Variant report

Variant	rs8111685
Chromosome Location	chr19:52076960-52076961
allele	C/T
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
ENSG00000167765	Chromatin interaction
ENSG00000269388	Chromatin interaction
ENSG00000267808	Chromatin interaction

Extended variants
information (count: 26 )
Associated
traits (count: 9 )

rSNPs within LD-proxies of this variant (count:18)

rs_ID	r²[population]
rs1125620	0.84[CHB][hapmap];0.94[CHD][hapmap];1.00[JPT][hapmap];0.92[ASN][1000 genomes]
rs1379284	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1585160	1.00[CEU][hapmap];0.90[CHB][hapmap];0.94[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];0.94[MEX][hapmap];0.89[MKK][hapmap];1.00[TSI][hapmap];0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs16982846	0.93[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17453522	0.95[CEU][hapmap];0.94[JPT][hapmap];0.81[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs1962189	0.83[JPT][hapmap];0.93[ASN][1000 genomes]
rs2305371	1.00[CEU][hapmap];1.00[GIH][hapmap];0.94[JPT][hapmap];0.89[MEX][hapmap];0.91[TSI][hapmap];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs2864106	0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2864108	0.91[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2864109	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3752129	1.00[CEU][hapmap];0.95[CHB][hapmap];0.97[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.94[MEX][hapmap];1.00[TSI][hapmap]
rs3752132	1.00[CEU][hapmap];0.89[CHB][hapmap];1.00[JPT][hapmap];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4308054	0.90[CHB][hapmap];0.89[JPT][hapmap];0.90[ASN][1000 genomes]
rs6509552	1.00[CEU][hapmap];1.00[GIH][hapmap];0.94[JPT][hapmap];0.90[MEX][hapmap];1.00[TSI][hapmap];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs7245838	1.00[CEU][hapmap];0.95[CHB][hapmap];0.97[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.89[MKK][hapmap];1.00[TSI][hapmap];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7249641	0.91[AMR][1000 genomes];0.87[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs8102214	0.84[CHB][hapmap];0.94[JPT][hapmap];0.92[ASN][1000 genomes]
rs8108872	0.81[ASW][hapmap];1.00[CEU][hapmap];0.95[CHB][hapmap];0.97[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.94[MEX][hapmap];0.89[MKK][hapmap];1.00[TSI][hapmap];0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[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:9)

SNP	Gene	Cis/trans	Tissue	Source
rs8111685	SBK2	cis	cerebellum	SCAN
rs8111685	ZNF808	cis	parietal	SCAN
rs8111685	ZNF544	cis	parietal	SCAN
rs8111685	ZNF175	cis	Esophagus Mucosa	GTEx
rs8111685	ZNF71	cis	cerebellum	SCAN
rs8111685	ZNF175	cis	Esophagus Muscularis	GTEx
rs8111685	TNNI3	cis	cerebellum	SCAN
rs8111685	ZNF175	Cis_1M	lymphoblastoid	RTeQTL
rs8111685	FCAR	cis	parietal	SCAN

Chromatin state (count:125 , 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	chr19:52075000-52077000	Flanking Active TSS	Osteobl	bone
3	chr19:52075200-52077000	Flanking Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
4	chr19:52075400-52084600	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
5	chr19:52075400-52087400	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
6	chr19:52075400-52090200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
7	chr19:52075600-52084400	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
8	chr19:52075600-52084400	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
9	chr19:52075600-52084600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
10	chr19:52075600-52084600	Weak transcription	iPS-20b Cell Line	embryonic stem cell
11	chr19:52075600-52084600	Weak transcription	Colonic Mucosa	Colon
12	chr19:52075600-52084800	Weak transcription	iPS-18 Cell Line	embryonic stem cell
13	chr19:52075600-52084800	Weak transcription	Fetal Kidney	kidney
14	chr19:52075600-52089200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
15	chr19:52075800-52077000	Enhancers	Psoas Muscle	Psoas
16	chr19:52075800-52077000	Flanking Active TSS	GM12878-XiMat	blood
17	chr19:52075800-52078000	Strong transcription	Thymus	Thymus
18	chr19:52075800-52079600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
19	chr19:52075800-52079600	Weak transcription	Primary B cells from cord blood	blood
20	chr19:52075800-52079800	Weak transcription	Gastric	stomach
21	chr19:52075800-52081800	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
22	chr19:52075800-52083600	Weak transcription	Primary T helper naive cells from peripheral blood	blood
23	chr19:52075800-52084200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
24	chr19:52075800-52084200	Weak transcription	HSMMtube	muscle
25	chr19:52075800-52085000	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
26	chr19:52075800-52090000	Weak transcription	Stomach Mucosa	stomach
27	chr19:52075800-52096800	Weak transcription	HepG2	liver
28	chr19:52076000-52077200	Transcr. at gene 5' and 3'	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
29	chr19:52076000-52077200	Transcr. at gene 5' and 3'	K562	blood
30	chr19:52076000-52084800	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
31	chr19:52076200-52077000	Genic enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
32	chr19:52076200-52077000	Genic enhancers	Adipose Nuclei	Adipose
33	chr19:52076200-52077000	Strong transcription	Fetal Lung	lung
34	chr19:52076200-52077200	Strong transcription	Brain Anterior Caudate	brain
35	chr19:52076200-52077200	Genic enhancers	Brain Germinal Matrix	brain
36	chr19:52076200-52077400	Strong transcription	Foreskin Melanocyte Primary Cells skin01	Skin
37	chr19:52076200-52077600	Strong transcription	Skeletal Muscle Male	skeletal muscle
38	chr19:52076200-52078000	Strong transcription	HUES6 Cell Line	embryonic stem cell
39	chr19:52076200-52078400	Strong transcription	A549	lung
40	chr19:52076200-52079800	Weak transcription	Brain Cingulate Gyrus	brain
41	chr19:52076200-52080600	Strong transcription	HUES48 Cell Line	embryonic stem cell
42	chr19:52076200-52080600	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
43	chr19:52076200-52084600	Weak transcription	Pancreatic Islets	Pancreatic Islet
44	chr19:52076200-52084800	Weak transcription	Fetal Heart	heart
45	chr19:52076200-52088200	Strong transcription	Monocytes-CD14+_RO01746	blood
46	chr19:52076400-52077000	Strong transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
47	chr19:52076400-52077000	Genic enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
48	chr19:52076400-52077000	Transcr. at gene 5' and 3'	Foreskin Fibroblast Primary Cells skin02	Skin
49	chr19:52076400-52077000	Strong transcription	Fetal Intestine Large	intestine
50	chr19:52076400-52077000	Strong transcription	Hela-S3	cervix

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