Variant report

Variant	rs71412688
Chromosome Location	chr14:56021539-56021540
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr14:56021535-56021702	MCF10A-Er-Src	breast:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr14:56017947..56022061-chr14:56043828..56047582,3	MCF-7	breast:

Variant related genes	Relation type
KTN1	TF binding region
ENSG00000126777	Chromatin interaction
ENSG00000186615	Chromatin interaction

Extended variants
information (count: 114 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:102)

rs_ID	r²[population]
rs10083303	0.88[AMR][1000 genomes]
rs10083353	0.88[AMR][1000 genomes]
rs10083431	0.84[AMR][1000 genomes]
rs10083493	0.88[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs10083499	0.84[AMR][1000 genomes]
rs10129890	0.81[AMR][1000 genomes]
rs10133729	0.80[AMR][1000 genomes]
rs10133962	0.88[AMR][1000 genomes]
rs10135426	0.84[AMR][1000 genomes]
rs10136155	0.88[AMR][1000 genomes]
rs10137340	0.84[AMR][1000 genomes]
rs10137364	0.84[AMR][1000 genomes]
rs10142497	0.88[AMR][1000 genomes]
rs10142757	0.88[AMR][1000 genomes]
rs10143002	0.88[AMR][1000 genomes]
rs10146604	0.84[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs10147380	0.84[AMR][1000 genomes]
rs10148983	0.88[AMR][1000 genomes]
rs10149408	0.84[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs10150498	0.84[AMR][1000 genomes]
rs10483643	0.80[AMR][1000 genomes]
rs10483645	1.00[AFR][1000 genomes]
rs10483646	1.00[AFR][1000 genomes]
rs10483648	1.00[AFR][1000 genomes]
rs10483650	1.00[AFR][1000 genomes]
rs12100753	0.84[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs12879564	1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12879705	0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12880362	1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12883972	0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12886406	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12892022	1.00[AFR][1000 genomes]
rs12892413	1.00[AFR][1000 genomes]
rs12893061	1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12893081	1.00[AFR][1000 genomes]
rs12893610	1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12893676	1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12893836	1.00[AFR][1000 genomes]
rs12894368	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12894613	1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13379151	0.84[AMR][1000 genomes]
rs13379340	0.84[AMR][1000 genomes]
rs13379342	0.88[AMR][1000 genomes]
rs13379343	0.88[AMR][1000 genomes]
rs13379353	0.84[AMR][1000 genomes]
rs17253716	1.00[AFR][1000 genomes]
rs17253723	1.00[AFR][1000 genomes]
rs17253744	1.00[AFR][1000 genomes]
rs17683614	1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs17683626	0.96[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs17683656	0.88[AMR][1000 genomes]
rs17683728	0.88[AMR][1000 genomes]
rs17685078	1.00[AFR][1000 genomes]
rs17685102	1.00[AFR][1000 genomes]
rs17744929	1.00[AFR][1000 genomes]
rs17745274	1.00[AFR][1000 genomes];0.92[AMR][1000 genomes];0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17745459	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17746033	0.88[AMR][1000 genomes]
rs17746106	0.81[AMR][1000 genomes]
rs17832371	1.00[AFR][1000 genomes]
rs17832389	1.00[AFR][1000 genomes]
rs2147114	1.00[AFR][1000 genomes];0.96[AMR][1000 genomes]
rs2274075	0.80[AMR][1000 genomes]
rs28380739	0.80[AMR][1000 genomes]
rs28392709	0.80[AMR][1000 genomes]
rs28478195	0.88[AMR][1000 genomes]
rs28513551	0.80[AMR][1000 genomes]
rs28549152	0.80[AMR][1000 genomes]
rs28581185	0.80[AMR][1000 genomes]
rs28681420	0.80[AMR][1000 genomes]
rs28831725	0.80[AMR][1000 genomes]
rs34136598	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34330219	1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34446601	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34719936	1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35230683	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35294669	1.00[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs35418987	1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35466279	1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35536987	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35830444	1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3736876	1.00[AFR][1000 genomes]
rs3742570	1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3742571	0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs45458197	1.00[AFR][1000 genomes]
rs45501402	1.00[AFR][1000 genomes]
rs71412689	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs71412690	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs71412693	1.00[AFR][1000 genomes]
rs71413577	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs71413578	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs7145064	0.87[AMR][1000 genomes]
rs7150841	1.00[AFR][1000 genomes];0.87[AMR][1000 genomes]
rs8007065	1.00[AFR][1000 genomes];0.96[AMR][1000 genomes]
rs8008528	1.00[AFR][1000 genomes];0.96[AMR][1000 genomes]
rs8009239	1.00[AFR][1000 genomes];0.96[AMR][1000 genomes]
rs8009608	0.88[AMR][1000 genomes]
rs8019218	0.87[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs9944028	0.88[AMR][1000 genomes]
rs9972177	0.84[AMR][1000 genomes]
rs9972178	0.88[AMR][1000 genomes]
rs9972180	0.88[AMR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:12 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv901958	chr14:55822095-56045411	Enhancers Weak transcription Flanking Active TSS Genic enhancers Strong transcription Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	20 gene(s)	inside rSNPs	diseases
2	nsv901960	chr14:55853724-56085130	Weak transcription Active TSS Flanking Active TSS Enhancers Strong transcription Genic enhancers Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	29 gene(s)	inside rSNPs	diseases
3	nsv901961	chr14:55853724-56101879	Enhancers Weak transcription Flanking Active TSS Strong transcription Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	30 gene(s)	inside rSNPs	diseases
4	nsv901962	chr14:55862956-56101879	Enhancers Flanking Bivalent TSS/Enh Strong transcription Active TSS Weak transcription Flanking Active TSS Genic enhancers ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	30 gene(s)	inside rSNPs	diseases
5	nsv901963	chr14:55871452-56085130	Enhancers Flanking Active TSS Weak transcription Active TSS Strong transcription ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	28 gene(s)	inside rSNPs	diseases
6	nsv901964	chr14:55871452-56101879	Enhancers Weak transcription Flanking Active TSS Active TSS ZNF genes & repeats Strong transcription Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	29 gene(s)	inside rSNPs	diseases
7	nsv564874	chr14:55879685-56027815	Flanking Active TSS Enhancers Weak transcription Active TSS Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases
8	nsv1051564	chr14:55895610-56130788	Enhancers Active TSS Weak transcription Strong transcription Flanking Active TSS Bivalent/Poised TSS Genic enhancers Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	27 gene(s)	inside rSNPs	diseases
9	nsv542103	chr14:55895610-56130788	Strong transcription Weak transcription Enhancers Active TSS Flanking Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	27 gene(s)	inside rSNPs	diseases
10	nsv1047054	chr14:55922287-56035579	Enhancers Flanking Active TSS ZNF genes & repeats Weak transcription Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Strong transcription Genic enhancers Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
11	nsv1037161	chr14:55928030-56039353	Weak transcription Flanking Active TSS Enhancers ZNF genes & repeats Active TSS Genic enhancers Bivalent Enhancer Strong transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
12	nsv901965	chr14:55976428-56101879	Active TSS Enhancers Weak transcription ZNF genes & repeats Flanking Active TSS Strong transcription Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	23 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs71412688	KTN1-AS1	cis	Skin Sun Exposed Lower leg	GTEx

Chromatin state (count:19 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr14:56010600-56026600	Weak transcription	Right Ventricle	heart
2	chr14:56010800-56024000	Weak transcription	A549	lung
3	chr14:56014000-56024000	Weak transcription	Pancreas	Pancrea
4	chr14:56014000-56031200	Weak transcription	Left Ventricle	heart
5	chr14:56018000-56021800	Weak transcription	Fetal Heart	heart
6	chr14:56018600-56023400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
7	chr14:56020800-56023400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
8	chr14:56020800-56023400	Weak transcription	Ovary	ovary
9	chr14:56020800-56023600	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
10	chr14:56020800-56024000	Weak transcription	Brain Inferior Temporal Lobe	brain
11	chr14:56021000-56023200	Weak transcription	Breast Myoepithelial Primary Cells	Breast
12	chr14:56021000-56023400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
13	chr14:56021000-56023400	Weak transcription	HMEC	breast
14	chr14:56021000-56023600	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
15	chr14:56021000-56023800	Weak transcription	NHEK	skin
16	chr14:56021000-56024000	Weak transcription	Aorta	Aorta
17	chr14:56021000-56026600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
18	chr14:56021200-56022000	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
19	chr14:56021200-56023600	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin

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