Variant report

Variant	rs7774208
Chromosome Location	chr6:24228243-24228244
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr6:24227048..24229838-chr6:24232947..24235192,3	MCF-7	breast:

Extended variants
information (count: 6 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:4)

rs_ID	r²[population]
rs12196541	0.82[CHD][hapmap]
rs12197537	0.85[ASN][1000 genomes]
rs4535539	0.90[CHD][hapmap]
rs9467087	0.87[EUR][1000 genomes];0.90[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1029930	chr6:23481989-24289948	Enhancers Flanking Active TSS Strong transcription Bivalent Enhancer Weak transcription Active TSS Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases
2	nsv427746	chr6:24221299-24305709	Weak transcription Enhancers Active TSS Genic enhancers Flanking Active TSS Strong transcription ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer	Chromatin interactive region	2 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs7774208	DCDC2	cis	parietal	SCAN
rs7774208	HIST1H1E	cis	parietal	SCAN
rs7774208	TDP2	cis	cerebellum	SCAN

Chromatin state (count:31 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:24206200-24231400	Weak transcription	Fetal Intestine Small	intestine
2	chr6:24214600-24235400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
3	chr6:24217800-24231600	Weak transcription	Rectal Smooth Muscle	rectum
4	chr6:24224800-24228800	Strong transcription	HepG2	liver
5	chr6:24225000-24229000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
6	chr6:24225000-24229200	Weak transcription	Pancreas	Pancrea
7	chr6:24226800-24229600	Enhancers	Cortex derived primary cultured neurospheres	brain
8	chr6:24227000-24228800	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
9	chr6:24227000-24230400	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
10	chr6:24227200-24229200	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
11	chr6:24227600-24229000	Enhancers	Brain Germinal Matrix	brain
12	chr6:24227600-24229200	Enhancers	Brain Anterior Caudate	brain
13	chr6:24227600-24229400	Enhancers	HUES48 Cell Line	embryonic stem cell
14	chr6:24227600-24229400	Enhancers	iPS-18 Cell Line	embryonic stem cell
15	chr6:24227600-24229400	Enhancers	Fetal Kidney	kidney
16	chr6:24227600-24229600	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
17	chr6:24227800-24229000	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
18	chr6:24227800-24229000	Weak transcription	Ovary	ovary
19	chr6:24227800-24229400	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
20	chr6:24227800-24229600	Enhancers	Fetal Lung	lung
21	chr6:24228000-24228400	Enhancers	Brain Inferior Temporal Lobe	brain
22	chr6:24228000-24228600	Enhancers	ES-WA7 Cell Line	embryonic stem cell
23	chr6:24228000-24228800	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
24	chr6:24228000-24229200	Enhancers	ES-I3 Cell Line	embryonic stem cell
25	chr6:24228000-24229200	Enhancers	H1 Cell Line	embryonic stem cell
26	chr6:24228000-24229200	Enhancers	iPS-15b Cell Line	embryonic stem cell
27	chr6:24228000-24229200	Enhancers	Fetal Stomach	stomach
28	chr6:24228000-24229400	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
29	chr6:24228000-24229600	Enhancers	HUES6 Cell Line	embryonic stem cell
30	chr6:24228000-24229600	Enhancers	HUES64 Cell Line	embryonic stem cell
31	chr6:24228200-24229200	Enhancers	iPS-20b Cell Line	embryonic stem cell

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links