Variant report

Variant	rs7747178
Chromosome Location	chr6:44307390-44307391
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:4)
CpG islands
(count:0)
Chromatin interactive
region (count:13)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:4 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	CTCF	chr6:44307340-44307490	BJ	skin:	n/a	n/a
2	CTCF	chr6:44307360-44307510	HCPEpiC	choroid plexus:	n/a	n/a
3	CTCF	chr6:44307260-44307410	HEK293	kidney:	n/a	n/a
4	CTCF	chr6:44305865-44307421	SK-N-SH	brain:	n/a	chr6:44306437-44306447 chr6:44306429-44306450 chr6:44307034-44307047 chr6:44306436-44306449 chr6:44306434-44306452

No data

(count:13 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr6:44299856..44303347-chr6:44304768..44307907,5	K562	blood:
2	chr6:44231961..44235036-chr6:44304302..44308085,4	MCF-7	breast:
3	chr6:44295218..44297676-chr6:44304954..44307920,2	K562	blood:
4	chr6:44247321..44249117-chr6:44305925..44308606,2	K562	blood:
5	chr6:44062217..44064228-chr6:44306668..44309028,2	K562	blood:
6	chr6:44279477..44281866-chr6:44305528..44307591,2	K562	blood:
7	chr6:44306430..44308872-chr6:44310895..44313358,2	K562	blood:
8	chr6:44229471..44232092-chr6:44306709..44308642,2	K562	blood:
9	chr6:44233695..44236268-chr6:44306586..44308563,3	K562	blood:
10	chr6:44235419..44235959-chr6:44307130..44307772,2	MCF-7	breast:
11	chr6:44236483..44238229-chr6:44307349..44309648,2	K562	blood:
12	chr6:44214075..44216789-chr6:44305650..44307657,3	MCF-7	breast:
13	chr6:44222748..44225647-chr6:44303433..44307988,6	K562	blood:

No data

No data

No data

Variant related genes	Relation type
SPATS1	TF binding region
ENSG00000096384	Chromatin interaction
ENSG00000178233	Chromatin interaction
ENSG00000146232	Chromatin interaction
ENSG00000124608	Chromatin interaction
ENSG00000157593	Chromatin interaction

Extended variants
information (count: 19 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:18)

rs_ID	r²[population]
rs12197830	0.95[AFR][1000 genomes]
rs1293207	0.85[YRI][hapmap]
rs1473563	0.85[YRI][hapmap];0.95[AFR][1000 genomes]
rs1473564	0.95[AFR][1000 genomes]
rs2026309	1.00[ASW][hapmap];0.80[AFR][1000 genomes]
rs2754769	0.85[YRI][hapmap]
rs490814	0.85[YRI][hapmap]
rs6458383	0.85[YRI][hapmap]
rs6458384	0.85[YRI][hapmap]
rs6458385	0.85[YRI][hapmap]
rs6908640	0.85[YRI][hapmap]
rs6912195	0.85[YRI][hapmap]
rs6931374	0.86[AFR][1000 genomes]
rs7763988	0.80[AFR][1000 genomes]
rs856597	0.85[YRI][hapmap]
rs9296429	0.90[AFR][1000 genomes]
rs9472254	0.95[AFR][1000 genomes]
rs994736	0.85[YRI][hapmap];0.90[AFR][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	nsv931987	chr6:43624625-44350167	Enhancers Flanking Bivalent TSS/Enh Weak transcription Genic enhancers Bivalent Enhancer Flanking Active TSS Strong transcription Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	201 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:12 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:44302600-44309600	Weak transcription	Monocytes-CD14+_RO01746	blood
2	chr6:44305000-44307400	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
3	chr6:44305200-44307400	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
4	chr6:44305400-44310400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
5	chr6:44306000-44307600	Enhancers	iPS-15b Cell Line	embryonic stem cell
6	chr6:44306200-44309200	Weak transcription	Brain Germinal Matrix	brain
7	chr6:44306400-44307800	Enhancers	Liver	Liver
8	chr6:44306800-44309200	Weak transcription	K562	blood
9	chr6:44307000-44308200	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
10	chr6:44307000-44308400	Enhancers	HMEC	breast
11	chr6:44307200-44307400	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
12	chr6:44307200-44307800	Enhancers	Gastric	stomach

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Input of quick search could be:

dbSNP/dbVar ID: rs12345 /nsv7879
a single nucleotide as 0-based coordinates: chr1:12345
chromosomal regions: chr1:12345-34567

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