Variant report

Variant	rs2562474
Chromosome Location	chr19:21646282-21646283
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 39 )
Associated
traits (count: 7 )

rSNPs within LD-proxies of this variant (count:31)

rs_ID	r²[population]
rs10420016	0.81[AMR][1000 genomes]
rs12974758	0.81[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs2562428	0.88[AMR][1000 genomes];0.89[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2562456	0.81[ASN][1000 genomes]
rs2562487	0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2650764	0.81[ASN][1000 genomes]
rs2650773	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2650784	0.81[ASN][1000 genomes]
rs2650793	0.81[AMR][1000 genomes]
rs2650801	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2650804	0.81[AMR][1000 genomes]
rs2650805	0.81[AMR][1000 genomes]
rs2650814	0.85[AFR][1000 genomes];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2650819	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2681389	0.81[AMR][1000 genomes]
rs2914646	0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2928211	0.81[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs2968072	0.81[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2968076	0.98[AFR][1000 genomes];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2968078	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs516519	0.82[EUR][1000 genomes]
rs56072098	0.85[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs627522	0.82[EUR][1000 genomes]
rs6511250	0.84[AMR][1000 genomes];0.83[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs6511253	0.80[AFR][1000 genomes];0.82[AMR][1000 genomes]
rs6511254	0.80[AFR][1000 genomes];0.82[AMR][1000 genomes]
rs6511256	0.81[AMR][1000 genomes]
rs7252585	0.81[ASN][1000 genomes]
rs8106025	0.98[AFR][1000 genomes];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9304986	0.81[AMR][1000 genomes]
rs9304987	0.82[AMR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:8 , 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	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

mRNA abundance (count:7)

SNP	Gene	Cis/trans	Tissue	Source
rs2562474	RP11-678G14.2	cis	Adipose Subcutaneous	GTEx
rs2562474	ZNF708	cis	Skin Sun Exposed Lower leg	GTEx
rs2562474	ZNF708	cis	lung	GTEx
rs2562474	CTD-2561J22.5	cis	Thyroid	GTEx
rs2562474	RP11-678G14.3	cis	Skin Sun Exposed Lower leg	GTEx
rs2562474	ZNF708	cis	Muscle Skeletal	GTEx
rs2562474	RP11-678G14.3	cis	Adipose Subcutaneous	GTEx

Chromatin state (count:81 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr19:21641200-21646400	Weak transcription	Brain Inferior Temporal Lobe	brain
2	chr19:21642600-21646800	Active TSS	K562	blood
3	chr19:21644600-21646400	Transcr. at gene 5' and 3'	Dnd41	blood
4	chr19:21645000-21647000	Active TSS	ES-I3 Cell Line	embryonic stem cell
5	chr19:21645000-21647000	Active TSS	HUES48 Cell Line	embryonic stem cell
6	chr19:21645200-21646600	Active TSS	ES-WA7 Cell Line	embryonic stem cell
7	chr19:21645200-21647000	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
8	chr19:21645200-21647000	Active TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
9	chr19:21645200-21647000	Active TSS	HUES6 Cell Line	embryonic stem cell
10	chr19:21645200-21647200	Active TSS	iPS-20b Cell Line	embryonic stem cell
11	chr19:21645400-21646800	Active TSS	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
12	chr19:21645400-21647000	Active TSS	HUES64 Cell Line	embryonic stem cell
13	chr19:21645400-21647000	Active TSS	iPS DF 19.11 Cell Line	embryonic stem cell
14	chr19:21645400-21647200	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
15	chr19:21645400-21647200	Active TSS	Primary hematopoietic stem cells short term culture	blood
16	chr19:21645600-21646800	Active TSS	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
17	chr19:21645600-21646800	Active TSS	iPS-15b Cell Line	embryonic stem cell
18	chr19:21645600-21646800	Active TSS	iPS DF 6.9 Cell Line	embryonic stem cell
19	chr19:21645600-21646800	Active TSS	ES-UCSF4 Cell Line	embryonic stem cell
20	chr19:21645600-21646800	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
21	chr19:21645600-21647000	Active TSS	H1 Cell Line	embryonic stem cell
22	chr19:21645600-21647000	Active TSS	H9 Cell Line	embryonic stem cell
23	chr19:21645600-21647000	Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
24	chr19:21645600-21647000	ZNF genes & repeats	Breast Myoepithelial Primary Cells	Breast
25	chr19:21645600-21647000	Active TSS	Primary hematopoietic stem cells	blood
26	chr19:21645800-21646400	Active TSS	Placenta	Placenta
27	chr19:21645800-21646800	Active TSS	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
28	chr19:21645800-21646800	Active TSS	iPS-18 Cell Line	embryonic stem cell
29	chr19:21645800-21646800	Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
30	chr19:21645800-21647000	ZNF genes & repeats	Foreskin Keratinocyte Primary Cells skin03	Skin
31	chr19:21645800-21647000	Active TSS	Brain Germinal Matrix	brain
32	chr19:21645800-21647000	Active TSS	Fetal Kidney	kidney
33	chr19:21645800-21647000	Active TSS	Ovary	ovary
34	chr19:21645800-21647000	ZNF genes & repeats	Thymus	Thymus
35	chr19:21646000-21646400	Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
36	chr19:21646000-21646600	Flanking Active TSS	Fetal Muscle Leg	muscle
37	chr19:21646000-21646800	Flanking Active TSS	H1 Derived Mesenchymal Stem Cells	ES cell derived
38	chr19:21646000-21646800	Active TSS	Primary T regulatory cells fromperipheralblood	blood
39	chr19:21646000-21646800	Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
40	chr19:21646000-21646800	Active TSS	Fetal Lung	lung
41	chr19:21646000-21646800	ZNF genes & repeats	Fetal Thymus	thymus
42	chr19:21646000-21646800	Active TSS	Pancreas	Pancrea
43	chr19:21646000-21646800	Active TSS	Placenta Amnion	Placenta Amnion
44	chr19:21646000-21647000	Bivalent Enhancer	Primary T cells fromperipheralblood	blood
45	chr19:21646000-21647000	Bivalent/Poised TSS	Primary T helper naive cells fromperipheralblood	blood
46	chr19:21646000-21647000	Active TSS	Brain Anterior Caudate	brain
47	chr19:21646000-21647000	Active TSS	Fetal Intestine Large	intestine
48	chr19:21646000-21647000	Active TSS	Fetal Intestine Small	intestine
49	chr19:21646000-21647000	Active TSS	Fetal Muscle Trunk	muscle
50	chr19:21646000-21647000	Active TSS	Rectal Mucosa Donor 29	rectum

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