Variant report

Variant	rs3108554
Chromosome Location	chr19:37172644-37172645
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr19:37170168..37172761-chr19:37172837..37175354,2	MCF-7	breast:
2	chr19:37171917..37174270-chr19:37177933..37180774,2	K562	blood:
3	chr19:37171965..37174267-chr19:37175474..37177630,2	K562	blood:

Variant related genes	Relation type
ENSG00000189042	Chromatin interaction
ENSG00000225975	Chromatin interaction

Extended variants
information (count: 69 )
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];0.90[ASN][1000 genomes]
rs1053064	1.00[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs12162275	0.86[AFR][1000 genomes];0.94[AMR][1000 genomes];0.91[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs12973307	0.86[AFR][1000 genomes];0.92[AMR][1000 genomes];0.92[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs12981751	0.94[AFR][1000 genomes]
rs2385640	0.89[AFR][1000 genomes];0.86[ASN][1000 genomes]
rs2462576	0.81[AFR][1000 genomes];0.85[ASN][1000 genomes]
rs2912401	0.90[EUR][1000 genomes]
rs2912402	0.83[AMR][1000 genomes];0.90[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2912406	0.84[AMR][1000 genomes];0.92[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2912416	0.84[AMR][1000 genomes];0.91[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2912417	0.84[AMR][1000 genomes];0.90[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2967424	0.89[EUR][1000 genomes]
rs2967455	0.85[AMR][1000 genomes];0.92[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2967470	0.85[AMR][1000 genomes];0.92[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs3096621	0.84[AMR][1000 genomes];0.92[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs3096626	0.83[EUR][1000 genomes]
rs3108169	0.93[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs3108170	0.86[AMR][1000 genomes];0.93[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs3108175	0.87[AMR][1000 genomes];0.93[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs3108180	0.84[AFR][1000 genomes];0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs3108198	0.97[AFR][1000 genomes];0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.89[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];0.89[ASN][1000 genomes]
rs3108207	1.00[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs3108213	0.84[AFR][1000 genomes];0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs3108220	0.81[AFR][1000 genomes];0.82[ASN][1000 genomes]
rs3108547	0.93[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs3108548	0.83[AMR][1000 genomes];0.90[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs3108551	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs3108553	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];0.92[ASN][1000 genomes]
rs3108561	0.97[AFR][1000 genomes];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs3108571	0.84[AFR][1000 genomes];0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs3108578	0.97[AFR][1000 genomes];0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs3108581	0.94[AFR][1000 genomes];0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs3108582	0.81[AFR][1000 genomes];0.86[ASN][1000 genomes]
rs3108587	0.83[AMR][1000 genomes];0.88[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs3108588	0.88[AFR][1000 genomes];0.86[ASN][1000 genomes]
rs3108595	0.84[AMR][1000 genomes];0.92[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs3108599	0.90[EUR][1000 genomes]
rs3108601	0.83[AMR][1000 genomes];0.91[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs3108611	0.93[AFR][1000 genomes];0.92[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs3111543	0.92[EUR][1000 genomes]
rs3111545	0.84[AMR][1000 genomes];0.91[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs3111546	0.91[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs71337534	0.89[AMR][1000 genomes];0.91[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs7254978	0.97[AFR][1000 genomes];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs8112546	0.91[AMR][1000 genomes];0.85[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs826979	0.81[ASN][1000 genomes]
rs826980	0.82[ASN][1000 genomes]
rs826986	0.80[AFR][1000 genomes];0.86[ASN][1000 genomes]
rs865448	0.88[AFR][1000 genomes];0.86[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	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
16	nsv470139	chr19:37171201-37264190	Flanking Active TSS Enhancers Weak transcription ZNF genes & repeats Active TSS Strong transcription 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	20 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs3108554	ZNF529	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:102 , 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	chr19:37165000-37177200	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
14	chr19:37165600-37177400	Weak transcription	iPS-18 Cell Line	embryonic stem cell
15	chr19:37167600-37177000	Weak transcription	Primary T killer memory cells from peripheral blood	blood
16	chr19:37167800-37177200	Weak transcription	Muscle Satellite Cultured Cells	--
17	chr19:37167800-37177400	Weak transcription	Colonic Mucosa	Colon
18	chr19:37168000-37177200	Weak transcription	NH-A	brain
19	chr19:37168400-37173400	ZNF genes & repeats	Breast Myoepithelial Primary Cells	Breast
20	chr19:37168800-37173000	ZNF genes & repeats	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
21	chr19:37168800-37173000	Strong transcription	Skeletal Muscle Male	skeletal muscle
22	chr19:37168800-37173200	ZNF genes & repeats	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
23	chr19:37168800-37173200	ZNF genes & repeats	Primary T helper cells fromperipheralblood	blood
24	chr19:37168800-37173200	ZNF genes & repeats	Monocytes-CD14+_RO01746	blood
25	chr19:37168800-37174600	ZNF genes & repeats	Primary hematopoietic stem cells G-CSF-mobilized Female	--
26	chr19:37168800-37176400	ZNF genes & repeats	Primary hematopoietic stem cells G-CSF-mobilized Male	--
27	chr19:37168800-37176400	ZNF genes & repeats	Liver	Liver
28	chr19:37169000-37173000	Strong transcription	Foreskin Fibroblast Primary Cells skin01	Skin
29	chr19:37169000-37173200	ZNF genes & repeats	Fetal Brain Female	brain
30	chr19:37169000-37173200	Strong transcription	Placenta	Placenta
31	chr19:37169200-37175400	Strong transcription	Primary B cells from cord blood	blood
32	chr19:37169200-37177200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
33	chr19:37169200-37177200	Weak transcription	Sigmoid Colon	Sigmoid Colon
34	chr19:37169200-37177800	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
35	chr19:37169400-37176800	Weak transcription	HSMMtube	muscle
36	chr19:37169400-37177200	Weak transcription	iPS-20b Cell Line	embryonic stem cell
37	chr19:37169600-37173400	Strong transcription	Dnd41	blood
38	chr19:37169600-37177400	Weak transcription	H1 Cell Line	embryonic stem cell
39	chr19:37169800-37173200	ZNF genes & repeats	Primary hematopoietic stem cells	blood
40	chr19:37170000-37176800	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
41	chr19:37170400-37173200	Strong transcription	Cortex derived primary cultured neurospheres	brain
42	chr19:37170400-37176800	Weak transcription	Brain Anterior Caudate	brain
43	chr19:37170400-37177400	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
44	chr19:37170600-37173800	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
45	chr19:37170600-37174000	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
46	chr19:37170600-37174600	Strong transcription	Brain Germinal Matrix	brain
47	chr19:37170600-37175400	Weak transcription	Brain Hippocampus Middle	brain
48	chr19:37170600-37176800	Weak transcription	Brain Cingulate Gyrus	brain
49	chr19:37170600-37177000	Weak transcription	Primary T helper naive cells from peripheral blood	blood
50	chr19:37170600-37177400	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived

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