Variant report

Variant	rs16982846
Chromosome Location	chr19:52077069-52077070
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	chr19:52075666..52078013-chr19:52102124..52103680,2	K562	blood:
2	chr19:52073066..52077206-chr19:52096074..52099799,4	K562	blood:

Variant related genes	Relation type
ENSG00000267808	Chromatin interaction
ENSG00000269388	Chromatin interaction
ENSG00000167765	Chromatin interaction

Extended variants
information (count: 25 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:17)

rs_ID	r²[population]
rs1125620	0.92[ASN][1000 genomes]
rs1379284	0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1585160	0.89[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs17453522	0.99[EUR][1000 genomes]
rs1962189	0.93[ASN][1000 genomes]
rs2305371	0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs2864106	0.89[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2864108	0.90[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2864109	0.90[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3752132	0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4308054	0.90[ASN][1000 genomes]
rs6509552	0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs7245838	0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7249641	0.89[AMR][1000 genomes];0.87[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs8102214	0.92[ASN][1000 genomes]
rs8108872	0.89[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs8111685	0.93[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:8 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1066308	chr19:51680133-52103974	Active TSS Weak transcription Flanking Active TSS Enhancers Strong transcription ZNF genes & repeats Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	71 gene(s)	inside rSNPs	diseases
2	nsv544049	chr19:51680133-52103974	Bivalent Enhancer Strong transcription Enhancers Active TSS Flanking Bivalent TSS/Enh Weak transcription Flanking Active TSS ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	71 gene(s)	inside rSNPs	diseases
3	nsv544051	chr19:51944903-52147459	Bivalent Enhancer Strong transcription Weak transcription Active TSS ZNF genes & repeats Flanking Active TSS Enhancers Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	26 gene(s)	inside rSNPs	diseases
4	esv2758504	chr19:51991896-52266700	Enhancers Strong transcription Transcr. at gene 5' and 3' Weak transcription Active TSS ZNF genes & repeats Flanking Active TSS Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	542 gene(s)	inside rSNPs	diseases
5	esv2758767	chr19:51991896-52604625	Flanking Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Weak transcription Active TSS Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh Strong transcription Enhancers Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	578 gene(s)	inside rSNPs	diseases
6	nsv469584	chr19:52001381-52151821	Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Active TSS Genic enhancers Transcr. at gene 5' and 3' Strong transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	25 gene(s)	inside rSNPs	diseases
7	nsv482654	chr19:52001381-52151821	Enhancers Strong transcription Weak transcription Bivalent Enhancer Active TSS Flanking Active TSS Genic enhancers ZNF genes & repeats 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	25 gene(s)	inside rSNPs	diseases
8	nsv579966	chr19:52075622-52131119	Enhancers Bivalent Enhancer Strong transcription Active TSS Flanking Active TSS Weak transcription ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	13 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs16982846	ZNF175	Cis_1M	lymphoblastoid	RTeQTL
rs16982846	ZNF175	cis	Esophagus Mucosa	GTEx
rs16982846	ZNF175	cis	Esophagus Muscularis	GTEx

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr19:52074800-52077400	Flanking Active TSS	HUVEC	blood vessel
2	chr19:52075400-52084600	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
3	chr19:52075400-52087400	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
4	chr19:52075400-52090200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
5	chr19:52075600-52084400	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
6	chr19:52075600-52084400	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
7	chr19:52075600-52084600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
8	chr19:52075600-52084600	Weak transcription	iPS-20b Cell Line	embryonic stem cell
9	chr19:52075600-52084600	Weak transcription	Colonic Mucosa	Colon
10	chr19:52075600-52084800	Weak transcription	iPS-18 Cell Line	embryonic stem cell
11	chr19:52075600-52084800	Weak transcription	Fetal Kidney	kidney
12	chr19:52075600-52089200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
13	chr19:52075800-52078000	Strong transcription	Thymus	Thymus
14	chr19:52075800-52079600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
15	chr19:52075800-52079600	Weak transcription	Primary B cells from cord blood	blood
16	chr19:52075800-52079800	Weak transcription	Gastric	stomach
17	chr19:52075800-52081800	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
18	chr19:52075800-52083600	Weak transcription	Primary T helper naive cells from peripheral blood	blood
19	chr19:52075800-52084200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
20	chr19:52075800-52084200	Weak transcription	HSMMtube	muscle
21	chr19:52075800-52085000	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
22	chr19:52075800-52090000	Weak transcription	Stomach Mucosa	stomach
23	chr19:52075800-52096800	Weak transcription	HepG2	liver
24	chr19:52076000-52077200	Transcr. at gene 5' and 3'	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
25	chr19:52076000-52077200	Transcr. at gene 5' and 3'	K562	blood
26	chr19:52076000-52084800	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
27	chr19:52076200-52077200	Strong transcription	Brain Anterior Caudate	brain
28	chr19:52076200-52077200	Genic enhancers	Brain Germinal Matrix	brain
29	chr19:52076200-52077400	Strong transcription	Foreskin Melanocyte Primary Cells skin01	Skin
30	chr19:52076200-52077600	Strong transcription	Skeletal Muscle Male	skeletal muscle
31	chr19:52076200-52078000	Strong transcription	HUES6 Cell Line	embryonic stem cell
32	chr19:52076200-52078400	Strong transcription	A549	lung
33	chr19:52076200-52079800	Weak transcription	Brain Cingulate Gyrus	brain
34	chr19:52076200-52080600	Strong transcription	HUES48 Cell Line	embryonic stem cell
35	chr19:52076200-52080600	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
36	chr19:52076200-52084600	Weak transcription	Pancreatic Islets	Pancreatic Islet
37	chr19:52076200-52084800	Weak transcription	Fetal Heart	heart
38	chr19:52076200-52088200	Strong transcription	Monocytes-CD14+_RO01746	blood
39	chr19:52076400-52077200	Genic enhancers	Primary T helper naive cells fromperipheralblood	blood
40	chr19:52076400-52077200	Strong transcription	Primary T helper cells fromperipheralblood	blood
41	chr19:52076400-52077200	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
42	chr19:52076400-52077200	Strong transcription	Duodenum Smooth Muscle	Duodenum
43	chr19:52076400-52077200	Strong transcription	Fetal Muscle Trunk	muscle
44	chr19:52076400-52077400	Strong transcription	Rectal Mucosa Donor 31	rectum
45	chr19:52076400-52078000	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
46	chr19:52076400-52078000	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
47	chr19:52076400-52078200	Strong transcription	iPS-15b Cell Line	embryonic stem cell
48	chr19:52076400-52078200	Strong transcription	Fetal Thymus	thymus
49	chr19:52076400-52078600	Strong transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
50	chr19:52076400-52078600	Strong transcription	Fetal Intestine Small	intestine

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links