Variant report

Variant	rs60297398
Chromosome Location	chr19:37159442-37159443
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	MAX	chr19:37159071-37159446	K562	blood:	n/a	chr19:37159316-37159327 chr19:37159316-37159326 chr19:37159288-37159304 chr19:37159193-37159202 chr19:37159318-37159325 chr19:37159317-37159326

No.	Distal block	Cell Line	Cell type
1	chr19:37129696..37132146-chr19:37158432..37159959,2	K562	blood:
2	chr19:37158057..37159719-chr19:37162849..37165565,2	MCF-7	breast:
3	chr19:37157483..37161085-chr19:37175435..37180024,4	MCF-7	breast:

Variant related genes	Relation type
ZNF461	TF binding region
ENSG00000225975	Chromatin interaction
ENSG00000189042	Chromatin interaction
ENSG00000197808	Chromatin interaction

Extended variants
information (count: 92 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:77)

rs_ID	r²[population]
rs1035777	0.95[AMR][1000 genomes];0.92[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs10402182	0.80[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs10403456	0.80[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs10407919	0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11084861	0.94[ASN][1000 genomes]
rs11666769	0.87[ASN][1000 genomes]
rs11667894	0.98[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11668432	0.90[ASN][1000 genomes]
rs11668689	0.99[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11669816	0.95[ASN][1000 genomes]
rs11670914	0.93[AMR][1000 genomes];0.90[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs11671382	0.93[AMR][1000 genomes];0.93[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11672098	0.93[AMR][1000 genomes];0.90[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs12608459	0.99[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12608512	0.92[ASN][1000 genomes]
rs12610555	0.89[ASN][1000 genomes]
rs12610572	0.93[AMR][1000 genomes];0.90[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1357879	0.91[AMR][1000 genomes];0.89[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs1464830	0.94[AMR][1000 genomes];0.93[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1464831	0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1525133	0.93[AMR][1000 genomes];0.90[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1673082	0.86[ASN][1000 genomes]
rs17272386	0.93[AMR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1985980	0.91[AMR][1000 genomes];0.90[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2052728	0.89[AMR][1000 genomes];0.91[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2162296	0.90[ASN][1000 genomes]
rs2194976	0.89[AMR][1000 genomes];0.91[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2912399	0.88[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2912400	0.84[ASN][1000 genomes]
rs2912404	0.81[ASN][1000 genomes]
rs2912408	0.87[ASN][1000 genomes]
rs2912412	0.89[AMR][1000 genomes];0.92[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2912440	0.83[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2912442	0.85[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2912443	0.89[ASN][1000 genomes]
rs2912444	0.88[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2912446	0.87[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2945964	0.85[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2967427	0.91[AMR][1000 genomes];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2967429	0.90[ASN][1000 genomes]
rs2967436	0.83[ASN][1000 genomes]
rs2967437	0.91[AMR][1000 genomes];0.90[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2967438	0.87[ASN][1000 genomes]
rs2967439	0.87[AMR][1000 genomes];0.90[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2967440	0.87[AMR][1000 genomes];0.90[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2967442	0.85[AMR][1000 genomes];0.92[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2967459	0.95[AMR][1000 genomes];0.93[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2967461	0.87[ASN][1000 genomes]
rs2967463	0.86[ASN][1000 genomes]
rs2967464	0.85[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs3096620	0.89[AMR][1000 genomes];0.92[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs3096637	0.85[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs3108593	0.91[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs3108605	0.93[AMR][1000 genomes];0.93[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs35299345	0.90[ASN][1000 genomes]
rs4806338	0.80[AMR][1000 genomes];0.99[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4806339	0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4806348	0.87[AMR][1000 genomes];0.85[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs4806349	0.93[AMR][1000 genomes];0.90[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs55940011	0.87[AMR][1000 genomes];0.89[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs55965207	0.86[AMR][1000 genomes];0.87[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs60213885	0.93[AMR][1000 genomes];0.90[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs61457535	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs61628442	0.87[ASN][1000 genomes]
rs6510551	0.87[AMR][1000 genomes];0.88[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs66717711	0.93[AMR][1000 genomes];0.90[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs66783290	0.95[ASN][1000 genomes]
rs67258954	0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs67995015	0.85[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs68012004	0.99[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7246216	0.80[AMR][1000 genomes];0.99[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7251805	0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs73609113	0.92[AMR][1000 genomes];0.90[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7507224	0.94[ASN][1000 genomes]
rs8100381	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs8108985	0.93[AMR][1000 genomes];0.90[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs826987	0.84[AMR][1000 genomes];0.89[EUR][1000 genomes];0.91[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:15 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1064851	chr19:36910259-37689721	Weak transcription ZNF genes & repeats Flanking Active TSS Strong transcription Enhancers Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	62 gene(s)	inside rSNPs	diseases
2	nsv1065698	chr19:36916796-37690124	Active TSS ZNF genes & repeats Weak transcription Strong transcription Enhancers Flanking Active TSS Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	61 gene(s)	inside rSNPs	diseases
3	nsv543999	chr19:36916796-37690124	Flanking Active TSS Active TSS Weak transcription ZNF genes & repeats Strong transcription Enhancers Genic 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	61 gene(s)	inside rSNPs	diseases
4	nsv529817	chr19:36930549-37654062	ZNF genes & repeats Weak transcription Enhancers Flanking Active TSS Active TSS Strong transcription Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS Genic enhancers Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	60 gene(s)	inside rSNPs	diseases
5	nsv833817	chr19:36978852-37195695	ZNF genes & repeats Weak transcription Active TSS Strong transcription Flanking Active TSS Enhancers 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	40 gene(s)	inside rSNPs	diseases
6	nsv918028	chr19:37020645-38014526	Weak transcription ZNF genes & repeats Active TSS Enhancers Flanking Active TSS Strong transcription Genic 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	73 gene(s)	inside rSNPs	diseases
7	esv3492171	chr19:37122012-37190210	Weak transcription Active TSS Bivalent/Poised TSS Strong transcription ZNF genes & repeats Flanking Active TSS Enhancers Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	20 gene(s)	inside rSNPs	n/a
8	esv3492172	chr19:37122562-37190060	Weak transcription ZNF genes & repeats Transcr. at gene 5' and 3' Strong transcription Active TSS Enhancers Flanking Active TSS Genic enhancers Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	20 gene(s)	inside rSNPs	n/a
9	esv3492173	chr19:37122562-37190060	Flanking Active TSS ZNF genes & repeats Strong transcription Transcr. at gene 5' and 3' Weak transcription Active TSS Enhancers Bivalent/Poised TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	20 gene(s)	inside rSNPs	n/a
10	nsv469794	chr19:37129858-37310257	Weak transcription Flanking Active TSS Strong transcription Active TSS ZNF genes & repeats Enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Genic enhancers Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	27 gene(s)	inside rSNPs	diseases
11	nsv482392	chr19:37129858-37310257	ZNF genes & repeats Weak transcription Strong transcription Active TSS Flanking Active TSS Enhancers Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	27 gene(s)	inside rSNPs	diseases
12	esv3420176	chr19:37130161-37207917	ZNF genes & repeats Genic enhancers Weak transcription Strong transcription Enhancers Flanking Active TSS Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	19 gene(s)	inside rSNPs	n/a
13	nsv1061250	chr19:37134068-37188771	ZNF genes & repeats Flanking Active TSS Weak transcription 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	18 gene(s)	inside rSNPs	n/a
14	esv34384	chr19:37134068-37330613	Strong transcription Weak transcription ZNF genes & repeats Enhancers Flanking Active TSS Active TSS Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	29 gene(s)	inside rSNPs	diseases
15	nsv817833	chr19:37146694-37357289	ZNF genes & repeats Weak transcription Enhancers Flanking Active TSS Strong transcription Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	33 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs60297398	ZNF567	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:100 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr19:37156600-37159600	Active TSS	Rectal Smooth Muscle	rectum
2	chr19:37156600-37160200	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
3	chr19:37156800-37159600	Active TSS	iPS-15b Cell Line	embryonic stem cell
4	chr19:37157000-37159600	Active TSS	Colonic Mucosa	Colon
5	chr19:37157400-37159800	ZNF genes & repeats	Fetal Brain Male	brain
6	chr19:37158400-37169000	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
7	chr19:37158600-37159600	Enhancers	Primary B cells from cord blood	blood
8	chr19:37158600-37159600	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
9	chr19:37158600-37159600	Enhancers	Gastric	stomach
10	chr19:37158600-37159600	Enhancers	Lung	lung
11	chr19:37158600-37159600	Enhancers	Spleen	Spleen
12	chr19:37158600-37159800	Enhancers	Primary B cells from peripheral blood	blood
13	chr19:37158600-37159800	Enhancers	Primary T cells fromperipheralblood	blood
14	chr19:37158600-37159800	Enhancers	Primary T helper naive cells fromperipheralblood	blood
15	chr19:37158600-37159800	Enhancers	Thymus	Thymus
16	chr19:37158600-37160000	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
17	chr19:37158600-37160200	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
18	chr19:37158600-37160200	Weak transcription	Primary T helper naive cells from peripheral blood	blood
19	chr19:37158600-37162000	Weak transcription	Rectal Mucosa Donor 31	rectum
20	chr19:37158600-37162800	Weak transcription	Brain Angular Gyrus	brain
21	chr19:37158600-37167400	Weak transcription	Muscle Satellite Cultured Cells	--
22	chr19:37158600-37167400	Weak transcription	Psoas Muscle	Psoas
23	chr19:37158600-37168800	Weak transcription	HUES48 Cell Line	embryonic stem cell
24	chr19:37158600-37168800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
25	chr19:37158600-37169000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
26	chr19:37158600-37169000	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
27	chr19:37158600-37169000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
28	chr19:37158600-37172800	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
29	chr19:37158600-37177200	Weak transcription	Fetal Kidney	kidney
30	chr19:37158600-37177400	Weak transcription	Placenta Amnion	Placenta Amnion
31	chr19:37158600-37177400	Weak transcription	NHDF-Ad	bronchial
32	chr19:37158600-37177800	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
33	chr19:37158800-37159600	Enhancers	Primary T regulatory cells fromperipheralblood	blood
34	chr19:37158800-37159600	ZNF genes & repeats	Fetal Adrenal Gland	Adrenal Gland
35	chr19:37158800-37159600	Enhancers	Fetal Heart	heart
36	chr19:37158800-37159800	ZNF genes & repeats	Foreskin Fibroblast Primary Cells skin01	Skin
37	chr19:37158800-37159800	ZNF genes & repeats	Brain Germinal Matrix	brain
38	chr19:37158800-37159800	ZNF genes & repeats	Skeletal Muscle Male	skeletal muscle
39	chr19:37158800-37160000	ZNF genes & repeats	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
40	chr19:37158800-37160200	Flanking Active TSS	Dnd41	blood
41	chr19:37158800-37166000	ZNF genes & repeats	Breast Myoepithelial Primary Cells	Breast
42	chr19:37159000-37159600	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
43	chr19:37159000-37159600	Enhancers	Primary T killer memory cells from peripheral blood	blood
44	chr19:37159000-37159600	ZNF genes & repeats	Fetal Muscle Trunk	muscle
45	chr19:37159000-37159600	ZNF genes & repeats	Fetal Stomach	stomach
46	chr19:37159000-37159600	Enhancers	Pancreas	Pancrea
47	chr19:37159000-37159800	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
48	chr19:37159000-37159800	Enhancers	Cortex derived primary cultured neurospheres	brain
49	chr19:37159000-37159800	Genic enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
50	chr19:37159000-37159800	Flanking Active TSS	Brain Anterior Caudate	brain

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