Variant report

Variant	rs55830504
Chromosome Location	chr19:37023389-37023390
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr19:37017700..37019947-chr19:37023301..37025958,2	K562	blood:
2	chr19:37020966..37023894-chr19:37025965..37028005,2	K562	blood:
3	chr19:37019316..37021481-chr19:37022356..37024677,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000228629	Chromatin interaction
ENSG00000254004	Chromatin interaction

Extended variants
information (count: 55 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:46)

rs_ID	r²[population]
rs17707014	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17707021	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17707033	0.87[ASN][1000 genomes]
rs2891868	0.84[AFR][1000 genomes];0.85[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs4514798	0.84[AFR][1000 genomes];0.85[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs4806328	0.90[AMR][1000 genomes]
rs4806333	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs4806340	0.81[AMR][1000 genomes]
rs55634974	0.89[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs55743839	0.87[AFR][1000 genomes];0.90[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs55801623	1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs55880628	0.98[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs55933007	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs56054915	0.89[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs56075402	0.90[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs56183102	0.87[AMR][1000 genomes]
rs56246998	0.81[AFR][1000 genomes];0.90[AMR][1000 genomes]
rs57126710	0.87[ASN][1000 genomes]
rs6510549	0.84[AFR][1000 genomes];0.85[AMR][1000 genomes]
rs7249099	0.87[AFR][1000 genomes];0.88[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs7257899	0.83[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs7259057	0.87[AMR][1000 genomes]
rs73032465	0.96[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs73032484	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73032489	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73032491	0.87[ASN][1000 genomes]
rs73032502	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73034106	0.87[ASN][1000 genomes]
rs73034109	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73034142	0.94[AMR][1000 genomes];0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73034176	0.84[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs73036297	0.81[AMR][1000 genomes]
rs73038105	0.81[AMR][1000 genomes]
rs73049817	0.90[AMR][1000 genomes]
rs73049826	0.81[AFR][1000 genomes];0.90[AMR][1000 genomes]
rs73049844	0.81[AMR][1000 genomes]
rs73049851	0.85[AMR][1000 genomes]
rs73049853	0.85[AMR][1000 genomes]
rs8100340	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs8102097	0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs8102474	0.87[ASN][1000 genomes]
rs8103917	0.85[AMR][1000 genomes]
rs8104893	0.90[AMR][1000 genomes]
rs8106144	0.87[ASN][1000 genomes]
rs8110140	0.87[AMR][1000 genomes]
rs8111192	0.87[AFR][1000 genomes];0.90[AMR][1000 genomes];0.87[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:9 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv833816	chr19:36824257-37034287	ZNF genes & repeats Active TSS Weak transcription Enhancers Flanking Active TSS Strong transcription Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	29 gene(s)	inside rSNPs	diseases
2	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
3	nsv911648	chr19:36914171-37047472	Weak transcription Active TSS Strong transcription ZNF genes & repeats Enhancers Flanking Active TSS Bivalent/Poised TSS Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	28 gene(s)	inside rSNPs	diseases
4	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
5	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
6	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
7	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
8	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
9	nsv1056134	chr19:37022039-37056943	Weak transcription ZNF genes & repeats Strong transcription Bivalent Enhancer Enhancers Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	n/a

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs55830504	ZNF567	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:52 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr19:37020200-37024000	Weak transcription	Aorta	Aorta
2	chr19:37020400-37024400	Weak transcription	Primary T helper naive cells from peripheral blood	blood
3	chr19:37020400-37024400	Weak transcription	Muscle Satellite Cultured Cells	--
4	chr19:37020400-37024600	Weak transcription	Brain Hippocampus Middle	brain
5	chr19:37020400-37025600	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
6	chr19:37020400-37025600	Weak transcription	Colon Smooth Muscle	Colon
7	chr19:37020400-37025800	Weak transcription	H9 Cell Line	embryonic stem cell
8	chr19:37020400-37025800	Weak transcription	Fetal Kidney	kidney
9	chr19:37020400-37025800	Weak transcription	Stomach Mucosa	stomach
10	chr19:37020400-37025800	Weak transcription	HSMM	muscle
11	chr19:37020400-37025800	Weak transcription	HSMMtube	muscle
12	chr19:37020400-37026000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
13	chr19:37020400-37034600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
14	chr19:37020600-37023400	Weak transcription	Placenta Amnion	Placenta Amnion
15	chr19:37020600-37023600	Weak transcription	Brain Substantia Nigra	brain
16	chr19:37020600-37023800	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
17	chr19:37020600-37024000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
18	chr19:37020600-37024000	Weak transcription	Brain Inferior Temporal Lobe	brain
19	chr19:37020600-37024000	Weak transcription	Rectal Smooth Muscle	rectum
20	chr19:37020600-37024400	Weak transcription	iPS-18 Cell Line	embryonic stem cell
21	chr19:37020600-37024400	Weak transcription	Fetal Heart	heart
22	chr19:37020600-37024600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
23	chr19:37020600-37025600	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
24	chr19:37020600-37025800	Weak transcription	iPS-15b Cell Line	embryonic stem cell
25	chr19:37020600-37025800	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
26	chr19:37020600-37025800	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
27	chr19:37020600-37025800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
28	chr19:37020600-37025800	Weak transcription	Placenta	Placenta
29	chr19:37020600-37025800	Weak transcription	Right Ventricle	heart
30	chr19:37020600-37027600	Weak transcription	Hela-S3	cervix
31	chr19:37021400-37061600	ZNF genes & repeats	Liver	Liver
32	chr19:37021600-37030000	ZNF genes & repeats	Primary hematopoietic stem cells	blood
33	chr19:37022600-37023400	Weak transcription	Fetal Lung	lung
34	chr19:37022600-37023600	Weak transcription	Primary T cells from cord blood	blood
35	chr19:37022600-37023600	Weak transcription	Primary T helper cells PMA-I stimulated	--
36	chr19:37022600-37023800	Weak transcription	Dnd41	blood
37	chr19:37022600-37024400	Weak transcription	Skeletal Muscle Female	skeletal muscle
38	chr19:37022600-37025400	Weak transcription	HUES64 Cell Line	embryonic stem cell
39	chr19:37022800-37061200	ZNF genes & repeats	Adipose Nuclei	Adipose
40	chr19:37023000-37023400	ZNF genes & repeats	Pancreas	Pancrea
41	chr19:37023000-37023600	Strong transcription	Ovary	ovary
42	chr19:37023000-37061800	ZNF genes & repeats	Duodenum Smooth Muscle	Duodenum
43	chr19:37023200-37024200	ZNF genes & repeats	Foreskin Fibroblast Primary Cells skin01	Skin
44	chr19:37023200-37024200	ZNF genes & repeats	Fetal Stomach	stomach
45	chr19:37023200-37025000	ZNF genes & repeats	Cortex derived primary cultured neurospheres	brain
46	chr19:37023200-37025000	ZNF genes & repeats	Foreskin Melanocyte Primary Cells skin03	Skin
47	chr19:37023200-37027000	ZNF genes & repeats	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
48	chr19:37023200-37031800	ZNF genes & repeats	A549	lung
49	chr19:37023200-37032600	ZNF genes & repeats	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
50	chr19:37023200-37048400	ZNF genes & repeats	IMR90 fetal lung fibroblasts Cell Line	lung

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links