Variant report

Variant	rs7299135
Chromosome Location	chr12:48413944-48413945
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr12:48406038..48410831-chr12:48411860..48418424,9	MCF-7	breast:
2	chr12:48391315..48400584-chr12:48411914..48418489,16	MCF-7	breast:
3	chr12:48399203..48400811-chr12:48412734..48415114,2	K562	blood:
4	chr12:48410357..48413530-chr12:48413703..48417962,3	K562	blood:

Variant related genes	Relation type
ENSG00000139219	Chromatin interaction

Extended variants
information (count: 78 )
Associated
traits (count: 5 )

rSNPs within LD-proxies of this variant (count:76)

rs_ID	r²[population]
rs10082861	0.82[CHB][hapmap];0.92[JPT][hapmap]
rs10219623	0.93[JPT][hapmap]
rs10875720	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10875722	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10875723	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10875724	0.82[CHB][hapmap];1.00[JPT][hapmap];0.95[ASN][1000 genomes]
rs10875725	0.90[CHB][hapmap];0.97[CHD][hapmap];0.93[JPT][hapmap];0.91[ASN][1000 genomes]
rs10875730	0.91[ASN][1000 genomes]
rs10875731	0.91[ASN][1000 genomes]
rs10875732	0.94[CHB][hapmap];0.92[JPT][hapmap];0.91[ASN][1000 genomes]
rs10875745	0.93[JPT][hapmap]
rs10875746	0.93[JPT][hapmap]
rs10875750	0.93[JPT][hapmap]
rs10875767	0.86[JPT][hapmap]
rs10875770	0.86[JPT][hapmap]
rs10875772	0.86[JPT][hapmap]
rs11168355	1.00[CHB][hapmap];1.00[CHD][hapmap];0.86[JPT][hapmap];0.93[ASN][1000 genomes]
rs11168357	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.96[ASN][1000 genomes]
rs11168369	0.94[CHB][hapmap];0.93[JPT][hapmap];0.91[ASN][1000 genomes]
rs11168371	0.95[CHB][hapmap];0.91[CHD][hapmap];0.93[JPT][hapmap];0.91[ASN][1000 genomes]
rs11168374	0.91[ASN][1000 genomes]
rs11168403	0.95[CHB][hapmap];0.93[JPT][hapmap]
rs11168413	0.93[JPT][hapmap]
rs11168414	0.93[JPT][hapmap]
rs11168418	0.93[JPT][hapmap]
rs11168420	0.93[JPT][hapmap]
rs11168421	0.93[JPT][hapmap]
rs11168425	0.93[JPT][hapmap]
rs11168427	0.93[JPT][hapmap]
rs11168433	0.93[JPT][hapmap]
rs11168450	0.91[GIH][hapmap];0.93[JPT][hapmap]
rs11168459	0.86[JPT][hapmap]
rs12296244	0.91[ASN][1000 genomes]
rs12297470	0.93[JPT][hapmap]
rs12304476	0.95[CHB][hapmap];0.88[CHD][hapmap];0.93[JPT][hapmap]
rs12305182	1.00[JPT][hapmap];0.93[ASN][1000 genomes]
rs12305511	0.93[JPT][hapmap]
rs12306451	0.95[CHB][hapmap];0.91[CHD][hapmap];0.93[JPT][hapmap]
rs12310813	0.93[JPT][hapmap]
rs12310999	0.91[ASN][1000 genomes]
rs12312134	0.86[JPT][hapmap]
rs17122666	0.83[CHD][hapmap];0.93[JPT][hapmap]
rs17122812	0.86[JPT][hapmap]
rs1859445	0.93[JPT][hapmap]
rs2012773	0.93[JPT][hapmap]
rs2079295	0.93[CHB][hapmap];1.00[JPT][hapmap];0.82[YRI][hapmap];0.92[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2107638	0.93[JPT][hapmap]
rs2228500	0.93[JPT][hapmap]
rs2269933	0.93[JPT][hapmap]
rs2269935	0.93[JPT][hapmap]
rs2269936	0.95[CHB][hapmap];0.93[JPT][hapmap];0.91[ASN][1000 genomes]
rs28459711	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3782910	0.95[CHB][hapmap];0.93[JPT][hapmap]
rs4760609	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.97[ASN][1000 genomes]
rs4760610	0.96[ASN][1000 genomes]
rs4760619	0.93[JPT][hapmap]
rs4760622	0.93[JPT][hapmap]
rs4760676	0.93[ASN][1000 genomes]
rs4760681	0.93[JPT][hapmap]
rs4760687	0.93[JPT][hapmap]
rs4760695	0.93[JPT][hapmap]
rs4760696	0.91[GIH][hapmap];0.93[JPT][hapmap]
rs4760697	0.91[GIH][hapmap];0.93[JPT][hapmap]
rs61918774	0.91[ASN][1000 genomes]
rs6580659	0.92[JPT][hapmap]
rs7135779	0.92[JPT][hapmap]
rs719008	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs725454	0.83[CHD][hapmap];0.93[JPT][hapmap]
rs7299271	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.88[MKK][hapmap];1.00[TSI][hapmap];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7299364	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7299762	0.93[AFR][1000 genomes];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs7486424	0.93[JPT][hapmap]
rs7964359	0.87[CHB][hapmap];0.87[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs8804	0.93[JPT][hapmap]
rs886588	0.94[CHB][hapmap];0.91[CHD][hapmap];0.93[JPT][hapmap]
rs989144	0.95[CHB][hapmap];0.93[JPT][hapmap]

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	nsv832401	chr12:48347453-48477999	Weak transcription Enhancers Bivalent Enhancer Genic enhancers Active TSS Flanking Bivalent TSS/Enh Strong transcription Bivalent/Poised TSS Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	29 gene(s)	inside rSNPs	diseases
2	esv2760677	chr12:48412410-48416967	Enhancers Weak transcription Bivalent Enhancer Active TSS Flanking Active TSS Bivalent/Poised TSS	Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	n/a

mRNA abundance (count:5)

SNP	Gene	Cis/trans	Tissue	Source
rs7299135	ZNF641	cis	Whole Blood	GTEx
rs7299135	SENP1	cis	cerebellum	SCAN
rs7299135	SMARCD1	cis	cerebellum	SCAN
rs7299135	ZNF641	cis	Muscle Skeletal	GTEx
rs7299135	RP1-228P16.1	cis	Skin Sun Exposed Lower leg	GTEx

Chromatin state (count:10 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:48399400-48415000	Weak transcription	Right Atrium	heart
2	chr12:48410600-48414800	Weak transcription	Hela-S3	cervix
3	chr12:48411600-48415000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
4	chr12:48411600-48415200	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
5	chr12:48412000-48415800	Weak transcription	Duodenum Mucosa	Duodenum
6	chr12:48412400-48415000	Weak transcription	Fetal Intestine Large	intestine
7	chr12:48412400-48415000	Weak transcription	Fetal Intestine Small	intestine
8	chr12:48412400-48415000	Weak transcription	Rectal Mucosa Donor 31	rectum
9	chr12:48412600-48415400	Weak transcription	HepG2	liver
10	chr12:48413600-48415400	Weak transcription	Right Ventricle	heart

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