Variant report

Variant	rs6805421
Chromosome Location	chr3:42728144-42728145
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr3:42727173..42729004-chr3:42733372..42735922,3	K562	blood:
2	chr3:42727358..42730131-chr3:42775132..42777505,2	MCF-7	breast:
3	chr3:42725723..42728637-chr3:42737292..42738802,2	K562	blood:
4	chr3:42724857..42728583-chr3:42742957..42746730,4	K562	blood:
5	chr3:42727541..42729253-chr3:42740076..42742004,2	K562	blood:

Variant related genes	Relation type
ENSG00000010282	Chromatin interaction
ENSG00000230970	Chromatin interaction

Extended variants
information (count: 7 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:6)

rs_ID	r²[population]
rs17030476	0.85[JPT][hapmap]
rs339699	0.83[ASN][1000 genomes]
rs339700	0.83[ASN][1000 genomes]
rs339703	0.96[CHD][hapmap];0.85[ASN][1000 genomes]
rs3890974	0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs72865703	0.82[ASN][1000 genomes]

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

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1002944	chr3:42559762-42728909	Strong transcription Flanking Active TSS Weak transcription Enhancers Genic enhancers Transcr. at gene 5' and 3' Active TSS ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	41 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs6805421	TTC21A	cis	parietal	SCAN
rs6805421	HHATL	cis	cerebellum	SCAN

Chromatin state (count:23 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:42724200-42729400	Enhancers	Fetal Heart	heart
2	chr3:42725200-42730000	Weak transcription	HUES64 Cell Line	embryonic stem cell
3	chr3:42725400-42737000	Weak transcription	Right Atrium	heart
4	chr3:42726200-42728200	Enhancers	Left Ventricle	heart
5	chr3:42726200-42730800	Weak transcription	HUES6 Cell Line	embryonic stem cell
6	chr3:42727000-42728200	Enhancers	Pancreas	Pancrea
7	chr3:42727000-42728200	Flanking Active TSS	Skeletal Muscle Female	skeletal muscle
8	chr3:42727000-42729800	Active TSS	Psoas Muscle	Psoas
9	chr3:42727400-42728600	Bivalent/Poised TSS	Fetal Muscle Leg	muscle
10	chr3:42727400-42728800	Enhancers	Right Ventricle	heart
11	chr3:42727400-42732800	Transcr. at gene 5' and 3'	Skeletal Muscle Male	skeletal muscle
12	chr3:42727600-42728400	Bivalent Enhancer	Primary hematopoietic stem cells short term culture	blood
13	chr3:42727600-42729000	Bivalent/Poised TSS	Fetal Muscle Trunk	muscle
14	chr3:42727600-42729600	Active TSS	HSMMtube	muscle
15	chr3:42727800-42728200	Bivalent Enhancer	Foreskin Melanocyte Primary Cells skin03	Skin
16	chr3:42727800-42728200	Bivalent Enhancer	Fetal Stomach	stomach
17	chr3:42727800-42728400	Weak transcription	Brain Anterior Caudate	brain
18	chr3:42727800-42729600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
19	chr3:42727800-42732400	Weak transcription	Brain Substantia Nigra	brain
20	chr3:42728000-42728200	Bivalent Enhancer	Ganglion Eminence derived primary cultured neurospheres	brain
21	chr3:42728000-42728200	Bivalent/Poised TSS	Fetal Lung	lung
22	chr3:42728000-42728400	Bivalent Enhancer	Foreskin Melanocyte Primary Cells skin01	Skin
23	chr3:42728000-42742800	Weak transcription	Gastric	stomach

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