Variant report

Variant	rs10420016
Chromosome Location	chr19:21688602-21688603
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr19:21510924..21513197-chr19:21688433..21691004,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000182141	Chromatin interaction

Extended variants
information (count: 68 )
Associated
traits (count: 7 )

rSNPs within LD-proxies of this variant (count:56)

rs_ID	r²[population]
rs10854048	0.81[ASN][1000 genomes]
rs10854050	0.82[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs10854051	0.82[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs11085462	0.82[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs11085465	0.81[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs11085468	0.81[EUR][1000 genomes]
rs11668606	0.82[AMR][1000 genomes];0.86[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs11671579	0.82[AMR][1000 genomes];0.84[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs12974758	0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1879234	1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2173727	0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2359155	0.93[AMR][1000 genomes];0.92[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2562398	0.88[AMR][1000 genomes];0.96[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2562408	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2562417	0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2562456	0.92[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs2562466	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2562468	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2562471	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2562474	0.81[AMR][1000 genomes]
rs2562487	0.84[AMR][1000 genomes];0.80[ASN][1000 genomes]
rs2562507	0.88[AMR][1000 genomes];0.96[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2562508	0.88[AMR][1000 genomes];0.96[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2650784	0.88[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs2650792	0.90[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2650793	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2650804	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2650805	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2650814	0.81[AMR][1000 genomes]
rs2650825	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2681370	0.82[AMR][1000 genomes];0.86[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2681377	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2681388	0.88[AMR][1000 genomes];0.96[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2681389	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2681391	0.86[AMR][1000 genomes];0.85[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2681392	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2681395	0.86[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2914646	0.92[AFR][1000 genomes];0.82[AMR][1000 genomes]
rs2946790	0.88[AMR][1000 genomes];0.96[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs35008138	0.88[AMR][1000 genomes];0.96[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs35099594	0.81[EUR][1000 genomes]
rs55771551	0.84[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs58001930	0.82[AMR][1000 genomes];0.86[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs62109226	0.83[AFR][1000 genomes]
rs62109227	0.83[AFR][1000 genomes]
rs62109228	0.83[AFR][1000 genomes]
rs62110163	0.88[AMR][1000 genomes];0.96[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs6511250	0.91[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs6511253	0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6511254	0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6511256	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6511258	0.97[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7252585	0.83[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs7259708	0.82[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs9304986	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9304987	0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:12 , 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	nsv833782	chr19:21663537-21845722	Weak transcription Enhancers Active TSS ZNF genes & repeats Strong transcription Bivalent/Poised TSS Flanking Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	23 gene(s)	inside rSNPs	diseases
9	nsv510759	chr19:21664791-21723191	Weak transcription ZNF genes & repeats Active TSS Flanking Active TSS Strong transcription Enhancers Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	18 gene(s)	inside rSNPs	diseases
10	nsv543941	chr19:21676223-21693215	Enhancers Flanking Active TSS Active TSS Weak transcription Transcr. at gene 5' and 3' ZNF genes & repeats Strong transcription Genic enhancers Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
11	esv2762028	chr19:21685778-21755476	ZNF genes & repeats Active TSS Weak transcription Enhancers Flanking Active TSS Strong transcription Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
12	nsv963024	chr19:21686690-21722618	Weak transcription Flanking Active TSS ZNF genes & repeats Strong transcription Active TSS Enhancers Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases

mRNA abundance (count:7)

SNP	Gene	Cis/trans	Tissue	Source
rs10420016	CTD-2561J22.5	cis	Thyroid	GTEx
rs10420016	ZNF708	cis	lung	GTEx
rs10420016	ZNF708	cis	Muscle Skeletal	GTEx
rs10420016	RP11-678G14.3	cis	Skin Sun Exposed Lower leg	GTEx
rs10420016	ZNF708	cis	Skin Sun Exposed Lower leg	GTEx
rs10420016	RP11-678G14.3	cis	Adipose Subcutaneous	GTEx
rs10420016	RP11-678G14.2	cis	Adipose Subcutaneous	GTEx

Chromatin state (count:125 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr19:21687600-21689400	Active TSS	Primary T cells effector/memory enriched fromperipheralblood	blood
2	chr19:21687600-21689600	Active TSS	Brain Germinal Matrix	brain
3	chr19:21687800-21689400	Active TSS	Brain Hippocampus Middle	brain
4	chr19:21687800-21689400	Active TSS	GM12878-XiMat	blood
5	chr19:21688000-21689000	Active TSS	Thymus	Thymus
6	chr19:21688000-21689200	Active TSS	NH-A	brain
7	chr19:21688000-21689400	Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
8	chr19:21688000-21689400	Active TSS	Brain Cingulate Gyrus	brain
9	chr19:21688000-21689400	Active TSS	Fetal Adrenal Gland	Adrenal Gland
10	chr19:21688000-21689400	Active TSS	Fetal Thymus	thymus
11	chr19:21688000-21689400	Active TSS	Right Ventricle	heart
12	chr19:21688000-21689600	Active TSS	ES-I3 Cell Line	embryonic stem cell
13	chr19:21688000-21689600	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
14	chr19:21688000-21689600	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
15	chr19:21688000-21689600	Active TSS	Muscle Satellite Cultured Cells	--
16	chr19:21688000-21689600	Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
17	chr19:21688000-21689600	Active TSS	Right Atrium	heart
18	chr19:21688000-21689600	Active TSS	NHEK	skin
19	chr19:21688000-21689800	Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
20	chr19:21688000-21689800	Active TSS	Brain Anterior Caudate	brain
21	chr19:21688000-21690000	Active TSS	H9 Derived Neuron Cultured Cells	ES cell derived
22	chr19:21688000-21690000	Active TSS	Brain Inferior Temporal Lobe	brain
23	chr19:21688000-21690200	Active TSS	Stomach Smooth Muscle	stomach
24	chr19:21688200-21688800	Active TSS	Primary hematopoietic stem cells	blood
25	chr19:21688200-21688800	Active TSS	Primary T helper memory cells from peripheral blood 1	blood
26	chr19:21688200-21688800	Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
27	chr19:21688200-21688800	Active TSS	Cortex derived primary cultured neurospheres	brain
28	chr19:21688200-21689000	Active TSS	Primary B cells from peripheral blood	blood
29	chr19:21688200-21689000	Active TSS	Primary hematopoietic stem cells short term culture	blood
30	chr19:21688200-21689000	Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
31	chr19:21688200-21689200	Active TSS	iPS-20b Cell Line	embryonic stem cell
32	chr19:21688200-21689200	Active TSS	iPS DF 6.9 Cell Line	embryonic stem cell
33	chr19:21688200-21689200	Active TSS	Primary T cells from cord blood	blood
34	chr19:21688200-21689200	Active TSS	Primary T helper naive cells from peripheral blood	blood
35	chr19:21688200-21689200	Active TSS	Primary T killer memory cells from peripheral blood	blood
36	chr19:21688200-21689200	Active TSS	Duodenum Smooth Muscle	Duodenum
37	chr19:21688200-21689200	Active TSS	Esophagus	oesophagus
38	chr19:21688200-21689200	Active TSS	Fetal Brain Male	brain
39	chr19:21688200-21689200	Active TSS	Fetal Intestine Small	intestine
40	chr19:21688200-21689200	Active TSS	Fetal Kidney	kidney
41	chr19:21688200-21689200	Active TSS	HUVEC	blood vessel
42	chr19:21688200-21689400	Active TSS	H1 Derived Mesenchymal Stem Cells	ES cell derived
43	chr19:21688200-21689400	Active TSS	H9 Cell Line	embryonic stem cell
44	chr19:21688200-21689400	Active TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
45	chr19:21688200-21689400	Active TSS	IMR90 fetal lung fibroblasts Cell Line	lung
46	chr19:21688200-21689400	Active TSS	iPS DF 19.11 Cell Line	embryonic stem cell
47	chr19:21688200-21689400	Active TSS	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
48	chr19:21688200-21689400	Active TSS	Primary T helper memory cells from peripheral blood 2	blood
49	chr19:21688200-21689400	Active TSS	Primary T helper cells PMA-I stimulated	--
50	chr19:21688200-21689400	Active TSS	Primary T killer naive cells fromperipheralblood	blood

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