Variant report

Variant	rs57299552
Chromosome Location	chr19:21504128-21504129
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr19:21503005..21505616-chr19:21507489..21509547,2	K562	blood:

Extended variants
information (count: 98 )
Associated
traits (count: 6 )

rSNPs within LD-proxies of this variant (count:88)

rs_ID	r²[population]
rs10414834	0.81[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs10424079	0.83[EUR][1000 genomes]
rs11666213	1.00[AFR][1000 genomes];0.81[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs11666447	0.85[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs11666525	1.00[AFR][1000 genomes];0.85[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs11666540	0.81[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs11667103	1.00[AFR][1000 genomes];0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11667361	0.81[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs11667392	0.82[AFR][1000 genomes];0.85[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11669033	1.00[AFR][1000 genomes];0.85[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs11669790	0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11670815	0.81[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs11670868	0.90[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs11672341	0.88[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs11672583	1.00[AFR][1000 genomes];0.90[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11673320	0.85[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs11879901	0.84[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs13346641	0.83[EUR][1000 genomes]
rs1621154	0.88[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1626404	0.88[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1762578	0.88[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17680605	0.90[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1781867	0.88[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1781872	0.83[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1967182	0.81[EUR][1000 genomes]
rs2061916	1.00[AFR][1000 genomes];0.90[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2154302	0.85[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs2358993	1.00[AFR][1000 genomes];0.90[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2359144	0.83[EUR][1000 genomes]
rs2359145	0.85[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs2562405	0.83[EUR][1000 genomes]
rs2562411	0.81[EUR][1000 genomes]
rs2562413	0.83[EUR][1000 genomes]
rs2562416	0.81[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs2650776	0.81[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs2650844	0.83[EUR][1000 genomes]
rs2650848	0.83[EUR][1000 genomes]
rs279807	0.85[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs279809	0.85[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2914646	0.84[AFR][1000 genomes]
rs3853837	1.00[AFR][1000 genomes];0.85[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs3853838	1.00[AFR][1000 genomes];0.85[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs4321312	0.81[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs4327181	0.95[EUR][1000 genomes]
rs4359573	1.00[AFR][1000 genomes];0.90[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4544364	1.00[AFR][1000 genomes];0.90[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4638726	0.85[EUR][1000 genomes]
rs516519	0.80[EUR][1000 genomes]
rs55756795	1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs55790393	0.86[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs55875743	1.00[AFR][1000 genomes];0.88[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs55899865	0.84[AFR][1000 genomes];0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs58412280	1.00[AFR][1000 genomes];0.90[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs60173523	0.81[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs61035285	0.86[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs62107465	0.84[AFR][1000 genomes];0.90[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62107468	0.89[EUR][1000 genomes]
rs62107469	1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62107472	0.88[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs62107479	1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62107531	1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62107532	0.88[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs62107534	0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62107536	0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62107539	1.00[AFR][1000 genomes];0.90[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62107540	0.84[AFR][1000 genomes];0.90[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62107541	1.00[AFR][1000 genomes];0.90[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62109225	1.00[AFR][1000 genomes];0.90[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62109226	0.91[AFR][1000 genomes];0.85[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs62109227	0.91[AFR][1000 genomes];0.85[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs62109228	0.91[AFR][1000 genomes];0.85[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs62109229	0.81[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs62110071	0.82[AFR][1000 genomes];0.85[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62110367	0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs62110377	1.00[AFR][1000 genomes];0.80[AMR][1000 genomes];0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62110416	1.00[AFR][1000 genomes];0.85[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs62110420	1.00[AFR][1000 genomes];0.85[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs62110424	1.00[AFR][1000 genomes];0.85[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs62110426	1.00[AFR][1000 genomes];0.83[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs62110428	1.00[AFR][1000 genomes];0.87[EUR][1000 genomes]
rs62110429	1.00[AFR][1000 genomes];0.81[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs627522	0.80[EUR][1000 genomes]
rs7246339	1.00[AFR][1000 genomes];0.85[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7251135	1.00[AFR][1000 genomes];0.85[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7258099	0.81[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs7258473	1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7258562	0.86[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs73537884	0.83[AMR][1000 genomes];0.98[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:10 , 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	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
5	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
6	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
7	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
8	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
9	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
10	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

mRNA abundance (count:6)

SNP	Gene	Cis/trans	Tissue	Source
rs57299552	ZNF708	cis	Skin Sun Exposed Lower leg	GTEx
rs57299552	ZNF708	cis	lung	GTEx
rs57299552	RP11-678G14.3	cis	Adipose Subcutaneous	GTEx
rs57299552	RP11-678G14.2	cis	Esophagus Muscularis	GTEx
rs57299552	ZNF708	cis	Muscle Skeletal	GTEx
rs57299552	RP11-678G14.2	cis	Whole Blood	GTEx

Chromatin state (count:116 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr19:21473800-21510400	Weak transcription	Fetal Heart	heart
2	chr19:21474800-21509800	Weak transcription	Fetal Brain Male	brain
3	chr19:21475200-21511200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
4	chr19:21481600-21505600	Weak transcription	K562	blood
5	chr19:21484400-21511000	Weak transcription	H9 Cell Line	embryonic stem cell
6	chr19:21485400-21508600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
7	chr19:21485400-21511200	Weak transcription	Gastric	stomach
8	chr19:21485600-21504200	Weak transcription	Pancreas	Pancrea
9	chr19:21487600-21508600	Weak transcription	Fetal Kidney	kidney
10	chr19:21487600-21511200	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
11	chr19:21488000-21505600	Weak transcription	Right Ventricle	heart
12	chr19:21488200-21511200	Weak transcription	Aorta	Aorta
13	chr19:21489000-21510800	Weak transcription	NH-A	brain
14	chr19:21489600-21506000	Weak transcription	iPS-18 Cell Line	embryonic stem cell
15	chr19:21489600-21509000	Weak transcription	Placenta	Placenta
16	chr19:21490200-21508800	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
17	chr19:21490200-21509200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
18	chr19:21492400-21506200	Weak transcription	Fetal Lung	lung
19	chr19:21492400-21508600	Weak transcription	Muscle Satellite Cultured Cells	--
20	chr19:21492400-21508800	Weak transcription	Fetal Intestine Large	intestine
21	chr19:21492400-21509000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
22	chr19:21492600-21509000	Weak transcription	Fetal Muscle Leg	muscle
23	chr19:21492800-21506600	Weak transcription	Fetal Thymus	thymus
24	chr19:21493000-21509200	Weak transcription	Fetal Intestine Small	intestine
25	chr19:21493600-21505400	Weak transcription	iPS-20b Cell Line	embryonic stem cell
26	chr19:21494200-21504600	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
27	chr19:21495400-21508400	Weak transcription	Fetal Brain Female	brain
28	chr19:21496200-21504600	Weak transcription	HSMMtube	muscle
29	chr19:21496400-21505600	Weak transcription	HepG2	liver
30	chr19:21496800-21509800	ZNF genes & repeats	Primary hematopoietic stem cells G-CSF-mobilized Male	--
31	chr19:21497400-21508600	ZNF genes & repeats	Primary T regulatory cells fromperipheralblood	blood
32	chr19:21497600-21511000	ZNF genes & repeats	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
33	chr19:21498000-21506800	ZNF genes & repeats	Primary hematopoietic stem cells G-CSF-mobilized Female	--
34	chr19:21498400-21510600	Weak transcription	HUVEC	blood vessel
35	chr19:21498400-21511200	Weak transcription	Placenta Amnion	Placenta Amnion
36	chr19:21498800-21510400	Weak transcription	Rectal Smooth Muscle	rectum
37	chr19:21499200-21506000	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
38	chr19:21499800-21505200	ZNF genes & repeats	Ganglion Eminence derived primary cultured neurospheres	brain
39	chr19:21500000-21509400	Weak transcription	Fetal Stomach	stomach
40	chr19:21500200-21505000	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
41	chr19:21500400-21506200	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
42	chr19:21500600-21505600	Weak transcription	Primary T helper naive cells from peripheral blood	blood
43	chr19:21500600-21506200	ZNF genes & repeats	GM12878-XiMat	blood
44	chr19:21500600-21509000	Weak transcription	Primary T cells from cord blood	blood
45	chr19:21500800-21506800	ZNF genes & repeats	Primary hematopoietic stem cells short term culture	blood
46	chr19:21501000-21504200	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
47	chr19:21501000-21504200	Weak transcription	Ovary	ovary
48	chr19:21501000-21504200	Weak transcription	Stomach Smooth Muscle	stomach
49	chr19:21501000-21504600	Weak transcription	Adipose Nuclei	Adipose
50	chr19:21501000-21504800	Enhancers	Brain Cingulate Gyrus	brain

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