Variant report

Variant	rs12988451
Chromosome Location	chr2:20669737-20669738
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:0)
CpG islands
(count:0)
Chromatin interactive
region (count:8)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:8 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr2:20665733..20672605-chr2:20815236..20823686,12	MCF-7	breast:
2	chr2:20664203..20670367-chr2:20692234..20698325,8	MCF-7	breast:
3	chr2:20667641..20670204-chr2:20848987..20852678,3	MCF-7	breast:
4	chr2:20642734..20659399-chr2:20663729..20679011,83	MCF-7	breast:
5	chr2:20667950..20670056-chr2:20708314..20710837,3	MCF-7	breast:
6	chr2:20578892..20581003-chr2:20669683..20672466,2	MCF-7	breast:
7	chr2:20643286..20659825-chr2:20662702..20680153,143	MCF-7	breast:
8	chr2:20669736..20672318-chr2:20836415..20838829,2	MCF-7	breast:

No data

Variant related genes	Relation type
ENSG00000143878	Chromatin interaction
ENSG00000118960	Chromatin interaction
ENSG00000228950	Chromatin interaction

Extended variants
information (count: 32 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:25)

rs_ID	r²[population]
rs1002162	0.85[CEU][hapmap]
rs10205221	1.00[CEU][hapmap];0.82[CHB][hapmap];1.00[JPT][hapmap];0.93[YRI][hapmap];0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11898154	0.81[CEU][hapmap]
rs13021908	0.81[CEU][hapmap]
rs1453051	0.85[CEU][hapmap]
rs168195	0.82[CEU][hapmap]
rs342105	0.92[CEU][hapmap];1.00[CHB][hapmap]
rs342114	0.80[CEU][hapmap]
rs342116	0.80[CEU][hapmap]
rs342117	0.92[CEU][hapmap];1.00[CHB][hapmap]
rs342118	0.88[CEU][hapmap];1.00[CHB][hapmap]
rs342119	0.92[CEU][hapmap];1.00[CHB][hapmap]
rs342123	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs342124	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs342125	0.92[CEU][hapmap];1.00[CHB][hapmap]
rs342126	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4666308	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4666401	0.81[CEU][hapmap]
rs4666402	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6531240	0.85[CEU][hapmap]
rs6704834	0.82[CEU][hapmap]
rs674534	0.96[CEU][hapmap];1.00[CHB][hapmap];0.82[JPT][hapmap];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs715670	1.00[CEU][hapmap];0.82[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs959058	1.00[CEU][hapmap];0.82[CHB][hapmap];1.00[JPT][hapmap];0.83[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs9917322	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][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	nsv873717	chr2:20625174-20756900	Active TSS Bivalent/Poised TSS Enhancers Bivalent Enhancer Weak transcription Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Flanking Active TSS Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	90 gene(s)	inside rSNPs	diseases
2	nsv873718	chr2:20627875-20752152	Weak transcription Enhancers Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	90 gene(s)	inside rSNPs	diseases
3	nsv873719	chr2:20628882-20756900	Enhancers Weak transcription Bivalent Enhancer Flanking Active TSS Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	90 gene(s)	inside rSNPs	diseases
4	nsv833537	chr2:20630092-20826816	Enhancers Weak transcription Flanking Active TSS Genic enhancers Strong transcription Transcr. at gene 5' and 3' Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	96 gene(s)	inside rSNPs	diseases
5	nsv873720	chr2:20645835-20756900	Active TSS Flanking Active TSS Weak transcription Enhancers Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	88 gene(s)	inside rSNPs	diseases
6	nsv873721	chr2:20645835-20759789	Enhancers Bivalent Enhancer Active TSS Weak transcription Transcr. at gene 5' and 3' Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	88 gene(s)	inside rSNPs	diseases
7	nsv873722	chr2:20652507-20705910	Enhancers Weak transcription Flanking Active TSS Bivalent Enhancer Genic enhancers Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	13 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	chr2:20653400-20674000	Weak transcription	Brain Inferior Temporal Lobe	brain
2	chr2:20656200-20671800	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
3	chr2:20664400-20672400	Weak transcription	Right Atrium	heart
4	chr2:20665400-20669800	Enhancers	Stomach Mucosa	stomach
5	chr2:20665400-20670400	Enhancers	Breast Myoepithelial Primary Cells	Breast
6	chr2:20666400-20671600	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
7	chr2:20666400-20672400	Weak transcription	Esophagus	oesophagus
8	chr2:20666400-20681800	Weak transcription	Colon Smooth Muscle	Colon
9	chr2:20666600-20671800	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
10	chr2:20667200-20671600	Weak transcription	NHEK	skin
11	chr2:20667200-20671800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
12	chr2:20667200-20672000	Weak transcription	Skeletal Muscle Male	skeletal muscle
13	chr2:20667400-20670000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
14	chr2:20667400-20672000	Weak transcription	Brain Anterior Caudate	brain
15	chr2:20667600-20670000	Weak transcription	Cortex derived primary cultured neurospheres	brain
16	chr2:20667600-20671800	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
17	chr2:20667600-20671800	Weak transcription	Skeletal Muscle Female	skeletal muscle
18	chr2:20667600-20673800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
19	chr2:20667600-20674000	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
20	chr2:20667800-20671600	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
21	chr2:20667800-20673000	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
22	chr2:20667800-20673800	Weak transcription	Brain Hippocampus Middle	brain
23	chr2:20668000-20674000	Weak transcription	Ovary	ovary
24	chr2:20668200-20670800	Weak transcription	Spleen	Spleen
25	chr2:20668200-20671800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
26	chr2:20668200-20671800	Weak transcription	Brain Substantia Nigra	brain
27	chr2:20668200-20672200	Weak transcription	Brain Cingulate Gyrus	brain
28	chr2:20668200-20674000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
29	chr2:20668400-20669800	Enhancers	Pancreas	Pancrea
30	chr2:20668600-20671600	Weak transcription	Placenta	Placenta
31	chr2:20668600-20672400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
32	chr2:20669200-20669800	Enhancers	Liver	Liver
33	chr2:20669400-20670800	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
34	chr2:20669600-20672000	Weak transcription	Gastric	stomach

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links