Variant report

Variant	rs3108553
Chromosome Location	chr19:37169927-37169928
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr19:37169916..37172252-chr19:37176189..37178987,2	MCF-7	breast:
2	chr19:37167853..37170740-chr19:37177122..37180031,2	K562	blood:

Variant related genes	Relation type
ENSG00000225975	Chromatin interaction
ENSG00000189042	Chromatin interaction

Extended variants
information (count: 68 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:53)

rs_ID	r²[population]
rs10411411	0.97[AFR][1000 genomes];0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1053064	1.00[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs12162275	0.86[AFR][1000 genomes];0.94[AMR][1000 genomes];0.91[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12973307	0.86[AFR][1000 genomes];0.92[AMR][1000 genomes];0.92[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12981751	0.94[AFR][1000 genomes]
rs2385640	0.89[AFR][1000 genomes];0.89[ASN][1000 genomes]
rs2462576	0.81[AFR][1000 genomes];0.88[ASN][1000 genomes]
rs2912401	0.90[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs2912402	0.83[AMR][1000 genomes];0.90[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2912406	0.84[AMR][1000 genomes];0.92[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2912416	0.84[AMR][1000 genomes];0.91[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2912417	0.84[AMR][1000 genomes];0.90[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2967424	0.89[EUR][1000 genomes]
rs2967455	0.85[AMR][1000 genomes];0.92[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2967470	0.85[AMR][1000 genomes];0.92[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs3096621	0.84[AMR][1000 genomes];0.92[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs3096626	0.83[EUR][1000 genomes]
rs3108169	0.93[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs3108170	0.86[AMR][1000 genomes];0.93[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs3108175	0.87[AMR][1000 genomes];0.93[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs3108180	0.84[AFR][1000 genomes];0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs3108198	0.97[AFR][1000 genomes];0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs3108199	0.94[EUR][1000 genomes]
rs3108200	0.95[AFR][1000 genomes];0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs3108207	1.00[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs3108213	0.84[AFR][1000 genomes];0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs3108220	0.81[AFR][1000 genomes];0.85[ASN][1000 genomes]
rs3108547	0.93[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3108548	0.83[AMR][1000 genomes];0.90[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs3108551	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3108554	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs3108558	0.98[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs3108561	0.97[AFR][1000 genomes];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs3108571	0.84[AFR][1000 genomes];0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs3108578	0.97[AFR][1000 genomes];0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs3108581	0.94[AFR][1000 genomes];0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs3108582	0.81[AFR][1000 genomes];0.89[ASN][1000 genomes]
rs3108587	0.83[AMR][1000 genomes];0.88[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs3108588	0.88[AFR][1000 genomes];0.89[ASN][1000 genomes]
rs3108595	0.84[AMR][1000 genomes];0.92[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs3108599	0.90[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs3108601	0.83[AMR][1000 genomes];0.91[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs3108611	0.93[AFR][1000 genomes];0.92[AMR][1000 genomes];0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs3111543	0.92[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs3111545	0.84[AMR][1000 genomes];0.91[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs3111546	0.91[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs71337534	0.89[AMR][1000 genomes];0.91[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7254978	0.97[AFR][1000 genomes];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs8112546	0.91[AMR][1000 genomes];0.85[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs826979	0.84[ASN][1000 genomes]
rs826980	0.85[ASN][1000 genomes]
rs826986	0.80[AFR][1000 genomes];0.89[ASN][1000 genomes]
rs865448	0.88[AFR][1000 genomes];0.89[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
rs3108553	ZNF529	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:104 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr19:37158600-37172800	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
2	chr19:37158600-37177200	Weak transcription	Fetal Kidney	kidney
3	chr19:37158600-37177400	Weak transcription	Placenta Amnion	Placenta Amnion
4	chr19:37158600-37177400	Weak transcription	NHDF-Ad	bronchial
5	chr19:37158600-37177800	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
6	chr19:37159000-37177000	Weak transcription	NHLF	lung
7	chr19:37159200-37177600	Weak transcription	H9 Cell Line	embryonic stem cell
8	chr19:37159400-37177600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
9	chr19:37159600-37176200	Weak transcription	Gastric	stomach
10	chr19:37159600-37177400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
11	chr19:37160000-37177000	Weak transcription	Fetal Heart	heart
12	chr19:37163200-37177200	Weak transcription	Pancreas	Pancrea
13	chr19:37163400-37171200	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
14	chr19:37165000-37177200	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
15	chr19:37165600-37177400	Weak transcription	iPS-18 Cell Line	embryonic stem cell
16	chr19:37166400-37170000	Weak transcription	Skeletal Muscle Female	skeletal muscle
17	chr19:37167600-37177000	Weak transcription	Primary T killer memory cells from peripheral blood	blood
18	chr19:37167800-37170000	Weak transcription	Brain Substantia Nigra	brain
19	chr19:37167800-37177200	Weak transcription	Muscle Satellite Cultured Cells	--
20	chr19:37167800-37177400	Weak transcription	Colonic Mucosa	Colon
21	chr19:37168000-37177200	Weak transcription	NH-A	brain
22	chr19:37168400-37173400	ZNF genes & repeats	Breast Myoepithelial Primary Cells	Breast
23	chr19:37168600-37170600	Strong transcription	Psoas Muscle	Psoas
24	chr19:37168800-37170000	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
25	chr19:37168800-37170200	ZNF genes & repeats	Foreskin Melanocyte Primary Cells skin01	Skin
26	chr19:37168800-37170200	ZNF genes & repeats	Fetal Intestine Large	intestine
27	chr19:37168800-37170400	ZNF genes & repeats	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
28	chr19:37168800-37170400	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
29	chr19:37168800-37170400	ZNF genes & repeats	Primary T helper cells PMA-I stimulated	--
30	chr19:37168800-37170400	ZNF genes & repeats	Cortex derived primary cultured neurospheres	brain
31	chr19:37168800-37170400	ZNF genes & repeats	Lung	lung
32	chr19:37168800-37170400	ZNF genes & repeats	Rectal Mucosa Donor 29	rectum
33	chr19:37168800-37170600	ZNF genes & repeats	H9 Derived Neuron Cultured Cells	ES cell derived
34	chr19:37168800-37170600	Strong transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
35	chr19:37168800-37170600	ZNF genes & repeats	Primary T regulatory cells fromperipheralblood	blood
36	chr19:37168800-37170600	ZNF genes & repeats	Ganglion Eminence derived primary cultured neurospheres	brain
37	chr19:37168800-37170600	ZNF genes & repeats	Adipose Nuclei	Adipose
38	chr19:37168800-37170600	ZNF genes & repeats	Brain Germinal Matrix	brain
39	chr19:37168800-37170600	Strong transcription	Brain Hippocampus Middle	brain
40	chr19:37168800-37170600	ZNF genes & repeats	Duodenum Mucosa	Duodenum
41	chr19:37168800-37170800	ZNF genes & repeats	H1 Derived Mesenchymal Stem Cells	ES cell derived
42	chr19:37168800-37170800	ZNF genes & repeats	Primary T cells fromperipheralblood	blood
43	chr19:37168800-37170800	ZNF genes & repeats	Primary T cells effector/memory enriched fromperipheralblood	blood
44	chr19:37168800-37170800	ZNF genes & repeats	Fetal Brain Male	brain
45	chr19:37168800-37170800	ZNF genes & repeats	Fetal Muscle Leg	muscle
46	chr19:37168800-37171000	Strong transcription	HUES48 Cell Line	embryonic stem cell
47	chr19:37168800-37171000	ZNF genes & repeats	Primary T cells from cord blood	blood
48	chr19:37168800-37171000	ZNF genes & repeats	Fetal Lung	lung
49	chr19:37168800-37171800	ZNF genes & repeats	Primary hematopoietic stem cells short term culture	blood
50	chr19:37168800-37171800	Strong transcription	Brain Angular Gyrus	brain

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