Variant report

Variant	rs7258901
Chromosome Location	chr19:21701504-21701505
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 137 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:124)

rs_ID	r²[population]
rs1012040	0.84[EUR][1000 genomes]
rs1021722	0.80[AMR][1000 genomes];0.96[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs10404462	0.82[AMR][1000 genomes];0.96[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs10406824	0.82[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs10406870	0.91[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs10411757	0.80[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs10412139	0.80[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs10412656	0.83[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs10414373	0.82[AMR][1000 genomes];0.96[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs10420166	0.82[AMR][1000 genomes];0.95[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs10423403	0.80[AMR][1000 genomes];0.96[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs11085455	0.96[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs12974329	0.84[AFR][1000 genomes]
rs1500400	0.82[AMR][1000 genomes];0.96[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs1500401	0.80[AMR][1000 genomes];0.96[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs1520071	0.80[AMR][1000 genomes];0.96[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs1520072	0.82[AMR][1000 genomes];0.96[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs1520073	0.82[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs1566474	0.83[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs1566476	0.83[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs1566477	0.83[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs1607664	0.82[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs16997924	0.83[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs1879235	0.82[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs1963056	0.82[AMR][1000 genomes];0.96[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs1984771	0.82[AMR][1000 genomes];0.96[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2056319	0.80[AMR][1000 genomes];0.96[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2062564	0.82[AMR][1000 genomes];0.96[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2090707	0.80[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs2133816	0.80[AMR][1000 genomes];0.96[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2133820	0.82[AMR][1000 genomes];0.96[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2133821	0.82[AMR][1000 genomes];0.96[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2173723	0.82[AMR][1000 genomes];0.96[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2173724	0.80[AMR][1000 genomes];0.96[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2246914	0.80[AMR][1000 genomes];0.96[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2262897	0.83[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs2359162	0.82[AMR][1000 genomes];0.96[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2454919	0.82[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs2562399	0.82[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs2562419	0.83[AMR][1000 genomes];0.93[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2562441	0.82[AMR][1000 genomes];0.96[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2562448	0.82[AMR][1000 genomes];0.96[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2562451	0.83[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs2562452	0.83[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs2562453	0.83[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs2562454	0.83[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs2562455	0.83[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs2562457	0.83[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs2562458	0.83[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs2562459	0.83[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs2562465	0.89[EUR][1000 genomes]
rs2562472	0.80[AMR][1000 genomes];0.95[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2562473	0.80[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs2562496	0.93[AMR][1000 genomes]
rs2650757	0.82[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs2650759	0.96[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2650760	0.80[AMR][1000 genomes];0.96[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2650778	0.83[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs2650779	0.83[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs2650780	0.83[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs2650781	0.83[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs2650782	0.83[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs2650783	0.83[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs2650785	0.83[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs2650786	0.83[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs2650787	0.83[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs2650788	0.80[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs2650791	0.82[AMR][1000 genomes];0.96[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2650794	0.80[AMR][1000 genomes];0.96[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2650799	0.80[AMR][1000 genomes];0.96[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2650806	0.82[AMR][1000 genomes];0.96[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2650807	0.82[AMR][1000 genomes];0.96[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2650808	0.83[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs2650827	0.80[AMR][1000 genomes];0.96[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2650829	0.82[AMR][1000 genomes];0.96[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2650830	0.95[EUR][1000 genomes]
rs2650834	0.80[AMR][1000 genomes];0.96[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2650835	0.82[AMR][1000 genomes];0.96[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2681365	0.80[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs2681366	0.82[AMR][1000 genomes];0.96[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2681368	0.80[AMR][1000 genomes];0.96[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2681371	0.80[AMR][1000 genomes];0.96[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2681372	0.80[AMR][1000 genomes];0.96[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2681375	0.82[AMR][1000 genomes];0.95[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2681380	0.80[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs2681382	0.82[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs2681383	0.82[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs2681384	0.80[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs2681390	0.80[AMR][1000 genomes];0.95[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2968081	0.83[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs34006898	0.96[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs34978316	0.88[EUR][1000 genomes]
rs35088652	0.96[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs35230828	0.86[AMR][1000 genomes];0.81[ASN][1000 genomes]
rs35245030	0.83[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs35366148	0.89[EUR][1000 genomes]
rs35506714	0.80[AMR][1000 genomes]
rs35991360	0.83[EUR][1000 genomes]
rs4332859	0.82[EUR][1000 genomes]
rs4462731	0.82[AFR][1000 genomes]
rs4574048	0.92[AMR][1000 genomes]
rs4611587	1.00[AMR][1000 genomes];0.81[ASN][1000 genomes]
rs58818104	0.89[EUR][1000 genomes]
rs59654184	0.95[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs62108277	0.83[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs62108331	0.96[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs62108332	0.86[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs62108335	0.84[EUR][1000 genomes]
rs6511255	0.84[AFR][1000 genomes]
rs6511261	0.96[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs7248097	0.92[AMR][1000 genomes];0.81[ASN][1000 genomes]
rs7254872	0.95[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs7257186	0.84[AFR][1000 genomes]
rs74167858	0.85[EUR][1000 genomes]
rs7507813	0.85[ASN][1000 genomes]
rs8100193	0.96[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs8100318	0.82[AMR][1000 genomes];0.96[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs8101900	0.83[AFR][1000 genomes]
rs8102699	0.91[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs8102854	0.96[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs8106433	0.96[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs8106840	0.82[AFR][1000 genomes]
rs8111788	0.96[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs8113259	0.82[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:13 , 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	esv3369003	chr19:21701297-21701726	ZNF genes & repeats Strong transcription Weak transcription	n/a	n/a	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs7258901	ZNF493	Cis_1M	lymphoblastoid	RTeQTL
rs7258901	ZNF738	Cis_1M	lymphoblastoid	RTeQTL
rs7258901	ZNF429	cis	Whole Blood	GTEx

Chromatin state (count:85 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr19:21689200-21702000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
2	chr19:21689200-21702000	Weak transcription	Stomach Mucosa	stomach
3	chr19:21689400-21701600	Weak transcription	Brain Substantia Nigra	brain
4	chr19:21689400-21701600	Weak transcription	Placenta Amnion	Placenta Amnion
5	chr19:21689400-21702000	Weak transcription	Left Ventricle	heart
6	chr19:21689400-21702000	Weak transcription	Right Ventricle	heart
7	chr19:21689600-21701600	Weak transcription	Skeletal Muscle Male	skeletal muscle
8	chr19:21689600-21702000	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
9	chr19:21690000-21701600	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
10	chr19:21690000-21701600	Weak transcription	Osteobl	bone
11	chr19:21690200-21701600	Weak transcription	Duodenum Smooth Muscle	Duodenum
12	chr19:21690200-21701600	Weak transcription	Stomach Smooth Muscle	stomach
13	chr19:21690600-21701600	Weak transcription	Primary T killer memory cells from peripheral blood	blood
14	chr19:21690600-21701600	Weak transcription	Skeletal Muscle Female	skeletal muscle
15	chr19:21691200-21701600	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
16	chr19:21691200-21702000	Weak transcription	Colon Smooth Muscle	Colon
17	chr19:21691400-21701600	Weak transcription	Brain Cingulate Gyrus	brain
18	chr19:21691400-21702000	Weak transcription	Ovary	ovary
19	chr19:21692400-21701600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
20	chr19:21695200-21702000	Weak transcription	Spleen	Spleen
21	chr19:21695400-21701600	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
22	chr19:21696800-21701600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
23	chr19:21696800-21702000	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
24	chr19:21697000-21702000	Weak transcription	Brain Inferior Temporal Lobe	brain
25	chr19:21698000-21702000	Weak transcription	Psoas Muscle	Psoas
26	chr19:21698400-21710800	ZNF genes & repeats	Primary hematopoietic stem cells G-CSF-mobilized Male	--
27	chr19:21698800-21701600	Weak transcription	Fetal Kidney	kidney
28	chr19:21699400-21705400	ZNF genes & repeats	Dnd41	blood
29	chr19:21699600-21707600	ZNF genes & repeats	Brain Germinal Matrix	brain
30	chr19:21699600-21720800	ZNF genes & repeats	Monocytes-CD14+_RO01746	blood
31	chr19:21699600-21727600	ZNF genes & repeats	Liver	Liver
32	chr19:21700000-21701600	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
33	chr19:21700200-21701600	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
34	chr19:21700600-21707800	ZNF genes & repeats	Primary neutrophils fromperipheralblood	blood
35	chr19:21700600-21707800	ZNF genes & repeats	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
36	chr19:21700800-21701600	Weak transcription	HSMM	muscle
37	chr19:21700800-21702000	Weak transcription	Brain Angular Gyrus	brain
38	chr19:21700800-21702000	Weak transcription	NH-A	brain
39	chr19:21700800-21702400	ZNF genes & repeats	iPS-15b Cell Line	embryonic stem cell
40	chr19:21700800-21703400	ZNF genes & repeats	Ganglion Eminence derived primary cultured neurospheres	brain
41	chr19:21700800-21704000	ZNF genes & repeats	H1 Cell Line	embryonic stem cell
42	chr19:21700800-21704400	ZNF genes & repeats	Primary T cells from cord blood	blood
43	chr19:21700800-21705400	ZNF genes & repeats	HUES64 Cell Line	embryonic stem cell
44	chr19:21700800-21706600	ZNF genes & repeats	Primary B cells from cord blood	blood
45	chr19:21700800-21706800	ZNF genes & repeats	Primary T regulatory cells fromperipheralblood	blood
46	chr19:21700800-21707200	ZNF genes & repeats	Cortex derived primary cultured neurospheres	brain
47	chr19:21700800-21711000	ZNF genes & repeats	Pancreatic Islets	Pancreatic Islet
48	chr19:21701000-21703000	ZNF genes & repeats	Fetal Brain Male	brain
49	chr19:21701000-21703200	ZNF genes & repeats	Primary hematopoietic stem cells short term culture	blood
50	chr19:21701000-21703200	ZNF genes & repeats	Fetal Intestine Large	intestine

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