Variant report

Variant	rs2649877
Chromosome Location	chr3:112961666-112961667
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 17 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:12)

rs_ID	r²[population]
rs2649876	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs4682476	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs58191991	1.00[AMR][1000 genomes]
rs58193594	1.00[AMR][1000 genomes]
rs58703340	1.00[AMR][1000 genomes]
rs60429373	1.00[AMR][1000 genomes]
rs61007952	1.00[AMR][1000 genomes]
rs6766106	1.00[AMR][1000 genomes]
rs6766186	1.00[AMR][1000 genomes]
rs7626435	1.00[AMR][1000 genomes]
rs7626507	1.00[AMR][1000 genomes]
rs7650980	1.00[AMR][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	esv3431441	chr3:112453467-113213252	Active TSS Flanking Active TSS Weak transcription Strong transcription ZNF genes & repeats Bivalent Enhancer Enhancers Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	43 gene(s)	inside rSNPs	diseases
2	nsv829677	chr3:112857075-113038987	Flanking Active TSS Enhancers Bivalent/Poised TSS Genic enhancers Weak transcription Active TSS ZNF genes & repeats Strong transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	11 gene(s)	inside rSNPs	diseases
3	nsv1003511	chr3:112858775-112989045	Weak transcription Enhancers Flanking Active TSS Strong transcription Flanking Bivalent TSS/Enh Active TSS Bivalent/Poised TSS Bivalent Enhancer Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
4	nsv1013506	chr3:112890608-113680951	Weak transcription Bivalent/Poised TSS Enhancers Strong transcription ZNF genes & repeats Genic enhancers Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	51 gene(s)	inside rSNPs	diseases
5	nsv877348	chr3:112914756-113012509	Weak transcription Enhancers Flanking Active TSS Strong transcription Bivalent Enhancer Genic enhancers Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	6 gene(s)	inside rSNPs	diseases

No data

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:112932000-112972800	Weak transcription	Aorta	Aorta
2	chr3:112951200-112967000	Weak transcription	Colonic Mucosa	Colon
3	chr3:112953800-112965600	Weak transcription	Right Atrium	heart
4	chr3:112954200-112965600	Weak transcription	Brain Substantia Nigra	brain
5	chr3:112957800-112961800	Enhancers	Rectal Smooth Muscle	rectum
6	chr3:112958400-112963000	Enhancers	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
7	chr3:112958600-112961800	Enhancers	Colon Smooth Muscle	Colon
8	chr3:112958600-112962200	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
9	chr3:112958600-112969000	Weak transcription	Spleen	Spleen
10	chr3:112958800-112962200	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
11	chr3:112958800-112962800	Enhancers	H1 Cell Line	embryonic stem cell
12	chr3:112959000-112962000	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
13	chr3:112959000-112962600	Enhancers	HUES48 Cell Line	embryonic stem cell
14	chr3:112959600-112961800	Enhancers	Fetal Adrenal Gland	Adrenal Gland
15	chr3:112959600-112963000	Enhancers	Fetal Brain Male	brain
16	chr3:112959800-112962200	Enhancers	Brain Anterior Caudate	brain
17	chr3:112959800-112963000	Enhancers	Primary hematopoietic stem cells short term culture	blood
18	chr3:112960000-112962000	Enhancers	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
19	chr3:112960200-112961800	Enhancers	HSMM	muscle
20	chr3:112960400-112961800	Enhancers	Fetal Stomach	stomach
21	chr3:112960400-112961800	Flanking Active TSS	NH-A	brain
22	chr3:112960400-112965800	Weak transcription	Skeletal Muscle Female	skeletal muscle
23	chr3:112960600-112961800	Flanking Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
24	chr3:112960600-112961800	Enhancers	Brain Hippocampus Middle	brain
25	chr3:112960600-112962200	Enhancers	Thymus	Thymus
26	chr3:112960800-112961800	Flanking Active TSS	Brain Germinal Matrix	brain
27	chr3:112960800-112961800	Flanking Active TSS	Fetal Brain Female	brain
28	chr3:112960800-112961800	Weak transcription	Ovary	ovary
29	chr3:112960800-112962000	Flanking Active TSS	iPS-20b Cell Line	embryonic stem cell
30	chr3:112960800-112962400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
31	chr3:112960800-112962400	Weak transcription	Esophagus	oesophagus
32	chr3:112960800-112962400	Weak transcription	Pancreas	Pancrea
33	chr3:112960800-112963400	Weak transcription	Fetal Heart	heart
34	chr3:112960800-112964600	Weak transcription	Fetal Muscle Trunk	muscle
35	chr3:112960800-112965600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
36	chr3:112960800-112965600	Weak transcription	Duodenum Smooth Muscle	Duodenum
37	chr3:112960800-112967000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
38	chr3:112961000-112961800	Flanking Active TSS	H9 Derived Neuron Cultured Cells	ES cell derived
39	chr3:112961000-112961800	Flanking Active TSS	Cortex derived primary cultured neurospheres	brain
40	chr3:112961000-112962400	Enhancers	Stomach Smooth Muscle	stomach
41	chr3:112961000-112962800	Enhancers	HUES64 Cell Line	embryonic stem cell
42	chr3:112961000-112962800	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
43	chr3:112961000-112965600	Weak transcription	Sigmoid Colon	Sigmoid Colon
44	chr3:112961200-112961800	Enhancers	H9 Cell Line	embryonic stem cell
45	chr3:112961200-112961800	Enhancers	Primary T cells from cord blood	blood
46	chr3:112961200-112962000	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
47	chr3:112961200-112962000	Flanking Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
48	chr3:112961200-112962600	Enhancers	Fetal Kidney	kidney
49	chr3:112961200-112962800	Enhancers	iPS-18 Cell Line	embryonic stem cell
50	chr3:112961200-112963000	Enhancers	HUES6 Cell Line	embryonic stem cell

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links