Variant report

Variant	rs7250360
Chromosome Location	chr19:21718822-21718823
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 88 )
Associated
traits (count: 37 )

rSNPs within LD-proxies of this variant (count:72)

rs_ID	r²[population]
rs1055753	0.95[JPT][hapmap]
rs11085447	0.88[CHD][hapmap];0.95[JPT][hapmap]
rs11085456	0.84[AFR][1000 genomes];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs11666680	0.95[AMR][1000 genomes];0.90[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs11667770	0.94[JPT][hapmap]
rs11668682	0.82[AMR][1000 genomes]
rs12461802	0.81[AFR][1000 genomes];0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs12609768	0.84[AMR][1000 genomes];0.88[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs12610154	0.94[AMR][1000 genomes];0.90[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs12973084	0.84[AFR][1000 genomes];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12974329	0.91[AMR][1000 genomes];0.89[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12975081	0.95[JPT][hapmap]
rs12981564	0.95[JPT][hapmap]
rs12981735	0.89[JPT][hapmap]
rs12982282	0.95[JPT][hapmap]
rs12985995	0.81[AFR][1000 genomes];0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1401926	0.89[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];1.00[GIH][hapmap];0.95[JPT][hapmap];0.91[LWK][hapmap];0.96[MEX][hapmap];0.92[MKK][hapmap];0.98[TSI][hapmap];0.90[YRI][hapmap];0.89[AMR][1000 genomes];0.86[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs1813234	0.88[CHD][hapmap];0.82[JPT][hapmap]
rs1879237	0.89[AMR][1000 genomes];0.86[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs1879238	0.89[AMR][1000 genomes];0.86[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2012013	0.82[CHB][hapmap];0.88[CHD][hapmap];0.95[JPT][hapmap]
rs2088762	0.87[CHD][hapmap];0.95[JPT][hapmap]
rs2133822	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.96[AMR][1000 genomes];0.90[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2170024	0.95[JPT][hapmap]
rs2650793	0.82[JPT][hapmap]
rs2650805	0.82[JPT][hapmap]
rs2650845	0.85[CHD][hapmap]
rs28898308	0.96[AMR][1000 genomes];0.91[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2914638	0.88[CHD][hapmap];0.95[JPT][hapmap]
rs34040704	0.87[AMR][1000 genomes];0.86[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs34497957	0.96[AMR][1000 genomes];0.89[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs35782355	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4315457	0.88[CHD][hapmap];0.95[JPT][hapmap]
rs4462731	0.96[AMR][1000 genomes];0.91[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs4621113	0.83[CHB][hapmap];0.90[JPT][hapmap]
rs56346453	0.85[AMR][1000 genomes]
rs6511239	0.95[JPT][hapmap]
rs6511253	0.82[JPT][hapmap]
rs6511255	0.81[AFR][1000 genomes];0.96[AMR][1000 genomes];0.91[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs6511259	0.83[AMR][1000 genomes];0.88[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs7247411	0.88[CHD][hapmap];0.95[JPT][hapmap]
rs7248601	0.89[JPT][hapmap]
rs7249412	0.95[JPT][hapmap]
rs7249636	0.88[CHD][hapmap];0.82[JPT][hapmap]
rs7250838	0.84[EUR][1000 genomes]
rs7251540	0.84[AFR][1000 genomes];0.84[AMR][1000 genomes];0.90[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs7251669	0.83[AFR][1000 genomes];0.81[AMR][1000 genomes];0.84[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs7252254	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.96[AMR][1000 genomes];0.91[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7252261	0.88[CHD][hapmap];0.95[JPT][hapmap]
rs7253249	0.96[CEU][hapmap];1.00[CHB][hapmap];0.84[JPT][hapmap]
rs7253559	0.89[AMR][1000 genomes];0.86[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7256389	0.90[AMR][1000 genomes];0.89[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs7257186	0.81[AFR][1000 genomes];0.96[AMR][1000 genomes];0.91[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7257857	0.88[CHD][hapmap];0.80[GIH][hapmap];0.95[JPT][hapmap];0.83[MEX][hapmap]
rs7259311	0.95[JPT][hapmap]
rs7259317	0.83[AMR][1000 genomes];0.88[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs73017722	0.96[AMR][1000 genomes];0.91[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7508671	0.80[CHB][hapmap];0.89[JPT][hapmap]
rs8099940	0.95[JPT][hapmap]
rs8101089	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[YRI][hapmap];0.95[AMR][1000 genomes];0.90[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs8101900	0.95[AMR][1000 genomes];0.91[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs8103325	0.88[CHD][hapmap];0.95[JPT][hapmap]
rs8103459	0.94[JPT][hapmap]
rs8106840	0.95[AMR][1000 genomes];0.91[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs8109536	0.89[AMR][1000 genomes];0.85[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs8109940	0.96[CEU][hapmap];1.00[CHB][hapmap];0.90[JPT][hapmap]
rs8110459	0.85[EUR][1000 genomes]
rs8110814	0.96[CEU][hapmap];0.88[CHB][hapmap];1.00[CHD][hapmap];0.91[GIH][hapmap];1.00[JPT][hapmap];0.98[TSI][hapmap];0.84[AMR][1000 genomes];0.88[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs8110967	0.95[JPT][hapmap]
rs8111885	0.89[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs924487	0.94[CHB][hapmap];0.91[JPT][hapmap]
rs9789284	0.83[AFR][1000 genomes];0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.90[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:16 , 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	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
11	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
12	nsv1059328	chr19:21691123-21775948	Weak transcription Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats Genic enhancers Flanking Active TSS Strong transcription Enhancers Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
13	nsv543942	chr19:21711611-21767567	Strong transcription ZNF genes & repeats Weak transcription Active TSS Enhancers Flanking Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
14	nsv543943	chr19:21713945-21759080	Weak transcription Strong transcription ZNF genes & repeats Active TSS Flanking Active TSS Enhancers Bivalent/Poised TSS Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
15	nsv543944	chr19:21713945-21767567	ZNF genes & repeats Weak transcription Enhancers Strong transcription Active TSS Flanking Bivalent TSS/Enh Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
16	nsv543945	chr19:21717518-21767567	Weak transcription ZNF genes & repeats Active TSS Bivalent/Poised TSS Enhancers Transcr. at gene 5' and 3' Strong transcription Flanking Active TSS Flanking Bivalent TSS/Enh Genic enhancers Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases

mRNA abundance (count:37)

SNP	Gene	Cis/trans	Tissue	Source
rs7250360	CTD-2561J22.5	cis	Thyroid	GTEx
rs7250360	CTD-2561J22.5	cis	Nerve Tibial	GTEx
rs7250360	ZNF826P	cis	parietal	SCAN
rs7250360	ZNF93	cis	cerebellum	SCAN
rs7250360	RP11-678G14.2	cis	Whole Blood	GTEx
rs7250360	CTD-2561J22.5	cis	Skin Sun Exposed Lower leg	GTEx
rs7250360	RP11-420K14.2	cis	Whole Blood	GTEx
rs7250360	CTD-2561J22.5	cis	lung	GTEx
rs7250360	ZNF429	cis	Muscle Skeletal	GTEx
rs7250360	ZNF708	cis	cerebellum	SCAN
rs7250360	CTD-2626G11.2	cis	Skin Sun Exposed Lower leg	GTEx
rs7250360	RP11-678G14.2	cis	lung	GTEx
rs7250360	ZNF429	cis	Whole Blood	GTEx
rs7250360	RP11-678G14.2	cis	Muscle Skeletal	GTEx
rs7250360	ZNF493	cis	cerebellum	SCAN
rs7250360	RP11-420K14.2	cis	Heart Left Ventricle	GTEx
rs7250360	RP11-678G14.3	cis	lung	GTEx
rs7250360	ZNF208	cis	parietal	SCAN
rs7250360	ZNF100	cis	Muscle Skeletal	GTEx
rs7250360	RP11-678G14.2	cis	Skin Sun Exposed Lower leg	GTEx
rs7250360	ZNF708	cis	Skin Sun Exposed Lower leg	GTEx
rs7250360	ZNF429	cis	parietal	SCAN
rs7250360	CTD-2561J22.5	cis	Adipose Subcutaneous	GTEx
rs7250360	RP11-678G14.3	cis	Adipose Subcutaneous	GTEx
rs7250360	ZNF43	cis	parietal	SCAN
rs7250360	C19orf50	cis	cerebellum	SCAN
rs7250360	RP11-678G14.3	cis	Skin Sun Exposed Lower leg	GTEx
rs7250360	RP11-678G14.2	cis	Adipose Subcutaneous	GTEx
rs7250360	RP11-678G14.3	cis	Whole Blood	GTEx
rs7250360	ZNF738	Cis_1M	lymphoblastoid	RTeQTL
rs7250360	CTD-2561J22.5	cis	Artery Tibial	GTEx
rs7250360	RP11-420K14.1	cis	Muscle Skeletal	GTEx
rs7250360	ZNF486	cis	cerebellum	SCAN
rs7250360	ZNF493	Cis_1M	lymphoblastoid	RTeQTL
rs7250360	RP11-678G14.2	cis	Thyroid	GTEx
rs7250360	ZNF429	cis	cerebellum	SCAN
rs7250360	RP11-678G14.3	cis	Muscle Skeletal	GTEx

Chromatin state (count:95 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr19:21699600-21720800	ZNF genes & repeats	Monocytes-CD14+_RO01746	blood
2	chr19:21699600-21727600	ZNF genes & repeats	Liver	Liver
3	chr19:21701000-21733400	ZNF genes & repeats	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
4	chr19:21701600-21720400	ZNF genes & repeats	Primary hematopoietic stem cells	blood
5	chr19:21702400-21721400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
6	chr19:21707000-21719000	Weak transcription	Stomach Mucosa	stomach
7	chr19:21709000-21722800	ZNF genes & repeats	Primary hematopoietic stem cells G-CSF-mobilized Female	--
8	chr19:21711600-21720400	ZNF genes & repeats	Breast Myoepithelial Primary Cells	Breast
9	chr19:21712000-21719200	Strong transcription	Skeletal Muscle Female	skeletal muscle
10	chr19:21712400-21720400	ZNF genes & repeats	Fetal Adrenal Gland	Adrenal Gland
11	chr19:21712600-21720200	ZNF genes & repeats	Pancreatic Islets	Pancreatic Islet
12	chr19:21713400-21719600	Strong transcription	Ovary	ovary
13	chr19:21713400-21720200	ZNF genes & repeats	Fetal Intestine Large	intestine
14	chr19:21713400-21720400	Strong transcription	Skeletal Muscle Male	skeletal muscle
15	chr19:21713400-21720800	ZNF genes & repeats	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
16	chr19:21713400-21720800	Strong transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
17	chr19:21713400-21721800	ZNF genes & repeats	Primary hematopoietic stem cells G-CSF-mobilized Male	--
18	chr19:21713400-21722000	ZNF genes & repeats	iPS-20b Cell Line	embryonic stem cell
19	chr19:21713400-21722800	ZNF genes & repeats	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
20	chr19:21714200-21721200	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
21	chr19:21714400-21719000	Weak transcription	Rectal Smooth Muscle	rectum
22	chr19:21714600-21723000	ZNF genes & repeats	HUES64 Cell Line	embryonic stem cell
23	chr19:21715200-21720600	ZNF genes & repeats	Fetal Lung	lung
24	chr19:21715200-21728600	ZNF genes & repeats	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
25	chr19:21715800-21719400	Weak transcription	Right Ventricle	heart
26	chr19:21715800-21720800	ZNF genes & repeats	Primary hematopoietic stem cells short term culture	blood
27	chr19:21716200-21720400	ZNF genes & repeats	Dnd41	blood
28	chr19:21716200-21722600	ZNF genes & repeats	Ganglion Eminence derived primary cultured neurospheres	brain
29	chr19:21716400-21720000	ZNF genes & repeats	Fetal Muscle Leg	muscle
30	chr19:21716400-21720600	ZNF genes & repeats	Cortex derived primary cultured neurospheres	brain
31	chr19:21716400-21720600	ZNF genes & repeats	Duodenum Mucosa	Duodenum
32	chr19:21716600-21720400	ZNF genes & repeats	Primary B cells from peripheral blood	blood
33	chr19:21716600-21720800	ZNF genes & repeats	Primary neutrophils fromperipheralblood	blood
34	chr19:21716800-21721000	ZNF genes & repeats	H1 Cell Line	embryonic stem cell
35	chr19:21717000-21720400	ZNF genes & repeats	Rectal Mucosa Donor 29	rectum
36	chr19:21717200-21720000	ZNF genes & repeats	Foreskin Keratinocyte Primary Cells skin03	Skin
37	chr19:21717200-21720200	ZNF genes & repeats	Primary T cells from cord blood	blood
38	chr19:21717200-21720400	ZNF genes & repeats	Primary T helper naive cells fromperipheralblood	blood
39	chr19:21717200-21720400	ZNF genes & repeats	Fetal Kidney	kidney
40	chr19:21717200-21720600	ZNF genes & repeats	IMR90 fetal lung fibroblasts Cell Line	lung
41	chr19:21717200-21720600	ZNF genes & repeats	Primary T cells fromperipheralblood	blood
42	chr19:21717400-21720600	ZNF genes & repeats	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
43	chr19:21717400-21720600	ZNF genes & repeats	Brain Germinal Matrix	brain
44	chr19:21717600-21719000	Weak transcription	Brain Angular Gyrus	brain
45	chr19:21717600-21719000	Weak transcription	Brain Cingulate Gyrus	brain
46	chr19:21717600-21719000	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
47	chr19:21717600-21719200	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
48	chr19:21718200-21720400	ZNF genes & repeats	Left Ventricle	heart
49	chr19:21718400-21719200	ZNF genes & repeats	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
50	chr19:21718400-21719200	ZNF genes & repeats	Aorta	Aorta

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