]
rs2562478	0.92[AFR][1000 genomes]
rs2562479	0.93[YRI][hapmap];0.93[AFR][1000 genomes]
rs2562480	0.93[AFR][1000 genomes]
rs2562481	0.98[AFR][1000 genomes]
rs2562482	0.92[AFR][1000 genomes]
rs2562485	0.89[AFR][1000 genomes]
rs2562486	0.93[YRI][hapmap];0.92[AFR][1000 genomes]
rs2562488	0.93[YRI][hapmap];0.92[AFR][1000 genomes]
rs2562489	0.86[AFR][1000 genomes]
rs2562490	0.85[AFR][1000 genomes]
rs2650761	0.83[AFR][1000 genomes]
rs2650762	0.83[AFR][1000 genomes]
rs2650765	0.83[AFR][1000 genomes]
rs2650796	1.00[AFR][1000 genomes]
rs2650813	0.83[AFR][1000 genomes]
rs2650816	0.86[AFR][1000 genomes]
rs2650818	1.00[AFR][1000 genomes]
rs2650820	0.92[AFR][1000 genomes]
rs2650821	0.92[AFR][1000 genomes]
rs2650822	0.92[AFR][1000 genomes]
rs2650823	0.92[AFR][1000 genomes]
rs2650824	0.82[AFR][1000 genomes]
rs2650837	0.88[AFR][1000 genomes]
rs28580140	0.86[AFR][1000 genomes]
rs28581819	0.83[AFR][1000 genomes]
rs2914653	0.81[AFR][1000 genomes]
rs2968077	1.00[AFR][1000 genomes]
rs987772	1.00[AFR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:9 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	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
2	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
3	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
4	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
5	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
6	esv3363678	chr19:21483148-21756908	Strong transcription Active TSS ZNF genes & repeats Weak transcription Flanking Active TSS Genic enhancers Enhancers 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	31 gene(s)	inside rSNPs	diseases
7	nsv578952	chr19:21535707-21868584	Genic enhancers Active TSS ZNF genes & repeats Enhancers Weak transcription Strong transcription Transcr. at gene 5' and 3' Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	34 gene(s)	inside rSNPs	diseases
8	esv3506838	chr19:21634362-21639360	Weak transcription ZNF genes & repeats Strong transcription	Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	n/a
9	nsv961284	chr19:21636687-21659271	Flanking Active TSS Bivalent Enhancer ZNF genes & repeats Active TSS Weak transcription Enhancers Strong transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	n/a

No data

Chromatin state (count:30 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr19:21629800-21641400	ZNF genes & repeats	HUES48 Cell Line	embryonic stem cell
2	chr19:21630000-21642000	ZNF genes & repeats	HUES64 Cell Line	embryonic stem cell
3	chr19:21630200-21643800	Strong transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
4	chr19:21630400-21643800	ZNF genes & repeats	Dnd41	blood
5	chr19:21633800-21641400	ZNF genes & repeats	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
6	chr19:21633800-21641400	ZNF genes & repeats	Primary hematopoietic stem cells G-CSF-mobilized Male	--
7	chr19:21634600-21641600	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
8	chr19:21635600-21642000	ZNF genes & repeats	iPS-20b Cell Line	embryonic stem cell
9	chr19:21635600-21642000	ZNF genes & repeats	Primary hematopoietic stem cells	blood
10	chr19:21635800-21641200	ZNF genes & repeats	H1 Cell Line	embryonic stem cell
11	chr19:21636200-21641000	ZNF genes & repeats	Primary neutrophils fromperipheralblood	blood
12	chr19:21636600-21639800	ZNF genes & repeats	iPS-18 Cell Line	embryonic stem cell
13	chr19:21636800-21640000	ZNF genes & repeats	ES-I3 Cell Line	embryonic stem cell
14	chr19:21636800-21641400	ZNF genes & repeats	HUES6 Cell Line	embryonic stem cell
15	chr19:21636800-21645800	Weak transcription	Fetal Kidney	kidney
16	chr19:21636800-21646200	Weak transcription	Fetal Heart	heart
17	chr19:21637200-21641000	ZNF genes & repeats	Primary hematopoietic stem cells short term culture	blood
18	chr19:21637400-21639800	ZNF genes & repeats	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
19	chr19:21638200-21640600	Weak transcription	Ovary	ovary
20	chr19:21638200-21642800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
21	chr19:21638400-21639400	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
22	chr19:21638400-21640600	Weak transcription	Brain Inferior Temporal Lobe	brain
23	chr19:21638600-21639600	Strong transcription	Fetal Lung	lung
24	chr19:21638800-21640600	Weak transcription	iPS-15b Cell Line	embryonic stem cell
25	chr19:21638800-21642600	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
26	chr19:21639000-21639600	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
27	chr19:21639200-21639400	ZNF genes & repeats	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
28	chr19:21639200-21639400	ZNF genes & repeats	H9 Cell Line	embryonic stem cell
29	chr19:21639200-21639400	ZNF genes & repeats	iPS DF 6.9 Cell Line	embryonic stem cell
30	chr19:21639200-21641400	ZNF genes & repeats	Primary hematopoietic stem cells G-CSF-mobilized Female	--

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