Variant report

Variant	rs9634261
Chromosome Location	chr12:48686871-48686872
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	chr12:48679787..48682010-chr12:48684412..48686927,2	K562	blood:
2	chr12:48677853..48680154-chr12:48686621..48688237,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000258234	Chromatin interaction

Extended variants
information (count: 117 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:99)

rs_ID	r²[population]
rs10082861	0.85[JPT][hapmap]
rs1021313	0.97[AMR][1000 genomes];0.91[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs10219623	0.87[JPT][hapmap]
rs10431526	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10437919	0.85[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs10437920	0.83[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs10467101	1.00[CEU][hapmap];0.94[CHB][hapmap];0.86[JPT][hapmap];0.95[AMR][1000 genomes];0.90[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs10875745	0.83[CHB][hapmap];0.87[JPT][hapmap]
rs10875746	0.87[JPT][hapmap]
rs10875750	0.83[CHB][hapmap];0.87[JPT][hapmap]
rs10875762	0.81[ASN][1000 genomes]
rs10875767	1.00[CEU][hapmap];0.94[CHB][hapmap];0.94[JPT][hapmap];0.83[AMR][1000 genomes];0.85[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs10875768	0.83[AMR][1000 genomes];0.84[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs10875769	0.83[ASN][1000 genomes]
rs10875770	1.00[CEU][hapmap];0.94[CHB][hapmap];0.93[JPT][hapmap];0.83[AMR][1000 genomes];0.86[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs10875772	1.00[CEU][hapmap];0.94[CHB][hapmap];0.93[JPT][hapmap];0.90[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs10875777	0.97[AMR][1000 genomes];0.91[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs10875778	0.81[AMR][1000 genomes];0.91[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs10875779	0.81[AMR][1000 genomes];0.91[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs10875782	0.84[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs10875792	1.00[CEU][hapmap];0.93[CHB][hapmap];1.00[JPT][hapmap];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10875793	1.00[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10875799	0.89[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs11168413	0.87[JPT][hapmap]
rs11168414	0.83[CHB][hapmap];0.87[JPT][hapmap]
rs11168418	0.83[CHB][hapmap];0.87[JPT][hapmap]
rs11168420	0.87[JPT][hapmap]
rs11168421	0.87[JPT][hapmap]
rs11168425	0.87[JPT][hapmap]
rs11168427	0.83[CHB][hapmap];0.87[JPT][hapmap]
rs11168433	0.83[CHB][hapmap];0.87[JPT][hapmap]
rs11168450	0.87[JPT][hapmap]
rs11168459	1.00[CEU][hapmap];0.94[CHB][hapmap];0.93[JPT][hapmap];0.83[AMR][1000 genomes];0.83[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs11168483	0.84[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs11168487	0.81[AMR][1000 genomes];0.91[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11168493	0.85[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs11168508	0.86[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11168510	0.83[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11168514	0.82[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11168516	1.00[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11168520	0.85[ASN][1000 genomes]
rs11168536	0.90[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs12227601	0.80[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12297470	0.83[CHB][hapmap];0.86[JPT][hapmap]
rs12300647	0.84[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs12305511	0.81[CEU][hapmap];0.83[CHB][hapmap];0.87[JPT][hapmap];0.83[ASN][1000 genomes]
rs12305647	0.83[ASN][1000 genomes]
rs12310813	0.83[CHB][hapmap];0.87[JPT][hapmap]
rs12312134	0.81[JPT][hapmap]
rs12313745	0.85[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs12317751	0.85[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs12318705	0.84[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs12322347	0.85[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs12322348	0.84[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs1471997	0.86[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];0.92[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs17122666	0.87[JPT][hapmap]
rs17122812	1.00[CEU][hapmap];0.94[CHB][hapmap];0.94[JPT][hapmap];0.83[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1859445	0.88[CHB][hapmap];0.87[JPT][hapmap]
rs2012773	0.87[JPT][hapmap]
rs2054903	0.85[CEU][hapmap];0.94[CHB][hapmap];0.93[JPT][hapmap];0.93[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2054904	0.93[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2107638	0.87[JPT][hapmap]
rs2171642	0.82[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs2228500	0.83[CHB][hapmap];0.87[JPT][hapmap]
rs2269933	0.87[JPT][hapmap]
rs2269935	0.83[CHB][hapmap];0.87[JPT][hapmap]
rs2279464	1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2409005	0.85[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs2634675	0.89[CHB][hapmap];1.00[JPT][hapmap];0.82[ASN][1000 genomes]
rs2732439	0.94[CHB][hapmap];1.00[JPT][hapmap];0.82[ASN][1000 genomes]
rs2732465	0.94[CHB][hapmap];1.00[JPT][hapmap];0.82[ASN][1000 genomes]
rs2898065	0.83[AFR][1000 genomes];0.97[AMR][1000 genomes];0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2898066	0.84[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs3185921	0.86[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];0.89[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs3751273	0.86[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];0.90[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs4760619	0.87[CHB][hapmap];0.87[JPT][hapmap]
rs4760622	0.81[CEU][hapmap];0.83[CHB][hapmap];0.87[JPT][hapmap];0.83[ASN][1000 genomes]
rs4760625	0.83[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4760681	0.83[CHB][hapmap];0.86[JPT][hapmap]
rs4760687	0.87[JPT][hapmap]
rs4760695	0.81[CEU][hapmap];0.83[CHB][hapmap];0.87[JPT][hapmap];0.83[ASN][1000 genomes]
rs4760696	0.87[JPT][hapmap]
rs4760697	0.87[JPT][hapmap]
rs4760699	0.86[ASN][1000 genomes]
rs61940962	0.83[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs61941003	0.81[AMR][1000 genomes];0.91[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs61941006	0.97[AMR][1000 genomes];0.91[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6580659	0.85[JPT][hapmap]
rs7135779	0.86[JPT][hapmap]
rs716553	0.85[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs725454	0.87[JPT][hapmap]
rs7297298	0.83[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7302466	0.84[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs7303055	0.85[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs7486008	0.85[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs7486424	0.87[JPT][hapmap]
rs7975956	0.84[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs8804	0.83[CHB][hapmap];0.87[JPT][hapmap]
rs9788082	0.88[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:18 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv2758307	chr12:48429702-48825499	Weak transcription Enhancers Active TSS Strong transcription Flanking Active TSS Flanking Bivalent TSS/Enh Genic enhancers Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	57 gene(s)	inside rSNPs	diseases
2	esv2759898	chr12:48429702-48825499	Weak transcription Strong transcription ZNF genes & repeats Genic enhancers Enhancers Active TSS Flanking Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	57 gene(s)	inside rSNPs	diseases
3	nsv8971	chr12:48536526-48758501	Flanking Active TSS Enhancers Weak transcription Bivalent Enhancer Strong transcription Bivalent/Poised TSS Genic enhancers Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	39 gene(s)	inside rSNPs	diseases
4	esv34439	chr12:48541757-48779562	Bivalent/Poised TSS Flanking Active TSS Weak transcription Active TSS Enhancers Strong transcription Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	39 gene(s)	inside rSNPs	diseases
5	esv2757502	chr12:48547128-48779562	Genic enhancers Flanking Active TSS Enhancers Bivalent Enhancer Weak transcription Flanking Bivalent TSS/Enh Active TSS Bivalent/Poised TSS ZNF genes & repeats Strong transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	39 gene(s)	inside rSNPs	diseases
6	nsv899062	chr12:48658212-48711867	Enhancers Active TSS Flanking Active TSS Weak transcription ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region	4 gene(s)	inside rSNPs	diseases
7	nsv899063	chr12:48664989-48713768	Flanking Active TSS Enhancers Active TSS Flanking Bivalent TSS/Enh Weak transcription Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region	4 gene(s)	inside rSNPs	diseases
8	nsv899064	chr12:48664989-48721832	Bivalent Enhancer Active TSS Flanking Active TSS Enhancers Weak transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region	5 gene(s)	inside rSNPs	diseases
9	nsv899065	chr12:48667019-48711867	Enhancers Flanking Active TSS Active TSS Weak transcription Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region	4 gene(s)	inside rSNPs	diseases
10	nsv899066	chr12:48667019-48713768	Active TSS Enhancers Bivalent Enhancer Weak transcription Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region	4 gene(s)	inside rSNPs	diseases
11	nsv427911	chr12:48670336-48979396	Weak transcription Strong transcription Flanking Active TSS Flanking Bivalent TSS/Enh Active TSS Enhancers Bivalent Enhancer ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	35 gene(s)	inside rSNPs	diseases
12	esv34952	chr12:48672333-48703533	Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Enhancers Weak transcription Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region	4 gene(s)	inside rSNPs	diseases
13	nsv469369	chr12:48675783-48711867	Enhancers Bivalent/Poised TSS Bivalent Enhancer Flanking Active TSS Active TSS Weak transcription Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region	4 gene(s)	inside rSNPs	diseases
14	nsv469370	chr12:48675783-48711867	Bivalent Enhancer Weak transcription Enhancers Active TSS Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region	4 gene(s)	inside rSNPs	diseases
15	nsv469372	chr12:48675783-48711867	Enhancers Flanking Active TSS Active TSS Bivalent/Poised TSS Weak transcription Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region	4 gene(s)	inside rSNPs	diseases
16	nsv470290	chr12:48675783-48711867	Weak transcription Active TSS Bivalent Enhancer Flanking Active TSS Enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region	4 gene(s)	inside rSNPs	diseases
17	nsv558791	chr12:48675783-48711867	Flanking Bivalent TSS/Enh Active TSS Weak transcription Enhancers Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region	4 gene(s)	inside rSNPs	diseases
18	nsv832402	chr12:48686761-48851020	Enhancers Weak transcription Flanking Active TSS Active TSS Strong transcription Flanking Bivalent TSS/Enh 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	26 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs9634261	RP1-228P16.1	cis	Adipose Subcutaneous	GTEx
rs9634261	RP1-228P16.1	cis	Thyroid	GTEx
rs9634261	RP1-228P16.1	cis	lung	GTEx

Chromatin state (count:4 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:48686000-48687400	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
2	chr12:48686000-48690800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
3	chr12:48686600-48687200	Weak transcription	Primary neutrophils fromperipheralblood	blood
4	chr12:48686800-48690200	Weak transcription	ES-I3 Cell Line	embryonic stem cell

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