Variant report

Variant	rs2122211
Chromosome Location	chr13:39268845-39268846
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	chr13:39265549..39268944-chr13:39270203..39272891,3	MCF-7	breast:
2	chr13:39260311..39263148-chr13:39268449..39271699,3	MCF-7	breast:

Variant related genes	Relation type
ENSG00000150893	Chromatin interaction

Extended variants
information (count: 3 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:1)

rs_ID	r²[population]
rs9634754	1.00[YRI][hapmap];0.84[AFR][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	nsv832584	chr13:39074265-39284724	Enhancers Flanking Active TSS Weak transcription Flanking Bivalent TSS/Enh Active TSS Strong transcription ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	diseases
2	nsv832585	chr13:39233307-39424375	Weak transcription Bivalent/Poised TSS Active TSS Enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Genic enhancers Bivalent Enhancer Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs2122211	CCNA1	cis	parietal	SCAN
rs2122211	CSNK1A1L	cis	cerebellum	SCAN

Chromatin state (count:20 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr13:39263600-39275400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
2	chr13:39263800-39275400	Weak transcription	HUES6 Cell Line	embryonic stem cell
3	chr13:39264000-39271000	Weak transcription	Fetal Muscle Trunk	muscle
4	chr13:39264200-39276800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
5	chr13:39264400-39271000	Weak transcription	Fetal Muscle Leg	muscle
6	chr13:39264400-39275800	Weak transcription	HUES48 Cell Line	embryonic stem cell
7	chr13:39264600-39270600	Active TSS	Fetal Adrenal Gland	Adrenal Gland
8	chr13:39265400-39275400	Weak transcription	HUES64 Cell Line	embryonic stem cell
9	chr13:39265800-39287200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
10	chr13:39268000-39270200	Weak transcription	Skeletal Muscle Female	skeletal muscle
11	chr13:39268000-39271000	Weak transcription	Psoas Muscle	Psoas
12	chr13:39268000-39271200	Weak transcription	Fetal Heart	heart
13	chr13:39268000-39284600	Weak transcription	Fetal Kidney	kidney
14	chr13:39268200-39276800	Weak transcription	H9 Cell Line	embryonic stem cell
15	chr13:39268200-39282400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
16	chr13:39268600-39271000	Weak transcription	Skeletal Muscle Male	skeletal muscle
17	chr13:39268800-39269600	Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
18	chr13:39268800-39269800	Enhancers	Fetal Intestine Large	intestine
19	chr13:39268800-39271800	Weak transcription	iPS-20b Cell Line	embryonic stem cell
20	chr13:39268800-39272200	Weak transcription	Cortex derived primary cultured neurospheres	brain

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links