Variant report

Variant	rs12972601
Chromosome Location	chr19:21491317-21491318
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 117 )
Associated
traits (count: 27 )

rSNPs within LD-proxies of this variant (count:107)

rs_ID	r²[population]
rs10854043	0.88[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs11085441	0.92[EUR][1000 genomes]
rs11085443	0.85[ASN][1000 genomes]
rs11085447	0.80[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs1142653	0.80[AMR][1000 genomes];0.88[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs11669588	0.82[AMR][1000 genomes];0.91[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs11882553	0.82[AFR][1000 genomes];0.86[AMR][1000 genomes];0.89[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs12459702	0.85[AFR][1000 genomes];0.88[AMR][1000 genomes];0.94[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs12461384	0.83[AMR][1000 genomes];0.92[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs12462022	0.94[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs12610331	0.85[AFR][1000 genomes];0.87[AMR][1000 genomes];0.93[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs12971736	0.86[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs12972339	0.85[AFR][1000 genomes];0.89[AMR][1000 genomes];0.94[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs12972580	0.80[AMR][1000 genomes];0.86[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs12974735	0.87[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs12975081	0.80[AMR][1000 genomes];0.88[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs12975464	0.88[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs12978116	0.82[AMR][1000 genomes];0.91[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs12980097	0.84[AFR][1000 genomes];0.83[AMR][1000 genomes];0.94[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs12981564	0.80[AMR][1000 genomes];0.88[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs12981735	0.80[AMR][1000 genomes];0.88[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs12981775	0.80[AMR][1000 genomes];0.88[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs12981777	0.82[AMR][1000 genomes];0.91[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs12982162	0.80[AMR][1000 genomes];0.88[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs12982282	0.80[AMR][1000 genomes];0.88[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs12982346	0.86[AFR][1000 genomes];0.89[AMR][1000 genomes];0.94[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs12983426	0.82[AMR][1000 genomes];0.91[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs12984300	0.87[AMR][1000 genomes];0.94[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs12984871	0.80[AMR][1000 genomes];0.85[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs1781863	0.81[ASN][1000 genomes]
rs1781873	0.93[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs1813234	0.82[ASN][1000 genomes]
rs1932088	0.81[AMR][1000 genomes];0.91[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs1963531	0.87[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs1963532	0.85[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2012013	0.80[AMR][1000 genomes];0.88[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2012038	0.80[AMR][1000 genomes];0.88[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2061917	0.88[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs2061918	0.87[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2061919	0.88[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2086317	0.80[AMR][1000 genomes];0.88[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2086318	0.80[AMR][1000 genomes];0.87[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2086320	0.84[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs2088762	0.80[AMR][1000 genomes];0.84[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2102072	0.84[EUR][1000 genomes]
rs2127404	0.80[AMR][1000 genomes];0.86[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2127405	0.80[AMR][1000 genomes];0.86[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2127406	0.80[AMR][1000 genomes];0.86[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2127407	0.80[AMR][1000 genomes];0.85[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2127408	0.80[AMR][1000 genomes];0.85[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2170024	0.84[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs2170025	0.85[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs2219840	0.80[AMR][1000 genomes];0.88[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2358982	0.80[AMR][1000 genomes];0.88[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2358983	0.80[AMR][1000 genomes];0.88[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2358985	0.80[AMR][1000 genomes];0.88[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2358986	0.80[AMR][1000 genomes];0.86[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2358988	0.80[AMR][1000 genomes];0.86[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2358989	0.85[EUR][1000 genomes]
rs2358990	0.80[AMR][1000 genomes];0.86[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2358991	0.85[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs2358992	0.85[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs2434997	0.85[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs28688205	0.93[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs2884601	0.80[AMR][1000 genomes];0.88[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2914638	0.88[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs2968025	0.82[EUR][1000 genomes]
rs35580411	0.83[AFR][1000 genomes];0.89[AMR][1000 genomes];0.94[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4315457	0.80[AMR][1000 genomes];0.88[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs4398213	0.82[ASN][1000 genomes]
rs4430876	0.80[ASN][1000 genomes]
rs4438422	0.80[AMR][1000 genomes];0.88[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs4525621	0.81[EUR][1000 genomes]
rs4566304	0.80[AMR][1000 genomes];0.88[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs6511222	0.85[AFR][1000 genomes];0.87[AMR][1000 genomes];0.94[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs6511229	0.80[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs6511231	0.80[AMR][1000 genomes];0.86[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs6511232	0.80[AMR][1000 genomes];0.86[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs6511233	0.83[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs7245920	0.80[AMR][1000 genomes];0.86[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs7247411	0.85[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs7252261	0.80[AMR][1000 genomes];0.88[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs7253178	0.81[AMR][1000 genomes];0.91[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs7256361	0.84[AFR][1000 genomes];0.82[AMR][1000 genomes];0.92[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs7257580	0.80[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs7257857	0.80[ASN][1000 genomes]
rs7258335	0.80[AMR][1000 genomes];0.86[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs7260369	0.86[AFR][1000 genomes];0.83[AMR][1000 genomes];0.94[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs7508030	0.87[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs7508044	0.83[EUR][1000 genomes]
rs7508045	0.83[EUR][1000 genomes]
rs7508072	0.81[EUR][1000 genomes]
rs7508087	0.83[EUR][1000 genomes]
rs7508092	0.81[AMR][1000 genomes];0.87[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs7508104	0.85[EUR][1000 genomes]
rs7508671	0.80[AMR][1000 genomes];0.87[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs8099940	0.80[AMR][1000 genomes];0.85[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs8103325	0.80[AMR][1000 genomes];0.86[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs8103459	0.80[AMR][1000 genomes];0.86[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs8103908	0.80[AMR][1000 genomes];0.86[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs8104017	0.80[AMR][1000 genomes];0.88[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs8106936	0.80[ASN][1000 genomes]
rs8110690	0.85[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs8110842	0.87[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs8110967	0.80[AMR][1000 genomes];0.88[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs8112059	0.83[AMR][1000 genomes];0.91[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs8112583	0.80[AMR][1000 genomes];0.85[EUR][1000 genomes];0.82[ASN][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	esv3385528	chr19:21030777-21495566	Active TSS Weak transcription Strong transcription ZNF genes & repeats Flanking Active TSS Genic enhancers Enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	32 gene(s)	inside rSNPs	diseases
2	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
3	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
4	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
5	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
6	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
7	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
8	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
9	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
10	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

mRNA abundance (count:27)

SNP	Gene	Cis/trans	Tissue	Source
rs12972601	RP11-678G14.2	cis	Artery Tibial	GTEx
rs12972601	ZNF493	Cis_1M	lymphoblastoid	RTeQTL
rs12972601	RP11-678G14.3	cis	Whole Blood	GTEx
rs12972601	RP11-420K14.2	cis	Heart Left Ventricle	GTEx
rs12972601	ZNF429	cis	Muscle Skeletal	GTEx
rs12972601	RP11-678G14.3	cis	lung	GTEx
rs12972601	RP11-678G14.2	cis	Muscle Skeletal	GTEx
rs12972601	CTD-2561J22.5	cis	Stomach	GTEx
rs12972601	CTD-2561J22.5	cis	Artery Tibial	GTEx
rs12972601	CTD-2561J22.5	cis	Adipose Subcutaneous	GTEx
rs12972601	CTD-2561J22.5	cis	Esophagus Muscularis	GTEx
rs12972601	LINC00664	cis	Adipose Subcutaneous	GTEx
rs12972601	RP11-678G14.3	cis	Skin Sun Exposed Lower leg	GTEx
rs12972601	ZNF738	Cis_1M	lymphoblastoid	RTeQTL
rs12972601	CTD-2561J22.5	cis	Thyroid	GTEx
rs12972601	ZNF708	cis	Skin Sun Exposed Lower leg	GTEx
rs12972601	RP11-678G14.2	cis	Thyroid	GTEx
rs12972601	RP11-678G14.3	cis	Adipose Subcutaneous	GTEx
rs12972601	RP11-678G14.2	cis	Whole Blood	GTEx
rs12972601	RP11-678G14.2	cis	lung	GTEx
rs12972601	RP11-678G14.2	cis	Adipose Subcutaneous	GTEx
rs12972601	ZNF429	cis	Whole Blood	GTEx
rs12972601	RP11-678G14.2	cis	Skin Sun Exposed Lower leg	GTEx
rs12972601	RP11-678G14.3	cis	Muscle Skeletal	GTEx
rs12972601	CTD-2561J22.5	cis	Nerve Tibial	GTEx
rs12972601	CTD-2561J22.5	cis	Skin Sun Exposed Lower leg	GTEx
rs12972601	CTD-2561J22.5	cis	lung	GTEx

Chromatin state (count:122 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr19:21465000-21496000	ZNF genes & repeats	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
2	chr19:21473800-21510400	Weak transcription	Fetal Heart	heart
3	chr19:21474400-21492400	ZNF genes & repeats	Primary hematopoietic stem cells G-CSF-mobilized Female	--
4	chr19:21474800-21509800	Weak transcription	Fetal Brain Male	brain
5	chr19:21475200-21511200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
6	chr19:21476800-21497600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
7	chr19:21477000-21494400	Weak transcription	Stomach Mucosa	stomach
8	chr19:21477200-21495000	Weak transcription	Brain Cingulate Gyrus	brain
9	chr19:21477600-21495800	Weak transcription	HepG2	liver
10	chr19:21478000-21497400	Weak transcription	Colon Smooth Muscle	Colon
11	chr19:21478200-21492600	Strong transcription	Primary T helper naive cells fromperipheralblood	blood
12	chr19:21478400-21500600	Weak transcription	Psoas Muscle	Psoas
13	chr19:21478600-21499200	Weak transcription	HMEC	breast
14	chr19:21481000-21500600	Weak transcription	NHLF	lung
15	chr19:21481200-21493000	Strong transcription	Primary T helper naive cells from peripheral blood	blood
16	chr19:21481600-21500000	Weak transcription	Skeletal Muscle Female	skeletal muscle
17	chr19:21481600-21500400	Weak transcription	iPS-15b Cell Line	embryonic stem cell
18	chr19:21481600-21505600	Weak transcription	K562	blood
19	chr19:21481800-21492600	Strong transcription	Fetal Muscle Leg	muscle
20	chr19:21481800-21493000	Strong transcription	Dnd41	blood
21	chr19:21481800-21493400	Strong transcription	Fetal Stomach	stomach
22	chr19:21482000-21492400	Strong transcription	Cortex derived primary cultured neurospheres	brain
23	chr19:21482000-21493200	Strong transcription	Fetal Muscle Trunk	muscle
24	chr19:21482000-21493800	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
25	chr19:21482400-21492800	Strong transcription	HUES64 Cell Line	embryonic stem cell
26	chr19:21483200-21492800	Strong transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
27	chr19:21483600-21493000	Strong transcription	Primary B cells from peripheral blood	blood
28	chr19:21484000-21492200	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
29	chr19:21484200-21492200	Weak transcription	Rectal Smooth Muscle	rectum
30	chr19:21484200-21494200	Strong transcription	Primary T helper cells fromperipheralblood	blood
31	chr19:21484400-21493200	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
32	chr19:21484400-21511000	Weak transcription	H9 Cell Line	embryonic stem cell
33	chr19:21484600-21492400	Strong transcription	Fetal Intestine Large	intestine
34	chr19:21484800-21491400	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
35	chr19:21484800-21492000	Weak transcription	Brain Hippocampus Middle	brain
36	chr19:21485000-21493000	Strong transcription	Primary T cells fromperipheralblood	blood
37	chr19:21485200-21494000	Weak transcription	NHDF-Ad	bronchial
38	chr19:21485200-21495000	Weak transcription	Brain Inferior Temporal Lobe	brain
39	chr19:21485400-21508600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
40	chr19:21485400-21511200	Weak transcription	Gastric	stomach
41	chr19:21485600-21497600	Weak transcription	Placenta Amnion	Placenta Amnion
42	chr19:21485600-21504200	Weak transcription	Pancreas	Pancrea
43	chr19:21486200-21492000	Weak transcription	Colonic Mucosa	Colon
44	chr19:21486200-21493000	Strong transcription	Duodenum Mucosa	Duodenum
45	chr19:21486400-21492000	Weak transcription	Brain Germinal Matrix	brain
46	chr19:21486400-21500400	Weak transcription	Spleen	Spleen
47	chr19:21487000-21492400	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
48	chr19:21487000-21492400	Strong transcription	Thymus	Thymus
49	chr19:21487200-21492600	Strong transcription	Sigmoid Colon	Sigmoid Colon
50	chr19:21487400-21492000	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived

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