Variant report

Variant	rs2292416
Chromosome Location	chr15:77943935-77943936
allele	C/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:3)
LncRNA
region (count:4)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:3 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr15:77936103..77940000-chr15:77942222..77946608,4	MCF-7	breast:
2	chr15:77938491..77940182-chr15:77942914..77944636,2	K562	blood:
3	chr15:77937910..77941005-chr15:77942503..77944690,3	K562	blood:

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

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-HMG20A-3	chr15:77943677-77943997	ENSG00000259666.1
2	lnc-HMG20A-3	chr15:77943677-77944620	NONHSAT047451
3	lnc-HMG20A-3	chr15:77943677-77944620	NONHSAT047452
4	lnc-HMG20A-3	chr15:77943677-77944620	NONHSAT047455

No data

Variant related genes	Relation type
ENSG00000259666	Chromatin interaction

Extended variants
information (count: 57 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:48)

rs_ID	r²[population]
rs11630768	0.85[CEU][hapmap];0.91[CHB][hapmap];0.92[JPT][hapmap];0.88[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs11633639	0.85[CEU][hapmap];0.91[CHB][hapmap];0.83[CHD][hapmap];0.93[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.91[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs11634778	0.92[CHB][hapmap];0.93[JPT][hapmap];0.97[ASN][1000 genomes]
rs11635239	1.00[CEU][hapmap];0.91[CHB][hapmap];0.93[JPT][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs11638318	0.91[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs11855155	0.85[CEU][hapmap];0.91[CHB][hapmap];0.83[CHD][hapmap];0.93[JPT][hapmap];1.00[TSI][hapmap];0.88[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs11856978	0.81[CHB][hapmap];0.81[JPT][hapmap]
rs11857045	0.82[CHB][hapmap];0.84[JPT][hapmap]
rs13329256	0.85[CEU][hapmap];0.91[CHB][hapmap];0.93[JPT][hapmap];1.00[TSI][hapmap];0.88[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs13329323	0.88[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs16969027	0.85[CEU][hapmap];0.91[CHB][hapmap];0.82[CHD][hapmap];0.93[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.88[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1877292	0.93[JPT][hapmap]
rs1877294	0.87[JPT][hapmap]
rs1877295	0.87[JPT][hapmap]
rs1877298	0.85[CEU][hapmap];0.81[CHB][hapmap];0.87[JPT][hapmap]
rs2292415	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[TSI][hapmap];0.87[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2292417	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28374408	0.84[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs28503184	0.84[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs28515899	0.91[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs56717248	0.88[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs56941158	0.91[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs60886924	0.92[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7165679	0.87[JPT][hapmap]
rs7171716	0.82[CHB][hapmap];0.87[JPT][hapmap]
rs73457842	0.88[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs73457843	0.88[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs74025333	0.84[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs74025334	0.91[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs74025342	0.94[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs74025352	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs8023571	0.82[JPT][hapmap]
rs8024724	0.82[CHB][hapmap];0.82[JPT][hapmap]
rs8024932	0.82[JPT][hapmap]
rs8026164	0.87[JPT][hapmap]
rs8026671	0.88[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs8027456	0.82[CHB][hapmap];0.86[JPT][hapmap]
rs8028788	0.85[CEU][hapmap];0.91[CHB][hapmap];0.82[CHD][hapmap];0.93[JPT][hapmap];0.88[TSI][hapmap];0.84[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs8043367	1.00[AMR][1000 genomes]
rs9652488	0.97[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs9806280	0.85[CEU][hapmap];0.91[CHB][hapmap];0.93[JPT][hapmap];0.81[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs9920101	0.87[JPT][hapmap]
rs9920113	0.82[CHB][hapmap];0.86[JPT][hapmap]
rs9920127	0.87[JPT][hapmap]
rs9920132	0.87[JPT][hapmap]
rs9920134	0.82[CHB][hapmap];0.85[JPT][hapmap]
rs9920869	0.87[JPT][hapmap]
rs9972481	0.85[CEU][hapmap];0.91[CHB][hapmap];0.93[JPT][hapmap];0.88[TSI][hapmap];0.84[EUR][1000 genomes];0.90[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:9 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1040852	chr15:77160237-78137541	Enhancers Flanking Active TSS Active TSS Strong transcription Weak transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	42 gene(s)	inside rSNPs	diseases
2	nsv916323	chr15:77485765-78121259	Enhancers Strong transcription Weak transcription Genic enhancers Bivalent Enhancer Active TSS Bivalent/Poised TSS Flanking Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	29 gene(s)	inside rSNPs	diseases
3	nsv833060	chr15:77816654-78035204	Weak transcription Bivalent Enhancer Enhancers Genic enhancers Flanking Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Strong transcription Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	15 gene(s)	inside rSNPs	diseases
4	esv1806097	chr15:77817889-78301377	Enhancers Weak transcription Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Strong transcription Active TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	30 gene(s)	inside rSNPs	diseases
5	nsv904415	chr15:77845959-77943935	Weak transcription Flanking Active TSS Strong transcription Enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Genic enhancers Active TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
6	nsv904416	chr15:77845959-77967416	Enhancers Flanking Active TSS Bivalent Enhancer Weak transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS Active TSS Strong transcription ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
7	nsv904418	chr15:77851535-77963887	Weak transcription Enhancers Bivalent/Poised TSS Flanking Active TSS Flanking Bivalent TSS/Enh Active TSS Bivalent Enhancer ZNF genes & repeats Strong transcription Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
8	nsv904419	chr15:77897197-77943935	Bivalent Enhancer Enhancers Weak transcription Bivalent/Poised TSS Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Genic enhancers Strong transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
9	nsv529491	chr15:77932659-78751516	Genic enhancers Bivalent Enhancer Enhancers Weak transcription Strong transcription Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	80 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:9 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:77937200-77946800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
2	chr15:77942600-77945000	Weak transcription	Rectal Mucosa Donor 31	rectum
3	chr15:77942600-77945600	Enhancers	Fetal Brain Male	brain
4	chr15:77943200-77945000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
5	chr15:77943200-77947200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
6	chr15:77943200-77951800	Weak transcription	H1 Cell Line	embryonic stem cell
7	chr15:77943400-77946400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
8	chr15:77943600-77944000	Bivalent Enhancer	HSMMtube	muscle
9	chr15:77943800-77945600	Weak transcription	Fetal Brain Female	brain

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