Variant report

Variant	rs16828066
Chromosome Location	chr2:187473632-187473633
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr2:187463673..187465188-chr2:187472518..187475154,2	MCF-7	breast:
2	chr2:187473194..187474789-chr2:187497969..187500920,2	K562	blood:
3	chr2:187473255..187475524-chr2:187477074..187478666,2	K562	blood:
4	chr2:187466949..187471073-chr2:187471987..187477288,6	MCF-7	breast:
5	chr2:187454467..187456170-chr2:187472478..187474784,2	MCF-7	breast:
6	chr2:187473139..187475194-chr2:187476719..187478486,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000138448	Chromatin interaction

Extended variants
information (count: 23 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:16)

rs_ID	r²[population]
rs10176423	1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs10190423	1.00[YRI][hapmap];0.88[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs13385496	0.93[AFR][1000 genomes]
rs13390676	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs13416778	1.00[YRI][hapmap];0.88[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs13421909	1.00[YRI][hapmap];0.88[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs13424365	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs16823857	1.00[YRI][hapmap];0.88[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs16828115	1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73979194	0.93[AFR][1000 genomes]
rs73979318	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73979328	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73979331	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs9288131	0.93[AFR][1000 genomes]
rs9288132	1.00[YRI][hapmap];0.93[AFR][1000 genomes]
rs9973509	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:7 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv2757844	chr2:187332780-187580547	Active TSS Enhancers Strong transcription Weak transcription Flanking Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	13 gene(s)	inside rSNPs	diseases
2	esv2759107	chr2:187332780-187580547	Enhancers Bivalent/Poised TSS Active TSS Genic enhancers Weak transcription Strong transcription Flanking Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	13 gene(s)	inside rSNPs	diseases
3	nsv875552	chr2:187393729-187505486	Weak transcription Active TSS Enhancers Genic enhancers Flanking Active TSS Strong transcription Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
4	nsv1014203	chr2:187413781-187477586	Weak transcription Active TSS Flanking Active TSS Enhancers Genic enhancers Strong transcription Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region	8 gene(s)	inside rSNPs	diseases
5	nsv536083	chr2:187413781-187477586	Flanking Active TSS Enhancers Weak transcription Flanking Bivalent TSS/Enh Genic enhancers Active TSS Strong transcription Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region	8 gene(s)	inside rSNPs	diseases
6	esv2756956	chr2:187416599-187492742	Enhancers Flanking Active TSS Strong transcription Weak transcription Active TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region	9 gene(s)	inside rSNPs	diseases
7	nsv818105	chr2:187423298-187481835	Weak transcription Enhancers Flanking Active TSS Active TSS Strong transcription Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region	8 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:102 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:187456000-187488200	Weak transcription	Primary T cells fromperipheralblood	blood
2	chr2:187456200-187508600	Weak transcription	Esophagus	oesophagus
3	chr2:187456200-187533000	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
4	chr2:187456400-187488200	Weak transcription	Fetal Thymus	thymus
5	chr2:187456400-187504000	Weak transcription	Fetal Muscle Trunk	muscle
6	chr2:187456600-187514000	Weak transcription	Thymus	Thymus
7	chr2:187456600-187520000	Weak transcription	Primary T helper cells fromperipheralblood	blood
8	chr2:187456800-187493400	Weak transcription	Brain Germinal Matrix	brain
9	chr2:187456800-187534400	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
10	chr2:187457200-187506000	Weak transcription	Liver	Liver
11	chr2:187457200-187533800	Weak transcription	Spleen	Spleen
12	chr2:187458000-187511400	Weak transcription	Primary T helper cells PMA-I stimulated	--
13	chr2:187458000-187529000	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
14	chr2:187458600-187477000	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
15	chr2:187459400-187505600	Weak transcription	NHLF	lung
16	chr2:187460200-187477200	Weak transcription	GM12878-XiMat	blood
17	chr2:187460200-187506200	Weak transcription	Small Intestine	intestine
18	chr2:187460800-187475600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
19	chr2:187460800-187486800	Weak transcription	Pancreatic Islets	Pancreatic Islet
20	chr2:187462000-187477600	Genic enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
21	chr2:187462600-187475800	Weak transcription	Lung	lung
22	chr2:187462600-187500600	Weak transcription	iPS-18 Cell Line	embryonic stem cell
23	chr2:187462800-187515400	Weak transcription	Gastric	stomach
24	chr2:187464400-187477000	Weak transcription	Duodenum Smooth Muscle	Duodenum
25	chr2:187464800-187536200	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
26	chr2:187465800-187529200	Weak transcription	Dnd41	blood
27	chr2:187466800-187533200	Weak transcription	Colonic Mucosa	Colon
28	chr2:187467000-187474200	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
29	chr2:187467200-187528600	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
30	chr2:187467400-187515800	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
31	chr2:187467600-187506000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
32	chr2:187468800-187504000	Weak transcription	NHDF-Ad	bronchial
33	chr2:187469000-187487200	Weak transcription	Fetal Muscle Leg	muscle
34	chr2:187469000-187501800	Weak transcription	Fetal Intestine Small	intestine
35	chr2:187469400-187487000	Weak transcription	Primary monocytes fromperipheralblood	blood
36	chr2:187469600-187488000	Weak transcription	Placenta Amnion	Placenta Amnion
37	chr2:187469600-187488200	Weak transcription	HUES48 Cell Line	embryonic stem cell
38	chr2:187469800-187477000	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
39	chr2:187470000-187475600	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
40	chr2:187470000-187475600	Weak transcription	Pancreas	Pancrea
41	chr2:187470000-187476000	Enhancers	Fetal Heart	heart
42	chr2:187470000-187476200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
43	chr2:187470000-187487200	Weak transcription	Stomach Smooth Muscle	stomach
44	chr2:187470000-187488000	Weak transcription	iPS-20b Cell Line	embryonic stem cell
45	chr2:187470000-187488600	Weak transcription	Fetal Stomach	stomach
46	chr2:187470200-187473800	Strong transcription	NH-A	brain
47	chr2:187470200-187475600	Weak transcription	K562	blood
48	chr2:187470200-187476800	Weak transcription	Brain Anterior Caudate	brain
49	chr2:187470200-187476800	Weak transcription	Brain Hippocampus Middle	brain
50	chr2:187470200-187482000	Weak transcription	Brain Inferior Temporal Lobe	brain

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