Variant report

Variant	rs2346176
Chromosome Location	chr2:46593299-46593300
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr2:46591157..46594128-chr2:46607853..46610004,2	MCF-7	breast:
2	chr2:46593206..46594772-chr2:46602945..46604592,2	K562	blood:
3	chr2:46484642..46486699-chr2:46592173..46593939,2	K562	blood:
4	chr2:46237927..46238645-chr2:46593172..46594132,3	MCF-7	breast:
5	chr2:46586164..46589641-chr2:46590092..46593590,4	K562	blood:
6	chr2:46593115..46594090-chr2:46688546..46689223,4	MCF-7	breast:
7	chr2:46593059..46594102-chr2:46688159..46689154,5	MCF-7	breast:

Variant related genes	Relation type
ENSG00000116016	Chromatin interaction

Extended variants
information (count: 8 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:4)

rs_ID	r²[population]
rs1530633	1.00[YRI][hapmap];0.88[AFR][1000 genomes]
rs1562452	1.00[YRI][hapmap]
rs3754556	0.87[MKK][hapmap];0.85[YRI][hapmap]
rs4953356	0.87[YRI][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	nsv1012446	chr2:45921682-46737036	Enhancers Weak transcription Bivalent Enhancer Flanking Active TSS Strong transcription Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	62 gene(s)	inside rSNPs	diseases
2	nsv916169	chr2:46310963-46622603	Weak transcription Enhancers Genic enhancers Strong transcription Bivalent/Poised TSS Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	25 gene(s)	inside rSNPs	diseases
3	esv2757795	chr2:46532812-46874151	Weak transcription Enhancers Active TSS Flanking Active TSS Strong transcription Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	52 gene(s)	inside rSNPs	diseases
4	esv2759046	chr2:46532812-46874151	Active TSS Enhancers Flanking Active TSS Strong transcription Weak transcription Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	52 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs2346176	SIX3	cis	cerebellum	SCAN

Chromatin state (count:82 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:46568000-46596600	Weak transcription	Colon Smooth Muscle	Colon
2	chr2:46573200-46613000	Strong transcription	Hela-S3	cervix
3	chr2:46574600-46607200	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
4	chr2:46574800-46613000	Weak transcription	HSMM	muscle
5	chr2:46580000-46594600	Weak transcription	Psoas Muscle	Psoas
6	chr2:46580600-46597200	Weak transcription	Fetal Heart	heart
7	chr2:46581200-46597000	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
8	chr2:46585200-46594600	Weak transcription	Brain Cingulate Gyrus	brain
9	chr2:46585400-46594000	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
10	chr2:46586600-46604000	Weak transcription	HSMMtube	muscle
11	chr2:46588600-46604800	Weak transcription	Stomach Mucosa	stomach
12	chr2:46588800-46596800	Weak transcription	Stomach Smooth Muscle	stomach
13	chr2:46588800-46597200	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
14	chr2:46588800-46598800	Weak transcription	Pancreatic Islets	Pancreatic Islet
15	chr2:46589000-46594800	Genic enhancers	Liver	Liver
16	chr2:46589200-46596200	Weak transcription	Skeletal Muscle Female	skeletal muscle
17	chr2:46589200-46597000	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
18	chr2:46589400-46594600	Weak transcription	Fetal Muscle Trunk	muscle
19	chr2:46589400-46596200	Weak transcription	Fetal Intestine Large	intestine
20	chr2:46589400-46596800	Weak transcription	Duodenum Smooth Muscle	Duodenum
21	chr2:46589600-46593600	Genic enhancers	A549	lung
22	chr2:46589600-46597000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
23	chr2:46589800-46594600	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
24	chr2:46589800-46594600	Weak transcription	Spleen	Spleen
25	chr2:46589800-46594800	Weak transcription	Colonic Mucosa	Colon
26	chr2:46589800-46597000	Weak transcription	Rectal Smooth Muscle	rectum
27	chr2:46589800-46616600	Weak transcription	Thymus	Thymus
28	chr2:46590000-46594400	Weak transcription	Primary hematopoietic stem cells	blood
29	chr2:46590000-46594800	Weak transcription	Right Ventricle	heart
30	chr2:46590000-46595400	Weak transcription	Fetal Thymus	thymus
31	chr2:46590200-46596400	Weak transcription	Esophagus	oesophagus
32	chr2:46590400-46593600	Weak transcription	Sigmoid Colon	Sigmoid Colon
33	chr2:46590400-46594400	Weak transcription	Fetal Intestine Small	intestine
34	chr2:46590400-46596400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
35	chr2:46590600-46594400	Weak transcription	Skeletal Muscle Male	skeletal muscle
36	chr2:46591000-46594600	Weak transcription	Aorta	Aorta
37	chr2:46591000-46594600	Weak transcription	Lung	lung
38	chr2:46591000-46594600	Weak transcription	Pancreas	Pancrea
39	chr2:46591000-46596200	Weak transcription	Ovary	ovary
40	chr2:46591000-46596400	Weak transcription	Gastric	stomach
41	chr2:46591000-46596800	Weak transcription	Primary T cells fromperipheralblood	blood
42	chr2:46591200-46595200	Weak transcription	Primary monocytes fromperipheralblood	blood
43	chr2:46591200-46595400	Weak transcription	Monocytes-CD14+_RO01746	blood
44	chr2:46591200-46596200	Weak transcription	Muscle Satellite Cultured Cells	--
45	chr2:46591200-46606400	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
46	chr2:46591400-46593600	Weak transcription	Left Ventricle	heart
47	chr2:46591400-46594200	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
48	chr2:46591400-46594600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
49	chr2:46591400-46596600	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
50	chr2:46591600-46594000	Enhancers	NHLF	lung

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