Variant report

Variant	rs6719049
Chromosome Location	chr2:47073302-47073303
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr2:47072385..47074201-chr2:47081615..47083494,2	K562	blood:

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-AC016722.1.1-1	chr2:47073015-47074176	XLOC_001458

Variant related genes	Relation type
ENSG00000239332	Chromatin interaction

Extended variants
information (count: 14 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:10)

rs_ID	r²[population]
rs1579862	0.96[CEU][hapmap];0.84[MEX][hapmap];0.90[TSI][hapmap];0.90[EUR][1000 genomes]
rs1579863	0.80[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs17774013	0.85[YRI][hapmap];0.87[AFR][1000 genomes];0.81[EUR][1000 genomes]
rs17774133	0.88[CEU][hapmap];0.92[GIH][hapmap];0.83[JPT][hapmap];0.94[MEX][hapmap];0.95[TSI][hapmap];0.91[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs1867821	0.88[CEU][hapmap];0.83[JPT][hapmap];0.91[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs1947109	0.87[EUR][1000 genomes]
rs55642514	0.90[AMR][1000 genomes]
rs6544931	0.87[TSI][hapmap]
rs7593289	0.91[GIH][hapmap]
rs7597025	0.87[TSI][hapmap]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv817517	chr2:46819371-47715140	Enhancers Weak transcription Genic enhancers Bivalent Enhancer Flanking Active TSS Strong transcription Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	152 gene(s)	inside rSNPs	diseases
2	nsv457352	chr2:47004788-47325973	Active TSS Enhancers Genic enhancers Strong transcription Weak transcription Flanking Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	37 gene(s)	inside rSNPs	diseases
3	nsv581749	chr2:47004788-47325973	Flanking Active TSS Enhancers Genic enhancers Strong transcription Weak transcription Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	37 gene(s)	inside rSNPs	diseases
4	nsv1004828	chr2:47056849-47814482	Weak transcription Enhancers Strong transcription Genic enhancers Flanking Active TSS Transcr. at gene 5' and 3' Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	144 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs6719049	CRIPT	cis	Liver	GTEx
rs6719049	CRIPT	cis	multi-tissue	Pritchard
rs6719049	MCFD2	cis	parietal	SCAN
rs6719049	MCFD2	cis	cerebellum	SCAN

Chromatin state (count:62 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:47067400-47073400	Weak transcription	Osteobl	bone
2	chr2:47069400-47073400	Weak transcription	Stomach Mucosa	stomach
3	chr2:47069400-47073600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
4	chr2:47069400-47082400	Enhancers	Breast Myoepithelial Primary Cells	Breast
5	chr2:47070200-47073800	Enhancers	Stomach Smooth Muscle	stomach
6	chr2:47070400-47073800	Enhancers	Colon Smooth Muscle	Colon
7	chr2:47070800-47073600	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
8	chr2:47072000-47074400	Enhancers	Fetal Lung	lung
9	chr2:47072000-47078400	Enhancers	Lung	lung
10	chr2:47072000-47078400	Enhancers	Right Ventricle	heart
11	chr2:47072000-47078600	Enhancers	Fetal Stomach	stomach
12	chr2:47072000-47078600	Enhancers	Ovary	ovary
13	chr2:47072200-47073800	Enhancers	Rectal Smooth Muscle	rectum
14	chr2:47072200-47077000	Enhancers	Placenta	Placenta
15	chr2:47072200-47078400	Enhancers	Left Ventricle	heart
16	chr2:47072200-47078600	Enhancers	Pancreas	Pancrea
17	chr2:47072200-47078800	Enhancers	Fetal Adrenal Gland	Adrenal Gland
18	chr2:47072400-47074200	Enhancers	Skeletal Muscle Male	skeletal muscle
19	chr2:47072400-47074400	Enhancers	Skeletal Muscle Female	skeletal muscle
20	chr2:47072400-47078600	Enhancers	Fetal Intestine Small	intestine
21	chr2:47072600-47074600	Enhancers	A549	lung
22	chr2:47072600-47077600	Enhancers	Brain Hippocampus Middle	brain
23	chr2:47072600-47078000	Enhancers	Small Intestine	intestine
24	chr2:47072600-47078400	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
25	chr2:47072600-47078400	Enhancers	Fetal Heart	heart
26	chr2:47072600-47078800	Enhancers	HUVEC	blood vessel
27	chr2:47072600-47080400	Enhancers	HMEC	breast
28	chr2:47072800-47073800	Enhancers	Colonic Mucosa	Colon
29	chr2:47072800-47074000	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
30	chr2:47072800-47074200	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
31	chr2:47072800-47074600	Enhancers	Duodenum Mucosa	Duodenum
32	chr2:47072800-47075200	Enhancers	Spleen	Spleen
33	chr2:47072800-47075400	Enhancers	Cortex derived primary cultured neurospheres	brain
34	chr2:47072800-47076000	Enhancers	Brain Substantia Nigra	brain
35	chr2:47072800-47076200	Enhancers	Fetal Muscle Leg	muscle
36	chr2:47072800-47077200	Enhancers	Brain Dorsolateral Prefrontal Cortex	brain
37	chr2:47072800-47078000	Enhancers	Fetal Intestine Large	intestine
38	chr2:47072800-47078600	Enhancers	Right Atrium	heart
39	chr2:47072800-47078600	Enhancers	NHDF-Ad	bronchial
40	chr2:47072800-47080200	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
41	chr2:47072800-47080400	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
42	chr2:47073000-47073400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
43	chr2:47073000-47073800	Enhancers	Rectal Mucosa Donor 31	rectum
44	chr2:47073000-47073800	Flanking Active TSS	NHEK	skin
45	chr2:47073000-47074000	Enhancers	Hela-S3	cervix
46	chr2:47073000-47074200	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
47	chr2:47073000-47074200	Enhancers	Fetal Brain Male	brain
48	chr2:47073000-47074400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
49	chr2:47073000-47075000	Enhancers	Fetal Brain Female	brain
50	chr2:47073000-47077000	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived

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