Variant report

Variant	rs562880
Chromosome Location	chr11:102338625-102338626
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr11:102320576..102325526-chr11:102337005..102343107,13	MCF-7	breast:
2	chr11:102321122..102328963-chr11:102333676..102341979,14	MCF-7	breast:

Variant related genes	Relation type
ENSG00000152558	Chromatin interaction
ENSG00000255337	Chromatin interaction

Extended variants
information (count: 15 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:7)

rs_ID	r²[population]
rs1893730	1.00[GIH][hapmap];1.00[TSI][hapmap];0.83[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs2096894	0.86[EUR][1000 genomes]
rs2155839	0.83[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs3897655	0.87[EUR][1000 genomes]
rs4754846	1.00[GIH][hapmap];1.00[TSI][hapmap];0.83[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs6590961	0.93[EUR][1000 genomes]
rs721916	0.95[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:8 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv3514195	chr11:102118479-102348362	Weak transcription Flanking Active TSS Active TSS Strong transcription Genic enhancers ZNF genes & repeats Enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	13 gene(s)	inside rSNPs	diseases
2	esv3514197	chr11:102118479-102348362	ZNF genes & repeats Enhancers Weak transcription Flanking Active TSS Active TSS Strong transcription Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	13 gene(s)	inside rSNPs	diseases
3	nsv1035567	chr11:102264516-102431607	Enhancers Weak transcription Flanking Active TSS Strong transcription Active TSS ZNF genes & repeats Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	8 gene(s)	inside rSNPs	diseases
4	nsv898334	chr11:102272884-102353192	Weak transcription Flanking Active TSS Strong transcription Enhancers Genic enhancers Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
5	nsv469990	chr11:102335609-102413943	Weak transcription Enhancers Flanking Active TSS Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
6	nsv556150	chr11:102335609-102415859	Enhancers Weak transcription Flanking Active TSS Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
7	nsv468854	chr11:102336617-102413943	Enhancers Weak transcription Active TSS Flanking Active TSS Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
8	nsv556151	chr11:102336617-102413943	Weak transcription Active TSS Flanking Active TSS Enhancers Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs562880	DYNC2H1	cis	parietal	SCAN

Chromatin state (count:65 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:102324600-102344600	Weak transcription	Colonic Mucosa	Colon
2	chr11:102333200-102340800	Enhancers	Primary T cells from cord blood	blood
3	chr11:102334800-102339200	Enhancers	Primary hematopoietic stem cells short term culture	blood
4	chr11:102334800-102345600	Enhancers	Primary T helper cells fromperipheralblood	blood
5	chr11:102335000-102338800	Enhancers	Primary T helper cells PMA-I stimulated	--
6	chr11:102335000-102339600	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
7	chr11:102335000-102343200	Enhancers	Primary T helper naive cells from peripheral blood	blood
8	chr11:102335000-102343200	Enhancers	Primary T killer naive cells fromperipheralblood	blood
9	chr11:102335000-102343600	Enhancers	Primary T killer memory cells from peripheral blood	blood
10	chr11:102335200-102343400	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
11	chr11:102335400-102342400	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
12	chr11:102335600-102342000	Enhancers	Primary T cells effector/memory enriched fromperipheralblood	blood
13	chr11:102336400-102338800	Enhancers	Rectal Mucosa Donor 29	rectum
14	chr11:102336400-102339800	Weak transcription	Primary monocytes fromperipheralblood	blood
15	chr11:102336600-102341400	Weak transcription	Primary neutrophils fromperipheralblood	blood
16	chr11:102336800-102339800	Weak transcription	Monocytes-CD14+_RO01746	blood
17	chr11:102337000-102339600	Enhancers	Fetal Thymus	thymus
18	chr11:102337000-102340000	Enhancers	Rectal Mucosa Donor 31	rectum
19	chr11:102337000-102341400	Enhancers	Colon Smooth Muscle	Colon
20	chr11:102337000-102343000	Enhancers	Placenta	Placenta
21	chr11:102337200-102339600	Enhancers	Sigmoid Colon	Sigmoid Colon
22	chr11:102337200-102340000	Weak transcription	Primary B cells from cord blood	blood
23	chr11:102337200-102340200	Weak transcription	Primary B cells from peripheral blood	blood
24	chr11:102337200-102340600	Enhancers	Fetal Intestine Small	intestine
25	chr11:102337200-102340800	Enhancers	Placenta Amnion	Placenta Amnion
26	chr11:102337400-102339200	Enhancers	Breast Myoepithelial Primary Cells	Breast
27	chr11:102337400-102339800	Weak transcription	Fetal Lung	lung
28	chr11:102337400-102339800	Enhancers	Stomach Mucosa	stomach
29	chr11:102337400-102340400	Enhancers	Fetal Intestine Large	intestine
30	chr11:102337400-102340800	Enhancers	Pancreas	Pancrea
31	chr11:102337400-102341000	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
32	chr11:102337400-102341000	Enhancers	HepG2	liver
33	chr11:102337400-102342400	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
34	chr11:102337400-102342600	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
35	chr11:102337600-102339000	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
36	chr11:102337600-102339600	Enhancers	NHEK	skin
37	chr11:102337600-102340600	Enhancers	Esophagus	oesophagus
38	chr11:102337600-102342800	Enhancers	HMEC	breast
39	chr11:102337800-102338800	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
40	chr11:102337800-102340200	Enhancers	Rectal Smooth Muscle	rectum
41	chr11:102338000-102340000	Weak transcription	Thymus	Thymus
42	chr11:102338000-102340200	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
43	chr11:102338000-102340200	Weak transcription	Gastric	stomach
44	chr11:102338000-102347000	Weak transcription	Small Intestine	intestine
45	chr11:102338200-102339200	Weak transcription	Primary T cells fromperipheralblood	blood
46	chr11:102338200-102340200	Weak transcription	Lung	lung
47	chr11:102338400-102339000	Enhancers	Brain Angular Gyrus	brain
48	chr11:102338400-102339400	Enhancers	Liver	Liver
49	chr11:102338400-102339800	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
50	chr11:102338400-102340000	Enhancers	K562	blood

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