Variant report

Variant	rs55888075
Chromosome Location	chr3:112960206-112960207
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 22 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:17)

rs_ID	r²[population]
rs11923623	1.00[EUR][1000 genomes]
rs16860704	0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs16860739	1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs16860784	1.00[EUR][1000 genomes]
rs16860788	1.00[EUR][1000 genomes]
rs17255413	0.97[EUR][1000 genomes]
rs17320507	0.92[ASN][1000 genomes]
rs3814401	1.00[EUR][1000 genomes]
rs3814405	1.00[EUR][1000 genomes]
rs41374946	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs55681309	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs55681380	1.00[EUR][1000 genomes]
rs55744928	0.82[EUR][1000 genomes]
rs55969905	1.00[EUR][1000 genomes]
rs56130902	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7614288	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs775221	1.00[EUR][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:79 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:112932000-112972800	Weak transcription	Aorta	Aorta
2	chr3:112943600-112960600	Weak transcription	Fetal Thymus	thymus
3	chr3:112951200-112967000	Weak transcription	Colonic Mucosa	Colon
4	chr3:112953800-112960600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
5	chr3:112953800-112965600	Weak transcription	Right Atrium	heart
6	chr3:112954200-112960400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
7	chr3:112954200-112965600	Weak transcription	Brain Substantia Nigra	brain
8	chr3:112954600-112960400	Weak transcription	HSMMtube	muscle
9	chr3:112957600-112960800	Enhancers	Ovary	ovary
10	chr3:112957800-112961800	Enhancers	Rectal Smooth Muscle	rectum
11	chr3:112958400-112960600	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
12	chr3:112958400-112960800	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
13	chr3:112958400-112960800	Enhancers	Duodenum Smooth Muscle	Duodenum
14	chr3:112958400-112963000	Enhancers	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
15	chr3:112958600-112960800	Genic enhancers	Breast Myoepithelial Primary Cells	Breast
16	chr3:112958600-112961800	Enhancers	Colon Smooth Muscle	Colon
17	chr3:112958600-112962200	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
18	chr3:112958600-112969000	Weak transcription	Spleen	Spleen
19	chr3:112958800-112960400	Enhancers	HUES64 Cell Line	embryonic stem cell
20	chr3:112958800-112960400	Genic enhancers	Fetal Stomach	stomach
21	chr3:112958800-112960400	Enhancers	Skeletal Muscle Female	skeletal muscle
22	chr3:112958800-112960800	Enhancers	Fetal Kidney	kidney
23	chr3:112958800-112961000	Enhancers	ES-I3 Cell Line	embryonic stem cell
24	chr3:112958800-112962200	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
25	chr3:112958800-112962800	Enhancers	H1 Cell Line	embryonic stem cell
26	chr3:112959000-112960600	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
27	chr3:112959000-112960600	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
28	chr3:112959000-112960800	Enhancers	iPS-20b Cell Line	embryonic stem cell
29	chr3:112959000-112960800	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
30	chr3:112959000-112960800	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
31	chr3:112959000-112961000	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
32	chr3:112959000-112961000	Enhancers	Cortex derived primary cultured neurospheres	brain
33	chr3:112959000-112961200	Enhancers	Placenta Amnion	Placenta Amnion
34	chr3:112959000-112962000	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
35	chr3:112959000-112962600	Enhancers	HUES48 Cell Line	embryonic stem cell
36	chr3:112959200-112961200	Weak transcription	Psoas Muscle	Psoas
37	chr3:112959200-112961400	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
38	chr3:112959600-112960400	Enhancers	Dnd41	blood
39	chr3:112959600-112960400	Enhancers	NH-A	brain
40	chr3:112959600-112960600	Enhancers	iPS DF 6.9 Cell Line	embryonic stem cell
41	chr3:112959600-112960600	Enhancers	Brain Inferior Temporal Lobe	brain
42	chr3:112959600-112960600	Enhancers	Osteobl	bone
43	chr3:112959600-112960800	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
44	chr3:112959600-112960800	Enhancers	Muscle Satellite Cultured Cells	--
45	chr3:112959600-112960800	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
46	chr3:112959600-112960800	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
47	chr3:112959600-112960800	Enhancers	Esophagus	oesophagus
48	chr3:112959600-112960800	Enhancers	Fetal Muscle Trunk	muscle
49	chr3:112959600-112960800	Enhancers	Pancreas	Pancrea
50	chr3:112959600-112960800	Enhancers	NHEK	skin

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links