Variant report

Variant	rs11879346
Chromosome Location	chr19:23427269-23427270
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr19:23426796..23428873-chr19:23431504..23433351,2	K562	blood:
2	chr19:23426796..23428873-chr19:23431504..23434558,3	K562	blood:

Variant related genes	Relation type
ENSG00000196081	Chromatin interaction

Extended variants
information (count: 47 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:22)

rs_ID	r²[population]
rs10401383	1.00[JPT][hapmap]
rs10403121	0.82[AMR][1000 genomes];0.83[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs10407768	0.82[AMR][1000 genomes];0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10422569	0.81[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs11085570	0.82[AMR][1000 genomes];0.83[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11666025	0.89[CHB][hapmap]
rs11667040	1.00[CHB][hapmap];0.94[JPT][hapmap];1.00[YRI][hapmap];0.91[AFR][1000 genomes];0.81[AMR][1000 genomes];0.83[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11667897	0.91[AFR][1000 genomes];0.81[AMR][1000 genomes];0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11670874	0.82[AMR][1000 genomes];0.83[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12610936	0.83[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12977336	0.87[AFR][1000 genomes];0.83[AMR][1000 genomes];0.84[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12979178	0.82[AMR][1000 genomes];0.83[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2054941	0.87[AFR][1000 genomes];0.83[AMR][1000 genomes];0.84[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs3180232	1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs34836272	0.82[AMR][1000 genomes];0.83[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs35256795	0.83[AFR][1000 genomes];0.81[AMR][1000 genomes];0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3851027	0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs59189024	0.84[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs7251426	0.87[ASN][1000 genomes]
rs7257176	0.82[AMR][1000 genomes];0.85[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs8111467	0.82[AMR][1000 genomes];0.83[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9676289	0.81[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];0.85[EUR][1000 genomes];0.97[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:25 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv34470	chr19:22922549-23659458	ZNF genes & repeats Flanking Active TSS Active TSS Enhancers Weak transcription Strong transcription 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	80 gene(s)	inside rSNPs	diseases
2	esv34907	chr19:22922549-23683097	Weak transcription ZNF genes & repeats Flanking Active TSS Flanking Bivalent TSS/Enh Strong transcription Active TSS Enhancers Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	80 gene(s)	inside rSNPs	diseases
3	nsv9686	chr19:22989454-23653750	Weak transcription Active TSS ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3' Strong transcription Enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	76 gene(s)	inside rSNPs	diseases
4	nsv817826	chr19:23000745-23620632	Active TSS Strong transcription ZNF genes & repeats Weak transcription Bivalent/Poised TSS Genic enhancers Flanking Active TSS Enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	75 gene(s)	inside rSNPs	diseases
5	esv3693269	chr19:23000745-23652839	Weak transcription Active TSS Strong transcription Enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Flanking Active TSS Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	76 gene(s)	inside rSNPs	diseases
6	esv2758491	chr19:23071299-23940467	ZNF genes & repeats Bivalent/Poised TSS Weak transcription Enhancers Flanking Bivalent TSS/Enh Flanking Active TSS Strong transcription Active TSS Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	87 gene(s)	inside rSNPs	diseases
7	nsv1065157	chr19:23091826-23812323	Weak transcription Transcr. at gene 5' and 3' ZNF genes & repeats Active TSS Flanking Active TSS Strong transcription Flanking Bivalent TSS/Enh Genic enhancers Enhancers Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	83 gene(s)	inside rSNPs	diseases
8	nsv543959	chr19:23091826-23812323	Active TSS Weak transcription Strong transcription Flanking Active TSS Enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	83 gene(s)	inside rSNPs	diseases
9	esv3424935	chr19:23111817-23495542	Weak transcription ZNF genes & repeats Active TSS Flanking Active TSS Transcr. at gene 5' and 3' Enhancers Strong transcription Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	48 gene(s)	inside rSNPs	diseases
10	esv3429878	chr19:23246650-23590744	Strong transcription ZNF genes & repeats Weak transcription Active TSS Enhancers Flanking Active TSS Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	52 gene(s)	inside rSNPs	diseases
11	esv3410568	chr19:23246670-23590714	Weak transcription ZNF genes & repeats Flanking Active TSS Strong transcription Enhancers Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Active TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	52 gene(s)	inside rSNPs	diseases
12	esv3433243	chr19:23249108-23585814	Strong transcription Weak transcription Active TSS ZNF genes & repeats Flanking Active TSS Flanking Bivalent TSS/Enh Enhancers Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	44 gene(s)	inside rSNPs	diseases
13	esv3387823	chr19:23265885-23590028	ZNF genes & repeats Weak transcription Strong transcription Enhancers Active TSS Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	47 gene(s)	inside rSNPs	diseases
14	esv3321838	chr19:23303462-23482478	Strong transcription Weak transcription Active TSS ZNF genes & repeats Flanking Active TSS Enhancers Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	19 gene(s)	inside rSNPs	diseases
15	esv3487542	chr19:23310521-23438770	ZNF genes & repeats Strong transcription Active TSS Weak transcription Flanking Active TSS Transcr. at gene 5' and 3' Enhancers Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
16	esv3487543	chr19:23310521-23438770	ZNF genes & repeats Weak transcription Active TSS Flanking Active TSS Strong transcription Enhancers Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
17	nsv911463	chr19:23327714-23430436	ZNF genes & repeats Weak transcription Enhancers Strong transcription Transcr. at gene 5' and 3' Active TSS Genic enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
18	nsv833789	chr19:23329463-23487797	Active TSS Weak transcription Enhancers Strong transcription Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	15 gene(s)	inside rSNPs	diseases
19	esv3440847	chr19:23361380-23481908	Weak transcription Strong transcription ZNF genes & repeats Genic enhancers Enhancers Flanking Active TSS Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	15 gene(s)	inside rSNPs	diseases
20	esv3446056	chr19:23361400-23481878	Weak transcription ZNF genes & repeats Flanking Active TSS Enhancers Genic enhancers Active TSS Strong transcription Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	15 gene(s)	inside rSNPs	diseases
21	nsv911464	chr19:23373200-23430436	ZNF genes & repeats Weak transcription Strong transcription Enhancers Genic enhancers Active TSS Flanking Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
22	nsv579033	chr19:23387788-23461424	Active TSS Strong transcription ZNF genes & repeats Weak transcription Flanking Active TSS Transcr. at gene 5' and 3' Enhancers Genic enhancers Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
23	nsv579034	chr19:23387788-23610784	ZNF genes & repeats Enhancers Weak transcription Active TSS Flanking Active TSS Strong transcription Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	43 gene(s)	inside rSNPs	diseases
24	nsv833790	chr19:23405972-23557520	ZNF genes & repeats Active TSS Weak transcription Flanking Active TSS Genic enhancers Strong transcription Enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	25 gene(s)	inside rSNPs	diseases
25	nsv961201	chr19:23410491-23434921	ZNF genes & repeats Active TSS Weak transcription Strong transcription Enhancers Flanking Active TSS Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs11879346	RP11-15H20.5	cis	Heart Left Ventricle	GTEx

Chromatin state (count:93 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr19:23398000-23431600	ZNF genes & repeats	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
2	chr19:23399600-23429000	ZNF genes & repeats	Primary hematopoietic stem cells G-CSF-mobilized Male	--
3	chr19:23400400-23430600	ZNF genes & repeats	Dnd41	blood
4	chr19:23400400-23432000	ZNF genes & repeats	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
5	chr19:23401800-23428200	ZNF genes & repeats	HUES6 Cell Line	embryonic stem cell
6	chr19:23402200-23431400	ZNF genes & repeats	Primary hematopoietic stem cells short term culture	blood
7	chr19:23404000-23431200	ZNF genes & repeats	Primary hematopoietic stem cells G-CSF-mobilized Female	--
8	chr19:23412600-23432000	Weak transcription	Pancreas	Pancrea
9	chr19:23413600-23431200	ZNF genes & repeats	Primary hematopoietic stem cells	blood
10	chr19:23413600-23431600	ZNF genes & repeats	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
11	chr19:23414200-23432200	Weak transcription	Gastric	stomach
12	chr19:23414200-23432200	Weak transcription	Ovary	ovary
13	chr19:23416800-23431600	ZNF genes & repeats	H9 Derived Neuron Cultured Cells	ES cell derived
14	chr19:23418400-23429600	ZNF genes & repeats	GM12878-XiMat	blood
15	chr19:23419800-23430000	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
16	chr19:23420600-23429000	ZNF genes & repeats	Primary B cells from cord blood	blood
17	chr19:23420600-23431600	ZNF genes & repeats	Foreskin Keratinocyte Primary Cells skin03	Skin
18	chr19:23421400-23427400	ZNF genes & repeats	Thymus	Thymus
19	chr19:23423400-23432200	Weak transcription	Left Ventricle	heart
20	chr19:23423800-23427600	ZNF genes & repeats	ES-I3 Cell Line	embryonic stem cell
21	chr19:23424000-23431600	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
22	chr19:23424200-23427400	ZNF genes & repeats	HUES64 Cell Line	embryonic stem cell
23	chr19:23424400-23431000	Strong transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
24	chr19:23424600-23431400	ZNF genes & repeats	Brain Germinal Matrix	brain
25	chr19:23424800-23431800	Weak transcription	Rectal Smooth Muscle	rectum
26	chr19:23424800-23431800	Weak transcription	Osteobl	bone
27	chr19:23425000-23427400	ZNF genes & repeats	Fetal Intestine Small	intestine
28	chr19:23425000-23427600	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
29	chr19:23425000-23431200	Strong transcription	HUES48 Cell Line	embryonic stem cell
30	chr19:23425000-23431800	Weak transcription	Primary T helper naive cells from peripheral blood	blood
31	chr19:23425000-23432000	Weak transcription	Brain Hippocampus Middle	brain
32	chr19:23425000-23432200	Weak transcription	Brain Angular Gyrus	brain
33	chr19:23425000-23432200	Weak transcription	HSMMtube	muscle
34	chr19:23425200-23428000	Strong transcription	Foreskin Fibroblast Primary Cells skin01	Skin
35	chr19:23425200-23430200	Weak transcription	Fetal Lung	lung
36	chr19:23425200-23430400	Strong transcription	H1 Cell Line	embryonic stem cell
37	chr19:23425200-23430400	Strong transcription	iPS-20b Cell Line	embryonic stem cell
38	chr19:23425200-23430400	Weak transcription	HepG2	liver
39	chr19:23425200-23430600	Weak transcription	Primary T helper cells PMA-I stimulated	--
40	chr19:23425200-23431400	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
41	chr19:23425200-23431800	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
42	chr19:23425200-23431800	Weak transcription	Primary T helper cells fromperipheralblood	blood
43	chr19:23425200-23431800	Weak transcription	NHDF-Ad	bronchial
44	chr19:23425200-23431800	Weak transcription	NHLF	lung
45	chr19:23425200-23432000	Weak transcription	Primary B cells from peripheral blood	blood
46	chr19:23425200-23432000	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
47	chr19:23425200-23432000	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
48	chr19:23425200-23432000	Weak transcription	Brain Anterior Caudate	brain
49	chr19:23425200-23432000	Weak transcription	Duodenum Smooth Muscle	Duodenum
50	chr19:23425200-23432000	Weak transcription	Fetal Brain Male	brain

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links