Variant report

Variant	rs3111543
Chromosome Location	chr19:37070123-37070124
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr19:37063335..37065551-chr19:37068652..37070249,2	MCF-7	breast:
2	chr1:90290948..90293135-chr19:37069121..37070641,2	K562	blood:
3	chr19:37062757..37067111-chr19:37067178..37071986,8	K562	blood:
4	chr19:37062757..37066475-chr19:37067178..37075829,11	K562	blood:
5	chr19:36703935..36706933-chr19:37068866..37070631,2	K562	blood:

Variant related genes	Relation type
ENSG00000196357	Chromatin interaction
ENSG00000186020	Chromatin interaction
ENSG00000233527	Chromatin interaction
ENSG00000167635	Chromatin interaction

Extended variants
information (count: 50 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:43)

rs_ID	r²[population]
rs10411411	0.88[EUR][1000 genomes]
rs1053064	0.88[AMR][1000 genomes];0.92[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs12162275	0.98[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs12973307	1.00[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2912401	0.91[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2912402	0.97[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2912406	0.85[AFR][1000 genomes];1.00[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2912416	0.81[AFR][1000 genomes];0.99[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2912417	0.81[AFR][1000 genomes];0.98[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2967424	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2967455	1.00[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2967470	0.83[AFR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs3096621	0.87[AFR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs3096626	0.89[AFR][1000 genomes];0.97[AMR][1000 genomes];0.91[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs3108169	0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs3108170	0.99[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs3108175	0.99[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs3108180	0.89[EUR][1000 genomes]
rs3108198	0.88[EUR][1000 genomes]
rs3108199	0.86[EUR][1000 genomes]
rs3108200	0.88[EUR][1000 genomes]
rs3108207	0.88[AMR][1000 genomes];0.92[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs3108213	0.88[EUR][1000 genomes]
rs3108547	0.92[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs3108548	0.98[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs3108551	0.92[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs3108553	0.92[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs3108554	0.92[EUR][1000 genomes]
rs3108558	0.89[EUR][1000 genomes]
rs3108561	0.89[EUR][1000 genomes]
rs3108571	0.88[EUR][1000 genomes]
rs3108578	0.88[EUR][1000 genomes]
rs3108581	0.88[EUR][1000 genomes]
rs3108587	0.96[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs3108595	0.82[AFR][1000 genomes];1.00[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs3108599	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3108601	0.99[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs3108611	0.97[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs3111545	0.99[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs3111546	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs71337534	0.83[EUR][1000 genomes]
rs7254978	0.94[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs8112546	0.92[EUR][1000 genomes];0.91[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:7 , 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	esv3334779	chr19:37050161-37076919	Active TSS Enhancers Weak transcription ZNF genes & repeats Strong transcription Flanking Active TSS Transcr. at gene 5' and 3' Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	18 gene(s)	inside rSNPs	n/a

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs3111543	ZNF529	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:124 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr19:37065600-37070200	Weak transcription	HSMMtube	muscle
2	chr19:37065600-37070200	Weak transcription	NHLF	lung
3	chr19:37065600-37081200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
4	chr19:37065600-37095400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
5	chr19:37065800-37071200	Weak transcription	Brain Substantia Nigra	brain
6	chr19:37065800-37072000	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
7	chr19:37065800-37072600	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
8	chr19:37065800-37075200	ZNF genes & repeats	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
9	chr19:37065800-37076600	Weak transcription	Stomach Mucosa	stomach
10	chr19:37065800-37078200	Weak transcription	Right Ventricle	heart
11	chr19:37066000-37070200	Weak transcription	Brain Anterior Caudate	brain
12	chr19:37066000-37081200	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
13	chr19:37066000-37081200	ZNF genes & repeats	Primary hematopoietic stem cells G-CSF-mobilized Female	--
14	chr19:37066200-37070200	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
15	chr19:37066200-37070200	Weak transcription	Fetal Brain Male	brain
16	chr19:37066200-37070200	Weak transcription	Fetal Heart	heart
17	chr19:37066200-37071400	Weak transcription	HepG2	liver
18	chr19:37066200-37073200	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
19	chr19:37066600-37070200	ZNF genes & repeats	Primary monocytes fromperipheralblood	blood
20	chr19:37066600-37072000	Strong transcription	HUVEC	blood vessel
21	chr19:37066600-37073200	Strong transcription	Fetal Muscle Leg	muscle
22	chr19:37066600-37073400	ZNF genes & repeats	Breast Myoepithelial Primary Cells	Breast
23	chr19:37066600-37073400	Strong transcription	Foreskin Fibroblast Primary Cells skin02	Skin
24	chr19:37066600-37073400	ZNF genes & repeats	Monocytes-CD14+_RO01746	blood
25	chr19:37066600-37074200	ZNF genes & repeats	IMR90 fetal lung fibroblasts Cell Line	lung
26	chr19:37066600-37074200	ZNF genes & repeats	Primary hematopoietic stem cells short term culture	blood
27	chr19:37066600-37080600	ZNF genes & repeats	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
28	chr19:37066800-37070200	ZNF genes & repeats	Fetal Intestine Large	intestine
29	chr19:37066800-37070200	ZNF genes & repeats	Fetal Intestine Small	intestine
30	chr19:37066800-37070600	ZNF genes & repeats	H1 Derived Mesenchymal Stem Cells	ES cell derived
31	chr19:37066800-37074400	ZNF genes & repeats	H9 Derived Neuron Cultured Cells	ES cell derived
32	chr19:37066800-37081000	Strong transcription	Dnd41	blood
33	chr19:37066800-37091400	ZNF genes & repeats	Primary hematopoietic stem cells G-CSF-mobilized Male	--
34	chr19:37067000-37070200	Strong transcription	Rectal Mucosa Donor 31	rectum
35	chr19:37067000-37072200	Strong transcription	Stomach Smooth Muscle	stomach
36	chr19:37067000-37073200	Strong transcription	Placenta	Placenta
37	chr19:37067000-37073800	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
38	chr19:37067000-37076200	ZNF genes & repeats	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
39	chr19:37067000-37076800	ZNF genes & repeats	GM12878-XiMat	blood
40	chr19:37067000-37080800	ZNF genes & repeats	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
41	chr19:37067000-37081200	ZNF genes & repeats	Liver	Liver
42	chr19:37067000-37081200	ZNF genes & repeats	Duodenum Smooth Muscle	Duodenum
43	chr19:37067200-37070400	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
44	chr19:37067200-37072000	Strong transcription	Primary T helper cells fromperipheralblood	blood
45	chr19:37067200-37072000	Strong transcription	HSMM	muscle
46	chr19:37067400-37072800	Strong transcription	Fetal Thymus	thymus
47	chr19:37067400-37074600	ZNF genes & repeats	Primary hematopoietic stem cells	blood
48	chr19:37067600-37070200	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
49	chr19:37067600-37070800	Strong transcription	Primary T helper naive cells from peripheral blood	blood
50	chr19:37067600-37071200	Strong transcription	Primary T cells from cord blood	blood

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links