Variant report

Variant	rs714948
Chromosome Location	chr19:45165912-45165913
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr19:45164861..45166953-chr19:45250378..45253353,2	MCF-7	breast:
2	chr19:45163507..45165937-chr19:45174707..45176258,2	MCF-7	breast:
3	chr19:45165601..45167675-chr19:45169237..45171055,2	MCF-7	breast:
4	chr19:45165424..45170809-chr19:45174095..45176705,6	MCF-7	breast:
5	chr19:45163718..45166142-chr19:45347949..45350163,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000186567	Chromatin interaction
ENSG00000069399	Chromatin interaction
ENSG00000130202	Chromatin interaction

Extended variants
information (count: 7 )
Associated
traits (count: 8 )

rSNPs within LD-proxies of this variant (count:2)

rs_ID	r²[population]
rs56261258	1.00[AFR][1000 genomes];0.83[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs8103315	1.00[ASW][hapmap];1.00[AFR][1000 genomes]

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	nsv1062812	chr19:45042262-45214796	Enhancers Flanking Active TSS Weak transcription Genic enhancers Active TSS ZNF genes & repeats Strong transcription Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA	20 gene(s)	inside rSNPs	diseases
2	nsv912116	chr19:45146103-45298069	Weak transcription Strong transcription Flanking Active TSS Enhancers Genic enhancers Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA	29 gene(s)	inside rSNPs	diseases
3	esv1811264	chr19:45162189-45170547	Strong transcription Genic enhancers Weak transcription Enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Active TSS	TF binding region CpG island Chromatin interactive region	5 gene(s)	inside rSNPs	diseases
4	esv1812642	chr19:45162189-45170547	Weak transcription Genic enhancers Strong transcription Enhancers ZNF genes & repeats Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	5 gene(s)	inside rSNPs	diseases
5	esv1812853	chr19:45163671-45170547	Strong transcription Weak transcription Enhancers ZNF genes & repeats Genic enhancers Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	5 gene(s)	inside rSNPs	diseases

mRNA abundance (count:8)

SNP	Gene	Cis/trans	Tissue	Source
rs714948	SHANK1	cis	cerebellum	SCAN
rs714948	SIGLEC9	cis	cerebellum	SCAN
rs714948	SNORD33	cis	cerebellum	SCAN
rs714948	CCDC61	cis	parietal	SCAN
rs714948	CEACAM19	cis	Artery Tibial	GTEx
rs714948	SLC1A5	cis	parietal	SCAN
rs714948	CEACAM19	cis	Thyroid	GTEx
rs714948	KLK12	cis	cerebellum	SCAN

Chromatin state (count:109 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr19:45148200-45170200	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
2	chr19:45149200-45167000	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
3	chr19:45149400-45167200	Strong transcription	HUES6 Cell Line	embryonic stem cell
4	chr19:45150200-45167200	Strong transcription	Primary hematopoietic stem cells short term culture	blood
5	chr19:45150600-45167200	Strong transcription	HUES64 Cell Line	embryonic stem cell
6	chr19:45150600-45167200	Strong transcription	Brain Germinal Matrix	brain
7	chr19:45150600-45167400	Strong transcription	HUES48 Cell Line	embryonic stem cell
8	chr19:45150600-45167400	Strong transcription	Primary monocytes fromperipheralblood	blood
9	chr19:45150600-45167400	Strong transcription	Rectal Mucosa Donor 29	rectum
10	chr19:45151000-45167800	Strong transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
11	chr19:45151200-45166400	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
12	chr19:45151200-45166400	Strong transcription	Cortex derived primary cultured neurospheres	brain
13	chr19:45151400-45167000	Strong transcription	Breast Myoepithelial Primary Cells	Breast
14	chr19:45152000-45167800	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
15	chr19:45152400-45166600	Strong transcription	Stomach Smooth Muscle	stomach
16	chr19:45152600-45166800	Strong transcription	Rectal Mucosa Donor 31	rectum
17	chr19:45152600-45167000	Strong transcription	HUVEC	blood vessel
18	chr19:45152600-45169200	Strong transcription	Osteobl	bone
19	chr19:45152600-45178200	Weak transcription	Fetal Heart	heart
20	chr19:45153000-45167000	Strong transcription	Gastric	stomach
21	chr19:45153000-45168600	Strong transcription	NH-A	brain
22	chr19:45153400-45168600	Strong transcription	Lung	lung
23	chr19:45154000-45173400	Weak transcription	Small Intestine	intestine
24	chr19:45155000-45168400	Weak transcription	Primary T cells from cord blood	blood
25	chr19:45156000-45166800	Strong transcription	HepG2	liver
26	chr19:45157000-45167600	Weak transcription	Pancreatic Islets	Pancreatic Islet
27	chr19:45157800-45168400	Strong transcription	Left Ventricle	heart
28	chr19:45158200-45166400	Strong transcription	Sigmoid Colon	Sigmoid Colon
29	chr19:45158600-45166800	Strong transcription	Duodenum Mucosa	Duodenum
30	chr19:45158600-45167400	Strong transcription	Monocytes-CD14+_RO01746	blood
31	chr19:45159400-45167800	Strong transcription	Pancreas	Pancrea
32	chr19:45160600-45166400	Strong transcription	Adipose Nuclei	Adipose
33	chr19:45160600-45166800	Strong transcription	Duodenum Smooth Muscle	Duodenum
34	chr19:45160600-45170800	Strong transcription	Fetal Intestine Small	intestine
35	chr19:45160800-45166000	Strong transcription	Fetal Stomach	stomach
36	chr19:45160800-45166800	Strong transcription	Right Ventricle	heart
37	chr19:45160800-45166800	Strong transcription	HMEC	breast
38	chr19:45160800-45167800	Strong transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
39	chr19:45160800-45170600	Strong transcription	Fetal Intestine Large	intestine
40	chr19:45161000-45166000	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
41	chr19:45161000-45166000	Strong transcription	Brain Hippocampus Middle	brain
42	chr19:45161000-45166200	Strong transcription	Brain Cingulate Gyrus	brain
43	chr19:45161000-45166400	Strong transcription	Esophagus	oesophagus
44	chr19:45161000-45167000	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
45	chr19:45161000-45167200	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
46	chr19:45161000-45167200	Strong transcription	Placenta	Placenta
47	chr19:45161000-45169200	Strong transcription	Foreskin Fibroblast Primary Cells skin01	Skin
48	chr19:45161200-45166200	Strong transcription	Brain Anterior Caudate	brain
49	chr19:45161200-45166200	Strong transcription	Rectal Smooth Muscle	rectum
50	chr19:45161200-45166400	Strong transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived

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