Variant report

Variant	rs6779561
Chromosome Location	chr3:42849818-42849819
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	TBL1XR1	chr3:42849788-42849903	K562	blood:	n/a	n/a
2	EP300	chr3:42849730-42849888	K562	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr3:42834430..42837380-chr3:42848485..42850165,2	K562	blood:
2	chr3:42845805..42849029-chr3:42849573..42852164,3	K562	blood:

Variant related genes	Relation type
KRBOX1	TF binding region
ENSG00000273291	TF binding region
HIGD1A	TF binding region
ENSG00000273328	TF binding region
ACKR2	TF binding region
ENSG00000181061	Chromatin interaction
ENSG00000144648	Chromatin interaction

Extended variants
information (count: 20 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:20)

rs_ID	r²[population]
rs11129975	0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs11129976	1.00[CEU][hapmap];0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11129977	0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11922832	1.00[CEU][hapmap];0.90[CHB][hapmap];0.94[CHD][hapmap];0.88[MEX][hapmap];1.00[TSI][hapmap];0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs12491179	0.86[CEU][hapmap];0.85[EUR][1000 genomes]
rs12639142	0.96[CEU][hapmap];0.95[GIH][hapmap];0.95[TSI][hapmap];0.97[EUR][1000 genomes]
rs13070029	0.97[EUR][1000 genomes]
rs13096498	1.00[CEU][hapmap];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2372110	0.92[EUR][1000 genomes]
rs339671	0.88[AMR][1000 genomes];0.92[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs339684	0.87[CEU][hapmap]
rs339731	0.91[CEU][hapmap];0.83[EUR][1000 genomes]
rs34868846	0.97[EUR][1000 genomes]
rs35584330	0.83[AMR][1000 genomes];0.91[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs3843369	0.83[AMR][1000 genomes];0.93[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs3846063	0.96[CEU][hapmap];0.93[GIH][hapmap];0.93[TSI][hapmap];0.90[EUR][1000 genomes]
rs4683332	1.00[CEU][hapmap];0.90[CHB][hapmap];0.94[CHD][hapmap];0.95[GIH][hapmap];0.88[MEX][hapmap];1.00[TSI][hapmap];0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs4683335	1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap];1.00[TSI][hapmap];0.90[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6442067	0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs7641046	1.00[CEU][hapmap];0.89[AMR][1000 genomes];1.00[EUR][1000 genomes];0.86[ASN][1000 genomes]

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs6779561	CCDC13-AS1	cis	Heart Left Ventricle	GTEx
rs6779561	CCDC13	cis	parietal	SCAN

Chromatin state (count:18 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:42846800-42856400	Weak transcription	Right Atrium	heart
2	chr3:42847000-42851000	Weak transcription	Placenta Amnion	Placenta Amnion
3	chr3:42847000-42852200	Weak transcription	Primary hematopoietic stem cells short term culture	blood
4	chr3:42847000-42852400	Weak transcription	Sigmoid Colon	Sigmoid Colon
5	chr3:42847200-42850000	Weak transcription	Placenta	Placenta
6	chr3:42847200-42850200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
7	chr3:42847200-42852000	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
8	chr3:42847200-42852200	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
9	chr3:42847200-42852200	Weak transcription	Rectal Mucosa Donor 31	rectum
10	chr3:42847200-42852400	Weak transcription	Pancreas	Pancrea
11	chr3:42847200-42856400	Weak transcription	NHEK	skin
12	chr3:42847400-42852800	Weak transcription	Fetal Heart	heart
13	chr3:42847400-42852800	Weak transcription	Stomach Mucosa	stomach
14	chr3:42847400-42856200	Weak transcription	Colonic Mucosa	Colon
15	chr3:42847600-42852200	Weak transcription	K562	blood
16	chr3:42849000-42852200	Weak transcription	HepG2	liver
17	chr3:42849400-42853000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
18	chr3:42849800-42856400	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links