Variant report

Variant	rs1879696
Chromosome Location	chr2:169769047-169769048
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	chr2:169755958..169758089-chr2:169767448..169770171,2	K562	blood:
2	chr2:169757947..169761015-chr2:169767482..169770079,3	MCF-7	breast:

Variant related genes	Relation type
ENSG00000152254	Chromatin interaction

Extended variants
information (count: 14 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:11)

rs_ID	r²[population]
rs10497346	0.92[EUR][1000 genomes]
rs12475693	0.83[AFR][1000 genomes]
rs16856159	0.86[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs16856161	0.84[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2232316	0.87[AFR][1000 genomes];0.82[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs2232328	0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3770568	0.84[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3821117	0.86[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs56135702	0.93[EUR][1000 genomes]
rs6730651	0.92[EUR][1000 genomes]
rs7606215	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv583599	chr2:169664227-169903096	Bivalent Enhancer Weak transcription Genic enhancers Strong transcription Enhancers Active TSS Flanking Active TSS ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	12 gene(s)	inside rSNPs	diseases
2	nsv459943	chr2:169756930-169799010	Bivalent/Poised TSS Enhancers Bivalent Enhancer Flanking Active TSS Weak transcription Flanking Bivalent TSS/Enh Active TSS ZNF genes & repeats Strong transcription Genic enhancers	TF binding region CpG island Chromatin interactive region miRNA target site	4 gene(s)	inside rSNPs	diseases
3	nsv583600	chr2:169756930-169799010	Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Enhancers Weak transcription Flanking Active TSS Bivalent Enhancer Strong transcription ZNF genes & repeats Genic enhancers	TF binding region CpG island Chromatin interactive region miRNA target site	4 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:34 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:169767200-169769400	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
2	chr2:169768200-169769200	Enhancers	ES-I3 Cell Line	embryonic stem cell
3	chr2:169768400-169769200	Enhancers	ES-WA7 Cell Line	embryonic stem cell
4	chr2:169768400-169769200	Enhancers	Cortex derived primary cultured neurospheres	brain
5	chr2:169768400-169769200	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
6	chr2:169768400-169769200	Enhancers	Fetal Brain Male	brain
7	chr2:169768400-169769400	Enhancers	iPS-20b Cell Line	embryonic stem cell
8	chr2:169768400-169769600	Enhancers	iPS-18 Cell Line	embryonic stem cell
9	chr2:169768400-169770400	Enhancers	H1 Cell Line	embryonic stem cell
10	chr2:169768400-169770400	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
11	chr2:169768400-169771400	Enhancers	H9 Cell Line	embryonic stem cell
12	chr2:169768600-169769200	Enhancers	Brain Germinal Matrix	brain
13	chr2:169768600-169769400	Enhancers	Brain Cingulate Gyrus	brain
14	chr2:169768600-169769400	Weak transcription	Pancreas	Pancrea
15	chr2:169768600-169771400	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
16	chr2:169768800-169769200	Bivalent Enhancer	HUES48 Cell Line	embryonic stem cell
17	chr2:169768800-169769200	Weak transcription	Breast Myoepithelial Primary Cells	Breast
18	chr2:169768800-169769200	Enhancers	Brain Hippocampus Middle	brain
19	chr2:169768800-169769800	Active TSS	Pancreatic Islets	Pancreatic Islet
20	chr2:169768800-169770000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
21	chr2:169769000-169769200	Bivalent Enhancer	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
22	chr2:169769000-169769200	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
23	chr2:169769000-169769200	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
24	chr2:169769000-169769200	Active TSS	Skeletal Muscle Male	skeletal muscle
25	chr2:169769000-169769400	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
26	chr2:169769000-169769400	Bivalent/Poised TSS	HUES6 Cell Line	embryonic stem cell
27	chr2:169769000-169769400	Flanking Bivalent TSS/Enh	iPS-15b Cell Line	embryonic stem cell
28	chr2:169769000-169769600	Active TSS	Skeletal Muscle Female	skeletal muscle
29	chr2:169769000-169769800	Bivalent/Poised TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
30	chr2:169769000-169769800	Active TSS	Brain Inferior Temporal Lobe	brain
31	chr2:169769000-169769800	Active TSS	Duodenum Smooth Muscle	Duodenum
32	chr2:169769000-169769800	Flanking Active TSS	Fetal Brain Female	brain
33	chr2:169769000-169769800	Bivalent/Poised TSS	Osteobl	bone
34	chr2:169769000-169770600	Enhancers	HUES64 Cell Line	embryonic stem cell

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links