Variant report

Variant	rs12680842
Chromosome Location	chr8:95582606-95582607
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr8:95580853..95582910-chr8:95652064..95654255,2	MCF-7	breast:

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-AC023632.1-2	chr8:95582338-95582725	NONHSAT127778

Variant related genes	Relation type
ENSG00000104413	Chromatin interaction

Extended variants
information (count: 71 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:64)

rs_ID	r²[population]
rs10104041	0.97[ASN][1000 genomes]
rs10111287	0.97[ASN][1000 genomes]
rs1023767	0.95[CHB][hapmap];0.93[CHD][hapmap];0.81[GIH][hapmap];0.95[JPT][hapmap];0.88[MEX][hapmap];0.95[ASN][1000 genomes]
rs1048029	0.96[ASN][1000 genomes]
rs1055800	1.00[CHB][hapmap];0.93[CHD][hapmap];0.81[GIH][hapmap];0.95[JPT][hapmap];0.88[MEX][hapmap];0.80[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs10956915	0.93[ASN][1000 genomes]
rs10956919	0.95[CEU][hapmap];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11986009	0.97[ASN][1000 genomes]
rs11992893	0.96[ASN][1000 genomes]
rs11998578	0.81[AFR][1000 genomes];0.86[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs12540967	0.97[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12541408	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.95[JPT][hapmap];0.96[LWK][hapmap];1.00[MEX][hapmap];0.90[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.90[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12543207	0.92[ASN][1000 genomes]
rs12543730	1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12549596	0.86[EUR][1000 genomes]
rs12678305	0.96[ASN][1000 genomes]
rs12679345	1.00[CHB][hapmap];0.93[CHD][hapmap];0.81[GIH][hapmap];0.95[JPT][hapmap];0.88[MEX][hapmap];0.80[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs12679785	0.86[CEU][hapmap];0.85[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs12680418	0.83[CHB][hapmap]
rs12680855	0.97[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12680965	0.80[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs12681564	0.93[ASN][1000 genomes]
rs13258635	0.86[CEU][hapmap];0.83[CHB][hapmap];0.84[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs1426172	0.86[EUR][1000 genomes]
rs1470153	0.96[ASN][1000 genomes]
rs16916874	0.96[ASN][1000 genomes]
rs16916881	0.81[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs1808488	0.86[EUR][1000 genomes]
rs1984711	0.87[EUR][1000 genomes]
rs1992370	1.00[CHB][hapmap];0.93[CHD][hapmap];0.81[GIH][hapmap];0.95[JPT][hapmap];0.88[MEX][hapmap];0.97[ASN][1000 genomes]
rs2114212	0.83[CHB][hapmap]
rs2304764	0.91[ASN][1000 genomes]
rs2381882	1.00[CHB][hapmap];0.93[CHD][hapmap];0.81[GIH][hapmap];0.95[JPT][hapmap];0.88[MEX][hapmap];0.96[ASN][1000 genomes]
rs2381885	0.80[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs28729295	0.97[ASN][1000 genomes]
rs28817653	0.85[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs34471170	0.86[EUR][1000 genomes]
rs4269508	0.80[ASN][1000 genomes]
rs4366055	0.93[ASN][1000 genomes]
rs4373498	0.96[ASN][1000 genomes]
rs4734282	0.83[EUR][1000 genomes]
rs4735297	0.94[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4735300	0.83[CHB][hapmap]
rs4735302	0.82[EUR][1000 genomes]
rs55897841	0.84[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs56042558	0.80[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs56302978	0.96[ASN][1000 genomes]
rs56716157	0.84[ASN][1000 genomes]
rs60655325	0.82[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs72674832	0.92[ASN][1000 genomes]
rs72674843	0.80[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs72674852	0.80[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs72674855	0.96[ASN][1000 genomes]
rs72674861	0.81[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs72674866	0.84[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs72674867	0.84[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs72674877	0.97[AFR][1000 genomes];0.99[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs72674881	0.85[EUR][1000 genomes]
rs7829886	0.92[ASN][1000 genomes]
rs957447	1.00[CHB][hapmap];0.88[CHD][hapmap];0.81[GIH][hapmap];0.95[JPT][hapmap];0.87[MEX][hapmap];0.80[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs957448	1.00[CHB][hapmap];0.93[CHD][hapmap];0.81[GIH][hapmap];0.95[JPT][hapmap];0.83[MEX][hapmap];0.96[ASN][1000 genomes]
rs9642927	0.86[EUR][1000 genomes]
rs9642928	0.86[EUR][1000 genomes]
rs9643346	0.86[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:7 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1017301	chr8:95273503-96248352	Weak transcription Enhancers Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh Strong transcription Bivalent Enhancer Bivalent/Poised TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	87 gene(s)	inside rSNPs	diseases
2	nsv539680	chr8:95273503-96248352	Enhancers Weak transcription Strong transcription Flanking Active TSS Genic enhancers Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	87 gene(s)	inside rSNPs	diseases
3	nsv532338	chr8:95296118-95971825	Enhancers Strong transcription Weak transcription Flanking Bivalent TSS/Enh Active TSS Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	61 gene(s)	inside rSNPs	diseases
4	nsv429928	chr8:95488800-95672033	Enhancers Weak transcription Flanking Active TSS Strong transcription Bivalent Enhancer Bivalent/Poised TSS Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	27 gene(s)	inside rSNPs	diseases
5	nsv1016339	chr8:95556054-95585807	Strong transcription Weak transcription Flanking Active TSS Transcr. at gene 5' and 3' Enhancers Active TSS ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
6	nsv1021702	chr8:95556054-95589194	Weak transcription Enhancers Flanking Active TSS Active TSS Strong transcription ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
7	nsv429929	chr8:95564533-95676894	Flanking Active TSS Weak transcription Flanking Bivalent TSS/Enh Enhancers Strong transcription Active TSS Bivalent Enhancer Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	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
rs12680842	KIAA1429	Cis_1M	lymphoblastoid	RTeQTL

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr8:95567000-95583000	Weak transcription	Duodenum Smooth Muscle	Duodenum
2	chr8:95567000-95584000	Weak transcription	Skeletal Muscle Female	skeletal muscle
3	chr8:95570000-95584400	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
4	chr8:95574000-95582800	Weak transcription	Fetal Muscle Leg	muscle
5	chr8:95575000-95584200	Weak transcription	Stomach Smooth Muscle	stomach
6	chr8:95577800-95582800	Weak transcription	Fetal Stomach	stomach

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