Variant report

Variant	rs3136646
Chromosome Location	chr19:39399277-39399278
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr19:39398838..39403067-chr19:39419638..39422578,4	MCF-7	breast:
2	chr19:39388731..39393423-chr19:39394024..39400037,10	K562	blood:
3	chr19:39337064..39339680-chr19:39397865..39400024,2	K562	blood:
4	chr19:39339924..39344199-chr19:39398243..39400684,3	MCF-7	breast:
5	chr19:39398169..39400794-chr19:39403289..39404909,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000104835	Chromatin interaction
ENSG00000104825	Chromatin interaction
ENSG00000068903	Chromatin interaction
ENSG00000104824	Chromatin interaction
ENSG00000128626	Chromatin interaction

Extended variants
information (count: 11 )
Associated
traits (count: 6 )

rSNPs within LD-proxies of this variant (count:6)

rs_ID	r²[population]
rs12975517	0.86[CEU][hapmap];0.80[EUR][1000 genomes]
rs12977011	0.86[CEU][hapmap]
rs12985277	0.87[CEU][hapmap];0.84[GIH][hapmap];0.94[MEX][hapmap];0.86[TSI][hapmap];1.00[YRI][hapmap];0.82[EUR][1000 genomes]
rs12985768	0.83[EUR][1000 genomes]
rs2241704	0.85[CHB][hapmap];0.92[JPT][hapmap]
rs4803045	0.93[CEU][hapmap];0.88[MEX][hapmap];0.83[TSI][hapmap]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1057899	chr19:39088319-39475493	Flanking Active TSS Flanking Bivalent TSS/Enh Genic enhancers Weak transcription Transcr. at gene 5' and 3' Enhancers Bivalent Enhancer Active TSS Strong transcription Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	82 gene(s)	inside rSNPs	diseases
2	esv1837023	chr19:39190588-39425722	Active TSS Enhancers Weak transcription Genic enhancers Flanking Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Strong transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	65 gene(s)	inside rSNPs	diseases
3	esv1798153	chr19:39338663-39399277	Weak transcription Flanking Active TSS Genic enhancers Enhancers Active TSS ZNF genes & repeats Strong transcription Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	38 gene(s)	inside rSNPs	diseases
4	nsv911676	chr19:39395654-39399277	Strong transcription Weak transcription Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Enhancers	Chromatin interactive region	7 gene(s)	inside rSNPs	diseases
5	nsv911677	chr19:39395654-39404457	Strong transcription Weak transcription Enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats Flanking Active TSS Genic enhancers Bivalent/Poised TSS Active TSS	TF binding region CpG island Chromatin interactive region	7 gene(s)	inside rSNPs	diseases

mRNA abundance (count:6)

SNP	Gene	Cis/trans	Tissue	Source
rs3136646	NFKBIB	Cis_1M	lymphoblastoid	RTeQTL
rs3136646	GPR4	cis	parietal	SCAN
rs3136646	LGALS14	cis	parietal	SCAN
rs3136646	CTC-360G5.9	cis	Skin Sun Exposed Lower leg	GTEx
rs3136646	MYPOP	cis	parietal	SCAN
rs3136646	NAPA	cis	parietal	SCAN

Chromatin state (count:118 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr19:39391200-39420800	Weak transcription	Small Intestine	intestine
2	chr19:39391400-39402200	Weak transcription	Fetal Brain Male	brain
3	chr19:39391600-39414800	Weak transcription	HMEC	breast
4	chr19:39391600-39420600	Weak transcription	Right Atrium	heart
5	chr19:39391800-39399600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
6	chr19:39391800-39400400	Weak transcription	Pancreatic Islets	Pancreatic Islet
7	chr19:39391800-39401800	Weak transcription	Fetal Lung	lung
8	chr19:39391800-39412200	Weak transcription	Osteobl	bone
9	chr19:39392000-39399600	Weak transcription	K562	blood
10	chr19:39392400-39399400	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
11	chr19:39392400-39414800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
12	chr19:39392600-39406000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
13	chr19:39392600-39414600	Weak transcription	Primary T killer memory cells from peripheral blood	blood
14	chr19:39392600-39418800	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
15	chr19:39393600-39400200	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
16	chr19:39393800-39400200	Strong transcription	Primary B cells from cord blood	blood
17	chr19:39394000-39401200	Strong transcription	Fetal Intestine Small	intestine
18	chr19:39394200-39401200	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
19	chr19:39394600-39401200	Strong transcription	Fetal Stomach	stomach
20	chr19:39394800-39399400	Strong transcription	Primary T helper cells fromperipheralblood	blood
21	chr19:39394800-39399800	Strong transcription	Primary monocytes fromperipheralblood	blood
22	chr19:39394800-39399800	Strong transcription	Duodenum Smooth Muscle	Duodenum
23	chr19:39394800-39400000	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
24	chr19:39394800-39400000	Strong transcription	Brain Cingulate Gyrus	brain
25	chr19:39394800-39400000	Strong transcription	Spleen	Spleen
26	chr19:39394800-39400200	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
27	chr19:39394800-39400200	Strong transcription	Dnd41	blood
28	chr19:39394800-39401000	Strong transcription	Gastric	stomach
29	chr19:39394800-39401800	Strong transcription	Breast Myoepithelial Primary Cells	Breast
30	chr19:39395000-39399400	Strong transcription	Primary T helper 17 cells PMA-I stimulated	--
31	chr19:39395000-39400000	Strong transcription	Primary neutrophils fromperipheralblood	blood
32	chr19:39395000-39400000	Strong transcription	Cortex derived primary cultured neurospheres	brain
33	chr19:39395000-39400000	Strong transcription	Monocytes-CD14+_RO01746	blood
34	chr19:39395000-39400200	Strong transcription	Duodenum Mucosa	Duodenum
35	chr19:39395000-39400200	Strong transcription	Lung	lung
36	chr19:39395000-39400400	Strong transcription	Brain Inferior Temporal Lobe	brain
37	chr19:39395000-39400400	Strong transcription	Fetal Muscle Trunk	muscle
38	chr19:39395000-39400400	Strong transcription	Stomach Smooth Muscle	stomach
39	chr19:39395000-39401000	Strong transcription	Adipose Nuclei	Adipose
40	chr19:39395000-39401200	Strong transcription	Skeletal Muscle Female	skeletal muscle
41	chr19:39395000-39401400	Strong transcription	Skeletal Muscle Male	skeletal muscle
42	chr19:39395000-39401600	Strong transcription	Fetal Muscle Leg	muscle
43	chr19:39395200-39399600	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
44	chr19:39395200-39399800	Strong transcription	Ovary	ovary
45	chr19:39395200-39400200	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
46	chr19:39395200-39400200	Strong transcription	Colonic Mucosa	Colon
47	chr19:39395200-39400800	Strong transcription	Thymus	Thymus
48	chr19:39395200-39401000	Strong transcription	Brain Hippocampus Middle	brain
49	chr19:39395200-39401200	Strong transcription	Right Ventricle	heart
50	chr19:39395400-39400400	Strong transcription	Esophagus	oesophagus

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