Variant report

Variant	rs11668109
Chromosome Location	chr19:41863777-41863778
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:2)
CpG islands
(count:0)
Chromatin interactive
region (count:6)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:2 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr19:41863628-41863868	K562	blood:	n/a	n/a
2	POLR2A	chr19:41863513-41864089	K562	blood:	n/a	n/a

No data

(count:6 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr19:41817873..41820006-chr19:41861978..41863961,2	MCF-7	breast:
2	chr19:41830987..41833840-chr19:41863132..41865918,2	MCF-7	breast:
3	chr19:41861604..41864575-chr19:41933607..41936595,2	MCF-7	breast:
4	chr19:41857382..41861361-chr19:41862121..41864311,4	MCF-7	breast:
5	chr19:41861983..41864638-chr19:41901106..41902845,2	K562	blood:
6	chr19:41773177..41775428-chr19:41862165..41864335,2	K562	blood:

No data

Variant related genes	Relation type
TGFB1	TF binding region
ENSG00000142046	Chromatin interaction
ENSG00000105323	Chromatin interaction
ENSG00000177191	Chromatin interaction
ENSG00000105329	Chromatin interaction

Extended variants
information (count: 13 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:11)

rs_ID	r²[population]
rs12462166	0.82[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs12983775	0.80[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs1549933	0.83[AMR][1000 genomes]
rs1800469	0.83[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs1982072	0.84[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs2241712	0.83[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs2241714	0.83[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs2241715	0.85[EUR][1000 genomes]
rs2317130	0.82[EUR][1000 genomes]
rs4803458	0.82[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs9797885	0.82[AMR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv1802868	chr19:41856886-41869392	Active TSS Enhancers Flanking Active TSS Weak transcription Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3' Strong transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region	17 gene(s)	inside rSNPs	diseases
2	nsv521311	chr19:41856886-41882712	Weak transcription Flanking Active TSS Active TSS Enhancers Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer Strong transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region	20 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs11668109	CTC-435M10.6	cis	Whole Blood	GTEx

Chromatin state (count:89 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr19:41859800-41868200	Weak transcription	Sigmoid Colon	Sigmoid Colon
2	chr19:41860000-41863800	Enhancers	Primary T cells effector/memory enriched fromperipheralblood	blood
3	chr19:41860200-41864000	Weak transcription	Small Intestine	intestine
4	chr19:41860200-41864800	Enhancers	Primary monocytes fromperipheralblood	blood
5	chr19:41860200-41865000	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
6	chr19:41860200-41869000	Weak transcription	Gastric	stomach
7	chr19:41860400-41864400	Enhancers	Primary mononuclear cells fromperipheralblood	Blood
8	chr19:41860400-41864800	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
9	chr19:41860400-41865800	Enhancers	Primary T cells fromperipheralblood	blood
10	chr19:41860400-41868200	Weak transcription	Rectal Mucosa Donor 31	rectum
11	chr19:41860400-41868600	Weak transcription	GM12878-XiMat	blood
12	chr19:41860400-41868800	Weak transcription	Hela-S3	cervix
13	chr19:41860400-41869000	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
14	chr19:41860400-41869000	Weak transcription	Brain Angular Gyrus	brain
15	chr19:41860400-41869000	Weak transcription	Rectal Smooth Muscle	rectum
16	chr19:41860400-41869200	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
17	chr19:41860400-41869200	Weak transcription	Cortex derived primary cultured neurospheres	brain
18	chr19:41860400-41869200	Weak transcription	HSMMtube	muscle
19	chr19:41860400-41869200	Weak transcription	HUVEC	blood vessel
20	chr19:41860400-41869200	Weak transcription	NHDF-Ad	bronchial
21	chr19:41860400-41869200	Weak transcription	NHLF	lung
22	chr19:41860400-41869400	Weak transcription	Aorta	Aorta
23	chr19:41860400-41869400	Weak transcription	Ovary	ovary
24	chr19:41860600-41864600	Enhancers	Primary hematopoietic stem cells	blood
25	chr19:41860600-41864600	Enhancers	Primary hematopoietic stem cells short term culture	blood
26	chr19:41860600-41864800	Enhancers	Fetal Thymus	thymus
27	chr19:41860600-41866800	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
28	chr19:41860600-41866800	Weak transcription	A549	lung
29	chr19:41860600-41868200	Weak transcription	Fetal Intestine Small	intestine
30	chr19:41860600-41868200	Weak transcription	Rectal Mucosa Donor 29	rectum
31	chr19:41860600-41868400	Weak transcription	Duodenum Mucosa	Duodenum
32	chr19:41860600-41868600	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
33	chr19:41860600-41868800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
34	chr19:41860600-41869000	Weak transcription	Duodenum Smooth Muscle	Duodenum
35	chr19:41860600-41869200	Weak transcription	Muscle Satellite Cultured Cells	--
36	chr19:41860600-41869200	Weak transcription	Brain Substantia Nigra	brain
37	chr19:41860600-41869200	Weak transcription	Esophagus	oesophagus
38	chr19:41860600-41869200	Weak transcription	Osteobl	bone
39	chr19:41860800-41868600	Weak transcription	Pancreas	Pancrea
40	chr19:41860800-41869200	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
41	chr19:41860800-41869200	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
42	chr19:41860800-41869200	Weak transcription	Placenta Amnion	Placenta Amnion
43	chr19:41860800-41869200	Weak transcription	Right Ventricle	heart
44	chr19:41861000-41868400	Weak transcription	Dnd41	blood
45	chr19:41861000-41868600	Weak transcription	Fetal Brain Female	brain
46	chr19:41861000-41869200	Weak transcription	Liver	Liver
47	chr19:41861200-41869200	Weak transcription	Fetal Kidney	kidney
48	chr19:41861400-41869000	Weak transcription	Breast Myoepithelial Primary Cells	Breast
49	chr19:41861600-41868400	Weak transcription	K562	blood
50	chr19:41861600-41868800	Weak transcription	Stomach Smooth Muscle	stomach

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