Variant report

Variant	rs2968040
Chromosome Location	chr19:21565070-21565071
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr19:21565048-21565276	MCF-7	breast:	n/a	n/a

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-ZNF738-1	chr19:21560191-21571384	NR_027130

Variant related genes	Relation type
ENSG00000268731	TF binding region
ENSG00000213976	TF binding region

Extended variants
information (count: 68 )
Associated
traits (count: 0)

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

rs_ID	r²[population]
rs1114305	0.97[AMR][1000 genomes];0.93[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs1875256	1.00[AFR][1000 genomes];0.81[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs2086319	1.00[AMR][1000 genomes];0.86[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2434996	0.97[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs2562402	0.94[AMR][1000 genomes];0.93[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2562409	0.97[AMR][1000 genomes];0.93[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs2562415	0.86[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs2562438	1.00[AMR][1000 genomes];0.86[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2650797	1.00[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2650798	1.00[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2650842	1.00[AMR][1000 genomes];0.86[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2650849	0.97[AMR][1000 genomes];0.93[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2650851	0.94[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2914626	0.94[AMR][1000 genomes];0.93[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2914627	0.94[AMR][1000 genomes];0.93[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2914635	0.89[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs2914645	1.00[AMR][1000 genomes];0.93[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2928188	0.94[AMR][1000 genomes];0.98[ASN][1000 genomes]
rs2928209	1.00[AMR][1000 genomes];0.86[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2928211	0.88[ASN][1000 genomes]
rs2928216	1.00[AMR][1000 genomes];0.86[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2928218	1.00[AMR][1000 genomes];0.86[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2937157	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.93[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2937174	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2968022	1.00[AMR][1000 genomes];0.86[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2968023	1.00[AMR][1000 genomes];0.86[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2968024	1.00[AMR][1000 genomes];0.86[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2968041	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2968045	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2968046	0.97[AMR][1000 genomes];0.93[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2968066	0.86[EUR][1000 genomes]
rs2968082	0.86[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs2968086	1.00[AMR][1000 genomes];0.86[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs472472	0.85[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs475162	0.94[AMR][1000 genomes];0.86[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs487991	0.86[EUR][1000 genomes]
rs489613	0.91[AMR][1000 genomes];0.81[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs489845	0.86[EUR][1000 genomes]
rs492271	0.91[AMR][1000 genomes];0.86[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs499445	0.91[AMR][1000 genomes];0.86[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs501563	0.85[AMR][1000 genomes];0.86[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs527060	0.88[AMR][1000 genomes];0.86[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs547516	0.85[AMR][1000 genomes];0.86[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs555596	0.91[AMR][1000 genomes];0.86[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs598959	0.86[EUR][1000 genomes]
rs600186	0.85[AMR][1000 genomes]
rs609806	0.91[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs612877	0.83[AMR][1000 genomes];0.86[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs627522	0.82[ASN][1000 genomes]
rs631436	0.91[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs651454	0.85[AMR][1000 genomes];0.86[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs8102235	0.94[AMR][1000 genomes];0.93[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs8112775	0.86[EUR][1000 genomes]
rs924485	1.00[AMR][1000 genomes];0.93[EUR][1000 genomes];0.98[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:14 , 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	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
6	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
7	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
8	nsv963023	chr19:21491992-21570395	Weak transcription ZNF genes & repeats Enhancers Flanking Active TSS Strong transcription Active TSS Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
9	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
10	esv1793996	chr19:21544242-21609607	Active TSS Strong transcription ZNF genes & repeats Weak transcription Enhancers Flanking Active TSS Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
11	esv1801985	chr19:21544242-21609607	ZNF genes & repeats Weak transcription Strong transcription Enhancers Genic enhancers Active TSS Flanking Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
12	esv1844586	chr19:21544242-21609607	Weak transcription Strong transcription ZNF genes & repeats Enhancers Flanking Active TSS Active TSS Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
13	esv1834499	chr19:21557835-21609607	Active TSS Weak transcription ZNF genes & repeats Strong transcription Transcr. at gene 5' and 3' Enhancers Flanking Active TSS Genic enhancers Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
14	esv1834993	chr19:21557835-21609607	Flanking Active TSS ZNF genes & repeats Strong transcription Weak transcription Active TSS Genic enhancers Enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:48 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr19:21543000-21566600	ZNF genes & repeats	H9 Derived Neuron Cultured Cells	ES cell derived
2	chr19:21543000-21566800	ZNF genes & repeats	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
3	chr19:21543400-21566400	ZNF genes & repeats	Brain Germinal Matrix	brain
4	chr19:21543400-21570600	ZNF genes & repeats	Monocytes-CD14+_RO01746	blood
5	chr19:21543600-21566400	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
6	chr19:21543800-21566600	ZNF genes & repeats	Primary hematopoietic stem cells G-CSF-mobilized Female	--
7	chr19:21543800-21567400	Strong transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
8	chr19:21544200-21567400	ZNF genes & repeats	Primary hematopoietic stem cells	blood
9	chr19:21544200-21567600	ZNF genes & repeats	Primary hematopoietic stem cells G-CSF-mobilized Male	--
10	chr19:21547400-21567600	ZNF genes & repeats	Primary T regulatory cells fromperipheralblood	blood
11	chr19:21547800-21571000	ZNF genes & repeats	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
12	chr19:21551000-21570800	ZNF genes & repeats	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
13	chr19:21552000-21570800	ZNF genes & repeats	iPS-20b Cell Line	embryonic stem cell
14	chr19:21555000-21566800	ZNF genes & repeats	HUES48 Cell Line	embryonic stem cell
15	chr19:21555800-21567000	ZNF genes & repeats	Dnd41	blood
16	chr19:21556800-21569400	ZNF genes & repeats	HUES64 Cell Line	embryonic stem cell
17	chr19:21558000-21565400	ZNF genes & repeats	ES-I3 Cell Line	embryonic stem cell
18	chr19:21558000-21566800	ZNF genes & repeats	Primary neutrophils fromperipheralblood	blood
19	chr19:21558000-21567400	ZNF genes & repeats	H1 Cell Line	embryonic stem cell
20	chr19:21558000-21567400	ZNF genes & repeats	Ganglion Eminence derived primary cultured neurospheres	brain
21	chr19:21560400-21567200	ZNF genes & repeats	Fetal Lung	lung
22	chr19:21560400-21567600	ZNF genes & repeats	Duodenum Mucosa	Duodenum
23	chr19:21560400-21568000	ZNF genes & repeats	Liver	Liver
24	chr19:21561000-21569800	ZNF genes & repeats	Duodenum Smooth Muscle	Duodenum
25	chr19:21561200-21565200	ZNF genes & repeats	Fetal Adrenal Gland	Adrenal Gland
26	chr19:21561200-21566600	ZNF genes & repeats	Primary hematopoietic stem cells short term culture	blood
27	chr19:21561400-21566800	ZNF genes & repeats	Fetal Brain Female	brain
28	chr19:21561400-21567600	ZNF genes & repeats	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
29	chr19:21561600-21565800	ZNF genes & repeats	Cortex derived primary cultured neurospheres	brain
30	chr19:21561800-21568000	ZNF genes & repeats	HUES6 Cell Line	embryonic stem cell
31	chr19:21562600-21566200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
32	chr19:21563200-21565200	ZNF genes & repeats	H1 Derived Mesenchymal Stem Cells	ES cell derived
33	chr19:21563200-21565400	ZNF genes & repeats	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
34	chr19:21563600-21566000	Weak transcription	Primary T killer memory cells from peripheral blood	blood
35	chr19:21563600-21566200	ZNF genes & repeats	H9 Cell Line	embryonic stem cell
36	chr19:21563800-21565200	Weak transcription	Fetal Kidney	kidney
37	chr19:21563800-21565600	Weak transcription	Right Ventricle	heart
38	chr19:21563800-21566000	Weak transcription	Primary T helper naive cells from peripheral blood	blood
39	chr19:21564200-21565200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
40	chr19:21564200-21565400	ZNF genes & repeats	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
41	chr19:21564400-21565400	ZNF genes & repeats	iPS DF 19.11 Cell Line	embryonic stem cell
42	chr19:21564600-21565200	ZNF genes & repeats	Fetal Intestine Small	intestine
43	chr19:21564600-21565400	ZNF genes & repeats	IMR90 fetal lung fibroblasts Cell Line	lung
44	chr19:21564600-21565400	ZNF genes & repeats	Ovary	ovary
45	chr19:21564800-21566000	Weak transcription	Primary B cells from cord blood	blood
46	chr19:21564800-21566000	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
47	chr19:21564800-21566000	Weak transcription	Rectal Smooth Muscle	rectum
48	chr19:21565000-21569800	ZNF genes & repeats	Primary T helper cells PMA-I stimulated	--

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