Variant report

Variant	rs1397400
Chromosome Location	chr2:21483555-21483556
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr2:21454261..21455870-chr2:21482924..21484730,2	K562	blood:
2	chr2:21466677..21468249-chr2:21482318..21484176,2	K562	blood:

Extended variants
information (count: 15 )
Associated
traits (count: 0)

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

rs_ID	r²[population]
rs12472945	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13002436	0.93[AMR][1000 genomes];0.92[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs13007394	0.82[EUR][1000 genomes]
rs13426161	0.94[ASN][1000 genomes]
rs35437800	0.81[EUR][1000 genomes]
rs35777541	0.86[AMR][1000 genomes]
rs6545183	0.99[ASN][1000 genomes]
rs6718442	0.80[ASN][1000 genomes]
rs67758164	0.86[AMR][1000 genomes]
rs7584773	0.89[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs870223	0.95[ASN][1000 genomes]
rs870570	0.91[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][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	nsv519215	chr2:21473751-21502727	Enhancers Weak transcription Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Strong transcription	Chromatin interactive region lncRNA	n/a	inside rSNPs	n/a
2	nsv1011486	chr2:21475803-22364002	Enhancers Weak transcription ZNF genes & repeats Flanking Active TSS Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
3	nsv535602	chr2:21475803-22364002	Enhancers Weak transcription ZNF genes & repeats Active TSS Bivalent Enhancer Flanking Active TSS Strong transcription Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:24 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:21473200-21488800	Enhancers	Brain Hippocampus Middle	brain
2	chr2:21473600-21487400	Enhancers	Brain Cingulate Gyrus	brain
3	chr2:21475200-21484600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
4	chr2:21476000-21488000	Enhancers	Brain Anterior Caudate	brain
5	chr2:21479000-21490400	Weak transcription	Spleen	Spleen
6	chr2:21479400-21494800	Enhancers	Brain Substantia Nigra	brain
7	chr2:21479600-21489200	Enhancers	Brain Inferior Temporal Lobe	brain
8	chr2:21479800-21484600	Weak transcription	Breast Myoepithelial Primary Cells	Breast
9	chr2:21481000-21483800	Enhancers	Brain Angular Gyrus	brain
10	chr2:21481200-21484600	Weak transcription	Fetal Muscle Trunk	muscle
11	chr2:21481200-21484600	Weak transcription	Fetal Muscle Leg	muscle
12	chr2:21481400-21484400	Weak transcription	Fetal Stomach	stomach
13	chr2:21481400-21487400	Weak transcription	Aorta	Aorta
14	chr2:21481600-21490200	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
15	chr2:21482000-21483800	Enhancers	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
16	chr2:21482200-21484200	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
17	chr2:21482200-21487200	Enhancers	Cortex derived primary cultured neurospheres	brain
18	chr2:21482400-21483800	Enhancers	Brain Dorsolateral Prefrontal Cortex	brain
19	chr2:21482600-21483600	Enhancers	HUES48 Cell Line	embryonic stem cell
20	chr2:21482600-21483800	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
21	chr2:21482600-21483800	Enhancers	Brain Germinal Matrix	brain
22	chr2:21482800-21483800	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
23	chr2:21483200-21483600	Enhancers	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
24	chr2:21483400-21490600	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links