Variant report

Variant	rs12453293
Chromosome Location	chr17:59778793-59778794
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr11:134093130..134095538-chr17:59777590..59779531,2	MCF-7	breast:
2	chr17:59771494..59775363-chr17:59775365..59778832,4	K562	blood:
3	chr17:59777669..59780570-chr17:59890560..59893186,2	MCF-7	breast:
4	chr17:59775287..59779545-chr17:59790270..59794482,5	MCF-7	breast:
5	chr17:59775949..59780769-chr17:59781104..59786917,12	MCF-7	breast:
6	chr17:59777901..59779551-chr17:59787087..59789823,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000151502	Chromatin interaction
ENSG00000151503	Chromatin interaction

Extended variants
information (count: 129 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:127)

rs_ID	r²[population]
rs1015771	0.87[EUR][1000 genomes]
rs10221278	0.93[AFR][1000 genomes];0.88[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs10438771	0.86[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs10468558	0.85[EUR][1000 genomes]
rs10515206	0.85[EUR][1000 genomes]
rs10515207	0.84[EUR][1000 genomes]
rs10515211	0.80[EUR][1000 genomes]
rs10853038	0.86[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs10853039	0.93[AFR][1000 genomes];0.87[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs11079445	0.85[EUR][1000 genomes]
rs11079446	0.86[EUR][1000 genomes]
rs11079448	0.86[EUR][1000 genomes]
rs11650471	0.86[EUR][1000 genomes]
rs11651510	0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11658539	0.80[EUR][1000 genomes]
rs11871753	0.87[EUR][1000 genomes]
rs12449319	0.86[EUR][1000 genomes]
rs12450027	0.85[EUR][1000 genomes]
rs12451862	0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12453801	0.86[EUR][1000 genomes]
rs12453966	0.86[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12603485	0.85[EUR][1000 genomes]
rs12603617	0.88[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs12937232	0.86[AMR][1000 genomes];0.95[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs12949659	0.80[EUR][1000 genomes]
rs12950438	0.87[EUR][1000 genomes]
rs1468577	0.80[EUR][1000 genomes]
rs1541346	0.85[EUR][1000 genomes]
rs16945500	0.86[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs17532528	0.85[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs1978244	0.80[EUR][1000 genomes]
rs1990337	0.80[EUR][1000 genomes]
rs1990338	0.80[EUR][1000 genomes]
rs2024188	0.87[EUR][1000 genomes]
rs2040608	0.85[EUR][1000 genomes]
rs2109252	0.87[EUR][1000 genomes]
rs2109254	0.87[EUR][1000 genomes]
rs2109255	0.87[EUR][1000 genomes]
rs2158006	0.83[EUR][1000 genomes]
rs2159450	0.87[EUR][1000 genomes]
rs2188731	0.85[EUR][1000 genomes]
rs2191247	0.86[EUR][1000 genomes]
rs2191249	0.87[EUR][1000 genomes]
rs2214184	0.89[AFR][1000 genomes];0.88[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs2378874	0.85[EUR][1000 genomes]
rs2378875	0.85[EUR][1000 genomes]
rs2378884	0.91[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2378902	0.87[EUR][1000 genomes]
rs2378905	0.80[EUR][1000 genomes]
rs2378906	0.80[EUR][1000 genomes]
rs28571892	0.87[EUR][1000 genomes]
rs2890012	0.86[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs2890013	0.88[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs2890021	0.87[EUR][1000 genomes]
rs36031690	0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs4309463	0.86[AMR][1000 genomes];0.95[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs4343344	0.81[AMR][1000 genomes];0.95[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs4580256	0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4968444	0.87[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs4968447	0.89[AMR][1000 genomes];0.95[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs4968577	0.85[EUR][1000 genomes]
rs4968579	0.86[EUR][1000 genomes]
rs4968580	0.86[EUR][1000 genomes]
rs4968582	0.86[EUR][1000 genomes]
rs4968584	0.86[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs4968585	0.86[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs4968588	0.82[AMR][1000 genomes];0.86[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs4988351	0.81[EUR][1000 genomes]
rs55797010	0.86[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs56284136	0.86[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs57099937	0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs57393813	0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61599541	0.88[AMR][1000 genomes];0.90[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs62068837	0.80[EUR][1000 genomes]
rs62070615	0.86[EUR][1000 genomes]
rs62070616	0.86[EUR][1000 genomes]
rs62070617	0.86[EUR][1000 genomes]
rs62070624	0.82[EUR][1000 genomes]
rs6504068	0.87[EUR][1000 genomes]
rs6504070	0.82[EUR][1000 genomes]
rs6504071	0.80[EUR][1000 genomes]
rs6504072	0.80[EUR][1000 genomes]
rs67273191	0.85[EUR][1000 genomes]
rs67938055	0.86[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs717961	0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs717962	0.90[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7207074	0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7207881	0.87[EUR][1000 genomes]
rs7212172	0.80[EUR][1000 genomes]
rs7212423	0.88[AMR][1000 genomes];0.95[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs7213329	0.80[EUR][1000 genomes]
rs7213470	0.84[AMR][1000 genomes];0.95[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs7213587	0.85[AMR][1000 genomes];0.95[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs7213759	0.87[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7214884	0.80[EUR][1000 genomes]
rs7215784	0.80[EUR][1000 genomes]
rs7216011	0.80[EUR][1000 genomes]
rs7216756	0.80[EUR][1000 genomes]
rs7216824	0.80[EUR][1000 genomes]
rs7217206	0.80[EUR][1000 genomes]
rs7217292	0.87[EUR][1000 genomes]
rs7220688	0.89[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7220719	0.83[AMR][1000 genomes];0.93[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs72841508	0.86[EUR][1000 genomes]
rs8074949	0.83[AMR][1000 genomes];0.94[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs8075370	0.83[AMR][1000 genomes];0.95[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs8075397	0.88[EUR][1000 genomes]
rs8077088	0.80[EUR][1000 genomes]
rs8078977	0.85[EUR][1000 genomes]
rs8182296	0.86[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9303449	0.86[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs9807012	0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs9895987	0.80[EUR][1000 genomes]
rs9896013	0.85[EUR][1000 genomes]
rs9897121	0.80[EUR][1000 genomes]
rs9897450	0.81[AMR][1000 genomes];0.95[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs9897928	0.87[EUR][1000 genomes]
rs9900559	0.80[EUR][1000 genomes]
rs9901428	0.85[EUR][1000 genomes]
rs9902995	0.87[EUR][1000 genomes]
rs9903041	0.85[EUR][1000 genomes]
rs9904292	0.80[EUR][1000 genomes]
rs9904294	0.95[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs9905870	0.88[AMR][1000 genomes];0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs9906313	0.87[EUR][1000 genomes]
rs9907299	0.80[EUR][1000 genomes]
rs991378	0.80[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	esv3378293	chr17:59744117-60124899	ZNF genes & repeats Strong transcription Weak transcription Flanking Active TSS Active TSS Enhancers Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	175 gene(s)	inside rSNPs	diseases
2	nsv908673	chr17:59767501-59926645	Weak transcription ZNF genes & repeats Genic enhancers Strong transcription Enhancers Flanking Active TSS Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	94 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:15 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr17:59763400-59792800	Weak transcription	NH-A	brain
2	chr17:59766000-59819000	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
3	chr17:59767600-59792800	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
4	chr17:59767600-59793200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
5	chr17:59771800-59794600	Weak transcription	HSMM	muscle
6	chr17:59775600-59780200	ZNF genes & repeats	Dnd41	blood
7	chr17:59777000-59780000	ZNF genes & repeats	Duodenum Smooth Muscle	Duodenum
8	chr17:59777200-59779200	ZNF genes & repeats	Cortex derived primary cultured neurospheres	brain
9	chr17:59777200-59779400	ZNF genes & repeats	HepG2	liver
10	chr17:59777200-59780000	ZNF genes & repeats	ES-I3 Cell Line	embryonic stem cell
11	chr17:59777400-59785600	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
12	chr17:59777800-59778800	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
13	chr17:59777800-59779800	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
14	chr17:59778200-59780600	ZNF genes & repeats	HUES64 Cell Line	embryonic stem cell
15	chr17:59778200-59805800	Weak transcription	Thymus	Thymus

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