Variant report

Variant	rs12941500
Chromosome Location	chr17:59646471-59646472
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:0)
CpG islands
(count:0)
Chromatin interactive
region (count:23)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

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

No.	Distal block	Cell Line	Cell type
1	chr17:59644855..59647910-chr17:59841335..59844150,3	MCF-7	breast:
2	chr17:59489860..59490823-chr17:59645940..59646503,2	MCF-7	breast:
3	chr17:59644698..59647505-chr20:52196256..52198648,3	MCF-7	breast:
4	chr17:57922174..57925590-chr17:59644631..59647005,4	MCF-7	breast:
5	chr17:59645361..59647604-chr20:52823496..52825003,2	MCF-7	breast:
6	chr17:56734257..56736743-chr17:59644680..59646726,2	MCF-7	breast:
7	chr17:59644967..59646707-chr3:49061145..49063463,2	MCF-7	breast:
8	chr17:59644033..59646771-chr20:55842643..55845574,2	MCF-7	breast:
9	chr11:88348048..88349548-chr17:59644695..59646956,2	MCF-7	breast:
10	chr17:59645769..59648011-chr17:59764387..59766837,2	MCF-7	breast:
11	chr17:59645174..59648291-chr20:49346675..49349528,3	MCF-7	breast:
12	chr17:59645078..59647528-chr20:52739899..52742175,2	MCF-7	breast:
13	chr17:59646337..59648248-chr20:55839360..55841998,2	MCF-7	breast:
14	chr10:93683550..93685113-chr17:59644992..59647516,2	MCF-7	breast:
15	chr17:59644566..59646787-chr20:49409333..49412308,3	MCF-7	breast:
16	chr17:59628231..59629240-chr17:59645949..59646723,4	MCF-7	breast:
17	chr17:59644932..59647511-chr20:49403932..49406632,2	MCF-7	breast:
18	chr17:59632406..59633060-chr17:59645700..59646561,2	MCF-7	breast:
19	chr17:59632363..59633272-chr17:59645757..59646684,4	MCF-7	breast:
20	chr17:59645929..59648016-chr20:61659710..61661386,2	MCF-7	breast:
21	chr17:59646374..59647932-chr20:49411300..49413192,2	MCF-7	breast:
22	chr17:59644866..59646960-chr7:2726523..2728836,2	MCF-7	breast:
23	chr17:59645061..59647542-chr4:153552803..153555273,2	MCF-7	breast:

No data

Variant related genes	Relation type
ENSG00000124243	Chromatin interaction
ENSG00000124171	Chromatin interaction
ENSG00000226308	Chromatin interaction
ENSG00000101144	Chromatin interaction
ENSG00000201524	Chromatin interaction
ENSG00000178035	Chromatin interaction
ENSG00000174945	Chromatin interaction
ENSG00000202077	Chromatin interaction
ENSG00000101132	Chromatin interaction

Extended variants
information (count: 30 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:28)

rs_ID	r²[population]
rs10438755	0.95[CEU][hapmap];0.88[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs10438756	0.95[CEU][hapmap];0.88[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs11650703	0.96[CEU][hapmap];0.84[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs11654397	0.89[CEU][hapmap];0.90[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs11655330	1.00[CEU][hapmap];1.00[CHB][hapmap];0.96[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.98[TSI][hapmap];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11869403	0.99[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12451513	0.86[ASW][hapmap];0.85[CEU][hapmap];0.84[CHB][hapmap];0.88[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.83[LWK][hapmap];1.00[MEX][hapmap];0.89[TSI][hapmap];0.83[AFR][1000 genomes];0.96[AMR][1000 genomes];0.85[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12451827	0.95[MEX][hapmap];0.91[TSI][hapmap];0.84[EUR][1000 genomes]
rs12452859	0.86[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs12939687	0.86[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs12943370	0.84[CEU][hapmap];0.82[EUR][1000 genomes]
rs12949631	0.96[CEU][hapmap];0.82[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs12952180	0.90[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12952542	0.84[EUR][1000 genomes]
rs1476799	0.81[CEU][hapmap];0.85[EUR][1000 genomes]
rs1476800	0.87[MEX][hapmap];0.81[TSI][hapmap]
rs1558275	0.86[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs1558276	0.86[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs1860414	0.96[CEU][hapmap];0.92[CHB][hapmap];1.00[JPT][hapmap];0.98[AMR][1000 genomes];0.89[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2079796	0.83[EUR][1000 genomes]
rs2378870	0.93[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs2378871	0.94[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs4583315	0.87[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs5024560	0.81[EUR][1000 genomes]
rs8064466	0.93[ASW][hapmap];0.92[CHB][hapmap];0.96[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.83[LWK][hapmap];0.87[MEX][hapmap];0.98[MKK][hapmap];0.85[TSI][hapmap];0.82[YRI][hapmap];0.90[AFR][1000 genomes];0.85[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs8070532	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];0.89[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs8071653	0.81[CEU][hapmap];0.83[MEX][hapmap];0.89[TSI][hapmap];0.87[EUR][1000 genomes]
rs977745	0.81[CEU][hapmap];0.87[MEX][hapmap];0.91[TSI][hapmap];0.86[EUR][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	nsv457864	chr17:59612041-59646764	Active TSS Enhancers Bivalent Enhancer Weak transcription Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent/Poised TSS	Chromatin interactive region	26 gene(s)	inside rSNPs	diseases
2	nsv575840	chr17:59612041-59646764	Enhancers Flanking Active TSS Weak transcription Bivalent Enhancer Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh	Chromatin interactive region	26 gene(s)	inside rSNPs	diseases

No data

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr17:59644400-59646800	Flanking Active TSS	A549	lung
2	chr17:59644400-59646800	Enhancers	HepG2	liver
3	chr17:59644600-59646800	Enhancers	Hela-S3	cervix
4	chr17:59646200-59646600	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
5	chr17:59646200-59646600	Enhancers	Rectal Mucosa Donor 31	rectum
6	chr17:59646200-59646800	Enhancers	Stomach Mucosa	stomach

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