Variant report

Variant	rs1778511
Chromosome Location	chr6:28229411-28229412
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:1)
CpG islands
(count:0)
Chromatin interactive
region (count:6)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:1 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr6:28229187-28229447	K562	blood:	n/a	n/a

No data

(count:6 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr6:28108136..28111844-chr6:28229127..28232755,4	K562	blood:
2	chr6:28228574..28231688-chr6:28301541..28303929,3	K562	blood:
3	chr6:28217539..28222258-chr6:28227412..28230016,4	MCF-7	breast:
4	chr6:28184440..28186086-chr6:28227732..28230449,2	K562	blood:
5	chr6:28228030..28230750-chr6:28318492..28321168,2	K562	blood:
6	chr6:28180865..28183340-chr6:28228825..28231312,2	K562	blood:

No data

Variant related genes	Relation type
ZKSCAN4	TF binding region
ENSG00000187626	Chromatin interaction
ENSG00000235109	Chromatin interaction
ENSG00000198315	Chromatin interaction

Extended variants
information (count: 57 )
Associated
traits (count: 7 )

rSNPs within LD-proxies of this variant (count:56)

rs_ID	r²[population]
rs10456362	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1076639	0.83[CHB][hapmap];1.00[JPT][hapmap];0.81[ASN][1000 genomes]
rs11755032	0.82[CHB][hapmap];1.00[JPT][hapmap];0.90[ASN][1000 genomes]
rs11965538	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs13200462	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1321505	0.93[CEU][hapmap]
rs1339899	0.82[CHB][hapmap];1.00[JPT][hapmap];0.88[ASN][1000 genomes]
rs1419183	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1679709	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1679732	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1778507	0.82[CHB][hapmap];1.00[JPT][hapmap];0.93[ASN][1000 genomes]
rs1778508	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1936365	0.86[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[AMR][1000 genomes];0.92[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs213239	1.00[JPT][hapmap]
rs213241	1.00[JPT][hapmap]
rs213243	1.00[JPT][hapmap]
rs213244	1.00[JPT][hapmap]
rs2743554	1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[ASN][1000 genomes]
rs2743555	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2799077	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.98[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2799079	1.00[CEU][hapmap];1.00[CHB][hapmap];0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs3757188	0.93[CEU][hapmap]
rs4713139	0.93[CEU][hapmap]
rs4713140	0.93[CEU][hapmap]
rs61127718	0.80[ASN][1000 genomes]
rs68141011	0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6901575	1.00[CEU][hapmap];0.92[CHB][hapmap];1.00[JPT][hapmap]
rs6905391	0.82[AMR][1000 genomes];0.92[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6920512	0.83[CHB][hapmap];0.91[ASN][1000 genomes]
rs735765	1.00[CEU][hapmap];0.92[EUR][1000 genomes]
rs7740487	0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs853676	0.86[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs853678	0.87[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs853679	0.86[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs853681	0.86[CEU][hapmap];0.91[CHB][hapmap];1.00[JPT][hapmap];0.90[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs853682	0.91[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs853685	0.86[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs853687	0.81[ASN][1000 genomes]
rs853688	0.87[ASN][1000 genomes]
rs853694	0.84[AMR][1000 genomes];0.92[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs9295765	0.83[CHB][hapmap];0.90[JPT][hapmap]
rs9366717	0.93[CEU][hapmap];0.82[CHB][hapmap];0.90[JPT][hapmap];0.81[EUR][1000 genomes]
rs9368561	0.80[EUR][1000 genomes]
rs9380064	0.93[CEU][hapmap]
rs9380069	0.93[CEU][hapmap]
rs9393908	0.88[JPT][hapmap];0.81[EUR][1000 genomes]
rs9461446	0.82[CHB][hapmap];1.00[JPT][hapmap];0.93[ASN][1000 genomes]
rs9461448	0.82[CHB][hapmap];1.00[JPT][hapmap];0.90[ASN][1000 genomes]
rs9461449	0.83[CHB][hapmap];1.00[JPT][hapmap];0.90[ASN][1000 genomes]
rs9468287	0.93[CEU][hapmap]
rs9468318	0.81[CEU][hapmap]
rs9468321	0.83[CHB][hapmap];1.00[JPT][hapmap];0.93[ASN][1000 genomes]
rs9468322	0.82[CHB][hapmap];1.00[JPT][hapmap];0.93[ASN][1000 genomes]
rs9468342	0.83[CHB][hapmap];1.00[JPT][hapmap];0.81[ASN][1000 genomes]
rs9468345	1.00[JPT][hapmap]
rs9986596	0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[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	nsv830620	chr6:28173997-28348033	Flanking Active TSS Strong transcription Active TSS Bivalent/Poised TSS Weak transcription ZNF genes & repeats Enhancers Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	51 gene(s)	inside rSNPs	diseases

mRNA abundance (count:7)

SNP	Gene	Cis/trans	Tissue	Source
rs1778511	AL022393.7	cis	Muscle Skeletal	GTEx
rs1778511	RP5-874C20.3	cis	Thyroid	GTEx
rs1778511	BTN3A2	Cis_chr	lymphoblastoid	RTeQTL
rs1778511	ZSCAN12	Cis_1M	lymphoblastoid	RTeQTL
rs1778511	ZKSCAN3	cis	Skin Sun Exposed Lower leg	GTEx
rs1778511	BTN3A2///BTN3A3	Cis_chr	lymphoblastoid	RTeQTL
rs1778511	RP5-874C20.3	cis	Esophagus Muscularis	GTEx

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:28227000-28232000	Weak transcription	Primary T helper cells fromperipheralblood	blood
2	chr6:28227000-28233800	Weak transcription	Primary T helper cells PMA-I stimulated	--
3	chr6:28227400-28234400	Weak transcription	HSMMtube	muscle
4	chr6:28227600-28229800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
5	chr6:28227600-28231600	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
6	chr6:28227600-28231600	Weak transcription	Muscle Satellite Cultured Cells	--
7	chr6:28227600-28233600	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
8	chr6:28227600-28233800	Weak transcription	Brain Cingulate Gyrus	brain
9	chr6:28227600-28233800	Weak transcription	HMEC	breast
10	chr6:28227800-28231600	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
11	chr6:28227800-28234400	Weak transcription	Right Atrium	heart
12	chr6:28228200-28229600	Weak transcription	Skeletal Muscle Male	skeletal muscle
13	chr6:28228200-28229800	Weak transcription	Right Ventricle	heart
14	chr6:28228200-28234600	Weak transcription	Left Ventricle	heart
15	chr6:28228400-28231400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
16	chr6:28228400-28233800	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
17	chr6:28228400-28234000	Weak transcription	Psoas Muscle	Psoas
18	chr6:28229400-28230000	Enhancers	Skeletal Muscle Female	skeletal muscle

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