Variant report

Variant	rs10023142
Chromosome Location	chr4:78271822-78271823
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr4:78269918..78271823-chr4:78272380..78274841,2	MCF-7	breast:
2	chr4:78270382..78272050-chr4:78274178..78276131,2	K562	blood:

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-CCNI-6	chr4:78271523-78272388	NONHSAT097053

Variant related genes	Relation type
ENSG00000248831	Chromatin interaction

Extended variants
information (count: 76 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:66)

rs_ID	r²[population]
rs10000203	1.00[CEU][hapmap];0.82[JPT][hapmap];1.00[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs10021013	0.92[ASN][1000 genomes]
rs10022216	1.00[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs10024634	1.00[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs10025816	1.00[CEU][hapmap];0.82[JPT][hapmap];1.00[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs10031995	1.00[CEU][hapmap];1.00[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs10034168	1.00[CEU][hapmap];0.81[CHB][hapmap];1.00[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs12502190	0.82[CEU][hapmap]
rs1559121	1.00[CEU][hapmap];0.81[CHB][hapmap]
rs17002568	1.00[CEU][hapmap];0.94[CHB][hapmap];0.94[JPT][hapmap];0.89[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs17002573	1.00[AMR][1000 genomes];0.88[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs17002574	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]
rs17002575	1.00[AMR][1000 genomes];0.88[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs17002578	1.00[CEU][hapmap];0.88[CHB][hapmap];1.00[AMR][1000 genomes];0.88[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs17002614	0.82[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs17002672	0.82[CEU][hapmap]
rs28408985	0.92[ASN][1000 genomes]
rs28470829	1.00[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs28509428	1.00[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs28510834	1.00[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs28558753	1.00[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs28640182	0.96[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs2866283	0.92[ASN][1000 genomes]
rs28697219	0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs28715173	0.82[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs28771770	0.86[AMR][1000 genomes]
rs28821633	0.86[AMR][1000 genomes]
rs28822468	0.82[AMR][1000 genomes]
rs28844066	0.86[AMR][1000 genomes]
rs28886989	0.86[AMR][1000 genomes]
rs3886412	1.00[CEU][hapmap];0.80[CHB][hapmap];1.00[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs4146559	0.82[CEU][hapmap]
rs4426805	1.00[CEU][hapmap];1.00[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs4447887	1.00[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs4643843	1.00[CEU][hapmap];0.96[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs4859826	0.85[CEU][hapmap];0.81[CHB][hapmap];0.94[JPT][hapmap];0.93[ASN][1000 genomes]
rs56704522	1.00[AMR][1000 genomes];0.88[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs57255185	0.86[AMR][1000 genomes]
rs57851138	0.86[AMR][1000 genomes]
rs57854205	1.00[AMR][1000 genomes];0.88[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs58210020	1.00[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs58493318	1.00[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs58763343	0.96[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs59017002	1.00[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs59225688	1.00[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs59383601	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs59548585	1.00[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs59817506	1.00[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs60084947	1.00[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs60847680	1.00[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs60994753	1.00[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs61041046	1.00[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs61482056	1.00[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs61559911	1.00[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs6819777	1.00[CEU][hapmap];0.87[CHB][hapmap];1.00[AMR][1000 genomes];0.88[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs6832224	0.86[AMR][1000 genomes]
rs6843981	1.00[CEU][hapmap];0.87[CHB][hapmap];1.00[JPT][hapmap];0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6848365	0.84[ASN][1000 genomes]
rs6849731	1.00[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][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]
rs72859841	0.86[AMR][1000 genomes]
rs72859843	0.86[AMR][1000 genomes]
rs72859844	0.86[AMR][1000 genomes]
rs7657699	0.82[CEU][hapmap]
rs7666881	0.93[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs9307270	0.82[CEU][hapmap];0.81[CHB][hapmap];0.94[JPT][hapmap];0.92[ASN][1000 genomes]
rs9994349	0.85[CEU][hapmap];0.80[CHB][hapmap]

Variant overlapped rSNPs/rCNVs (count:10 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1006017	chr4:78139780-78312974	Enhancers ZNF genes & repeats Weak transcription Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
2	nsv1002683	chr4:78170317-78281331	Enhancers Weak transcription ZNF genes & repeats Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Active TSS	TF binding region Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
3	nsv1010450	chr4:78182037-78317840	Enhancers Weak transcription ZNF genes & repeats Flanking Active TSS Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
4	nsv1004824	chr4:78188691-78312974	Enhancers ZNF genes & repeats Weak transcription Bivalent Enhancer Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
5	nsv1000447	chr4:78191608-78291173	Weak transcription Enhancers ZNF genes & repeats Bivalent Enhancer Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh	TF binding region Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
6	esv3468255	chr4:78237484-78277631	Enhancers Weak transcription ZNF genes & repeats Flanking Active TSS	TF binding region Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
7	esv5935	chr4:78237568-78277734	Weak transcription ZNF genes & repeats Flanking Active TSS Enhancers	TF binding region Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
8	esv3468256	chr4:78237627-78277552	Enhancers Weak transcription ZNF genes & repeats Flanking Active TSS	TF binding region Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
9	esv1845782	chr4:78237955-78321598	Enhancers Weak transcription ZNF genes & repeats Bivalent Enhancer Flanking Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
10	nsv829974	chr4:78240718-78415642	Weak transcription Enhancers Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	2 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	chr4:78269800-78272000	Enhancers	HMEC	breast
2	chr4:78270000-78272000	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
3	chr4:78270000-78273000	Weak transcription	Stomach Mucosa	stomach
4	chr4:78271400-78272000	Enhancers	Fetal Intestine Small	intestine
5	chr4:78271400-78272600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
6	chr4:78271800-78276800	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin

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