Variant report

Variant	rs248321
Chromosome Location	chr5:179371900-179371901
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	chr5:179366779..179369050-chr5:179370265..179372456,2	MCF-7	breast:
2	chr5:179369823..179371965-chr5:179382794..179386815,3	MCF-7	breast:

Variant related genes	Relation type
ENSG00000113269	Chromatin interaction
ENSG00000249876	Chromatin interaction

Extended variants
information (count: 14 )
Associated
traits (count: 5 )

rSNPs within LD-proxies of this variant (count:9)

rs_ID	r²[population]
rs155576	0.84[CEU][hapmap]
rs155577	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs156097	0.83[ASN][1000 genomes]
rs190328	0.80[CEU][hapmap]
rs248327	0.84[AFR][1000 genomes]
rs248329	0.84[AFR][1000 genomes]
rs248330	0.84[CEU][hapmap];1.00[LWK][hapmap];0.87[TSI][hapmap];0.81[YRI][hapmap];0.84[AFR][1000 genomes]
rs248332	0.81[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs27010	0.84[CEU][hapmap];0.84[TSI][hapmap]

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	nsv531997	chr5:179107599-179588082	Enhancers Strong transcription Flanking Active TSS ZNF genes & repeats Weak transcription Genic enhancers Flanking Bivalent TSS/Enh Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	339 gene(s)	inside rSNPs	diseases
2	nsv1030437	chr5:179235423-179649944	Enhancers Strong transcription Flanking Active TSS Active TSS Weak transcription ZNF genes & repeats Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	189 gene(s)	inside rSNPs	diseases
3	nsv537982	chr5:179235423-179649944	Active TSS Weak transcription Flanking Active TSS Genic enhancers Strong transcription Bivalent/Poised TSS Enhancers Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	189 gene(s)	inside rSNPs	diseases
4	nsv948909	chr5:179249099-179772640	Weak transcription Active TSS Flanking Active TSS Enhancers Strong transcription ZNF genes & repeats Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	175 gene(s)	inside rSNPs	diseases
5	nsv830561	chr5:179365637-179537012	Weak transcription Enhancers ZNF genes & repeats Strong transcription Flanking Active TSS Genic enhancers Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	153 gene(s)	inside rSNPs	diseases

mRNA abundance (count:5)

SNP	Gene	Cis/trans	Tissue	Source
rs248321	PDLIM7	cis	cerebellum	SCAN
rs248321	BTNL3	cis	cerebellum	SCAN
rs248321	LOC202181	cis	parietal	SCAN
rs248321	DOK3	cis	cerebellum	SCAN
rs248321	CANX	cis	parietal	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:179344600-179381600	Weak transcription	Fetal Brain Male	brain
2	chr5:179347200-179381000	Weak transcription	Brain Angular Gyrus	brain
3	chr5:179347400-179372000	Weak transcription	Brain Germinal Matrix	brain
4	chr5:179351000-179372200	Weak transcription	Monocytes-CD14+_RO01746	blood
5	chr5:179354200-179381400	Weak transcription	Fetal Brain Female	brain
6	chr5:179359000-179381000	Weak transcription	Brain Substantia Nigra	brain
7	chr5:179359000-179381200	Weak transcription	Brain Inferior Temporal Lobe	brain
8	chr5:179359400-179373000	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
9	chr5:179360200-179377400	Weak transcription	Primary hematopoietic stem cells short term culture	blood
10	chr5:179361200-179372200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
11	chr5:179363400-179373800	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
12	chr5:179366600-179372200	Weak transcription	Cortex derived primary cultured neurospheres	brain
13	chr5:179366600-179382000	Weak transcription	Fetal Lung	lung
14	chr5:179367000-179374000	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
15	chr5:179367400-179381400	Weak transcription	Duodenum Mucosa	Duodenum
16	chr5:179368400-179381400	Weak transcription	Left Ventricle	heart
17	chr5:179368800-179372000	Weak transcription	Fetal Stomach	stomach
18	chr5:179369000-179381000	Weak transcription	Brain Hippocampus Middle	brain
19	chr5:179369000-179381400	Weak transcription	Duodenum Smooth Muscle	Duodenum
20	chr5:179369800-179381400	Weak transcription	Ovary	ovary
21	chr5:179370000-179382800	Weak transcription	Lung	lung
22	chr5:179370200-179392800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
23	chr5:179370400-179372200	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
24	chr5:179370400-179372200	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
25	chr5:179370400-179374000	Weak transcription	Primary monocytes fromperipheralblood	blood
26	chr5:179370400-179374200	Weak transcription	Primary neutrophils fromperipheralblood	blood
27	chr5:179370400-179376800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
28	chr5:179370600-179372000	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
29	chr5:179370800-179374000	Weak transcription	Liver	Liver
30	chr5:179370800-179380800	Weak transcription	Adipose Nuclei	Adipose
31	chr5:179370800-179386800	Weak transcription	HepG2	liver
32	chr5:179371000-179381400	Weak transcription	Colon Smooth Muscle	Colon
33	chr5:179371800-179372000	Active TSS	Stomach Smooth Muscle	stomach
34	chr5:179371800-179377400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links