Variant report

Variant	rs11111917
Chromosome Location	chr12:104565620-104565621
allele	A/C
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:6)
LncRNA
region (count:1)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

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

No.	Distal block	Cell Line	Cell type
1	chr12:104560247..104562977-chr12:104565263..104567117,2	K562	blood:
2	chr12:104564791..104567133-chr12:104568799..104572664,3	K562	blood:
3	chr12:104530242..104531948-chr12:104564445..104566644,3	K562	blood:
4	chr12:104564345..104567467-chr12:104679276..104682233,3	K562	blood:
5	chr12:104526354..104529452-chr12:104565610..104568678,3	MCF-7	breast:
6	chr12:104530438..104533662-chr12:104564030..104567253,5	K562	blood:

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

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-TXNRD1-2	chr12:104565551-104565814	ENSG00000257193

No data

Variant related genes	Relation type
ENSG00000120837	Chromatin interaction
ENSG00000198431	Chromatin interaction

Extended variants
information (count: 35 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:30)

rs_ID	r²[population]
rs11111916	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.91[LWK][hapmap];0.95[MEX][hapmap];0.91[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.92[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11111940	0.89[CHD][hapmap];0.90[JPT][hapmap]
rs11613944	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11829709	0.87[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11836726	0.81[ASW][hapmap];1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];0.92[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.84[MKK][hapmap];1.00[TSI][hapmap];0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs17806643	0.85[MEX][hapmap]
rs4246260	0.91[CEU][hapmap];0.94[CHB][hapmap];0.94[CHD][hapmap];1.00[JPT][hapmap];0.85[MEX][hapmap];0.89[MKK][hapmap];0.81[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs4246261	0.81[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs4321026	0.86[ASN][1000 genomes]
rs4371000	0.95[AFR][1000 genomes];0.85[AMR][1000 genomes];0.98[ASN][1000 genomes]
rs4445711	0.81[CHD][hapmap];0.90[JPT][hapmap]
rs4522249	0.87[ASN][1000 genomes]
rs4592489	0.81[ASN][1000 genomes]
rs4964256	0.80[ASN][1000 genomes]
rs4964626	0.92[AFR][1000 genomes];0.85[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs4964628	0.94[ASW][hapmap];0.91[CEU][hapmap];0.89[CHB][hapmap];0.97[CHD][hapmap];1.00[JPT][hapmap];0.95[LWK][hapmap];0.86[MEX][hapmap];0.84[MKK][hapmap];0.96[YRI][hapmap];0.92[AFR][1000 genomes];0.82[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs4964678	0.86[ASN][1000 genomes]
rs61939220	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6539125	0.82[JPT][hapmap]
rs7297296	0.86[ASN][1000 genomes]
rs7297956	0.82[CHD][hapmap];0.85[JPT][hapmap]
rs7957744	0.91[CEU][hapmap];0.89[CHB][hapmap];1.00[JPT][hapmap];0.82[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs7958262	0.90[JPT][hapmap]
rs7961381	0.87[AFR][1000 genomes];0.86[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs7966970	0.86[ASN][1000 genomes]
rs7969538	0.83[AFR][1000 genomes];0.84[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs7972172	0.94[ASW][hapmap];0.84[CHB][hapmap];0.92[CHD][hapmap];1.00[JPT][hapmap];0.93[LWK][hapmap];0.86[MEX][hapmap];0.85[MKK][hapmap];0.87[YRI][hapmap];0.90[AFR][1000 genomes];0.85[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs7975524	0.81[ASN][1000 genomes]
rs9668556	0.80[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs9705582	0.83[AFR][1000 genomes];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1045725	chr12:104524153-104614108	Enhancers Weak transcription Genic enhancers ZNF genes & repeats Flanking Active TSS Flanking Bivalent TSS/Enh Active TSS Bivalent/Poised TSS Strong transcription Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	32 gene(s)	inside rSNPs	n/a
2	nsv541586	chr12:104524153-104614108	Enhancers Active TSS Weak transcription Genic enhancers Flanking Active TSS Strong transcription Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	32 gene(s)	inside rSNPs	n/a
3	esv1842062	chr12:104531180-104638773	Weak transcription Flanking Active TSS Enhancers Flanking Bivalent TSS/Enh Active TSS Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	33 gene(s)	inside rSNPs	n/a
4	nsv899493	chr12:104548613-104703228	Flanking Active TSS Active TSS Enhancers Strong transcription Weak transcription Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	30 gene(s)	inside rSNPs	diseases
5	nsv899494	chr12:104561521-104806232	Flanking Active TSS Weak transcription Genic enhancers Active TSS Enhancers Strong transcription Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	34 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	chr12:104560600-104565800	Weak transcription	Spleen	Spleen
2	chr12:104564400-104566200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
3	chr12:104565200-104566000	Flanking Active TSS	K562	blood
4	chr12:104565400-104565800	Enhancers	Placenta	Placenta
5	chr12:104565600-104566200	Enhancers	iPS-15b Cell Line	embryonic stem cell
6	chr12:104565600-104566200	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
7	chr12:104565600-104566400	Enhancers	H1 Cell Line	embryonic stem cell
8	chr12:104565600-104566400	Enhancers	HUES6 Cell Line	embryonic stem cell
9	chr12:104565600-104566600	Enhancers	ES-I3 Cell Line	embryonic stem cell

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