Variant report

Variant	rs2407794
Chromosome Location	chr13:50184262-50184263
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	chr13:50182731..50184724-chr13:50185681..50187681,2	K562	blood:
2	chr13:49874144..49875850-chr13:50184194..50186636,2	MCF-7	breast:

Extended variants
information (count: 126 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:111)

rs_ID	r²[population]
rs11616920	0.89[CEU][hapmap];0.83[JPT][hapmap];0.87[EUR][1000 genomes]
rs12017701	0.87[EUR][1000 genomes]
rs12428474	0.82[CEU][hapmap];0.83[JPT][hapmap];0.87[EUR][1000 genomes]
rs12583946	0.87[EUR][1000 genomes]
rs12585072	0.89[CEU][hapmap];0.83[JPT][hapmap];0.86[EUR][1000 genomes]
rs12585079	0.83[EUR][1000 genomes]
rs17069328	0.88[CEU][hapmap];0.81[JPT][hapmap];0.86[EUR][1000 genomes]
rs17073145	0.88[CEU][hapmap];0.81[JPT][hapmap];0.87[EUR][1000 genomes]
rs17073150	0.89[CEU][hapmap];0.83[JPT][hapmap];0.87[EUR][1000 genomes]
rs1830629	0.88[AFR][1000 genomes];0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2002407	0.84[EUR][1000 genomes]
rs2274279	0.87[EUR][1000 genomes]
rs2274280	0.87[EUR][1000 genomes]
rs2274281	0.89[CEU][hapmap];0.82[JPT][hapmap];0.86[EUR][1000 genomes]
rs2274282	0.89[CEU][hapmap];0.83[JPT][hapmap]
rs2274283	0.87[EUR][1000 genomes]
rs2407793	0.98[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2897768	0.98[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3751381	0.89[CEU][hapmap];0.82[JPT][hapmap];0.86[EUR][1000 genomes]
rs3751382	0.85[EUR][1000 genomes]
rs3751383	0.88[CEU][hapmap];0.81[JPT][hapmap];0.86[EUR][1000 genomes]
rs3764082	0.87[EUR][1000 genomes]
rs4344626	0.98[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4595700	0.98[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs56250426	0.87[EUR][1000 genomes]
rs56744999	0.88[AFR][1000 genomes];0.94[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs59416746	0.87[EUR][1000 genomes]
rs61961364	0.87[EUR][1000 genomes]
rs6561546	0.97[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6561547	0.98[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6561548	0.91[AFR][1000 genomes];0.96[AMR][1000 genomes];0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6561549	0.92[AFR][1000 genomes];0.96[AMR][1000 genomes];0.93[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs66897547	0.96[AFR][1000 genomes];0.90[AMR][1000 genomes];0.84[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs67275254	0.87[EUR][1000 genomes]
rs7140107	0.85[EUR][1000 genomes]
rs7320475	0.87[EUR][1000 genomes]
rs7325667	0.88[CEU][hapmap];0.81[JPT][hapmap];0.87[EUR][1000 genomes]
rs7327293	0.94[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7328126	0.87[EUR][1000 genomes]
rs7328536	0.88[CEU][hapmap];0.82[JPT][hapmap];0.87[EUR][1000 genomes]
rs7328860	0.88[CEU][hapmap];0.81[JPT][hapmap];0.87[EUR][1000 genomes]
rs7331252	0.98[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7332484	0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7332771	0.98[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7332926	0.94[CEU][hapmap]
rs7334012	0.94[CEU][hapmap]
rs7336758	0.87[EUR][1000 genomes]
rs7337705	0.86[EUR][1000 genomes]
rs7338090	0.89[CEU][hapmap];0.83[JPT][hapmap];0.87[EUR][1000 genomes]
rs7339079	0.83[EUR][1000 genomes]
rs7981952	0.87[EUR][1000 genomes]
rs7983030	0.89[CEU][hapmap];0.88[JPT][hapmap];0.87[EUR][1000 genomes]
rs7983672	0.82[EUR][1000 genomes]
rs7986417	0.89[CEU][hapmap];0.83[JPT][hapmap];0.87[EUR][1000 genomes]
rs7987338	0.87[EUR][1000 genomes]
rs7987806	0.89[CEU][hapmap];0.83[JPT][hapmap];0.87[EUR][1000 genomes]
rs7987956	0.87[EUR][1000 genomes]
rs7988350	0.86[EUR][1000 genomes]
rs7988844	0.86[EUR][1000 genomes]
rs7989915	0.88[CEU][hapmap];0.82[JPT][hapmap];0.87[EUR][1000 genomes]
rs7990896	0.84[EUR][1000 genomes]
rs8001878	0.87[EUR][1000 genomes]
rs9562893	0.83[EUR][1000 genomes]
rs9562894	0.85[EUR][1000 genomes]
rs9562897	0.87[EUR][1000 genomes]
rs9562898	0.87[EUR][1000 genomes]
rs9562899	0.88[CEU][hapmap];0.81[JPT][hapmap];0.87[EUR][1000 genomes]
rs9562900	0.88[CEU][hapmap];0.81[JPT][hapmap];0.87[EUR][1000 genomes]
rs9568243	0.87[EUR][1000 genomes]
rs9568246	0.88[CEU][hapmap];0.81[JPT][hapmap];0.86[EUR][1000 genomes]
rs9568247	0.88[CEU][hapmap];0.81[JPT][hapmap];0.87[EUR][1000 genomes]
rs9568248	0.87[EUR][1000 genomes]
rs9568249	0.87[EUR][1000 genomes]
rs9568250	0.84[EUR][1000 genomes]
rs9568251	0.89[CEU][hapmap];0.83[JPT][hapmap];0.87[EUR][1000 genomes]
rs9568252	0.89[CEU][hapmap];0.83[JPT][hapmap];0.87[EUR][1000 genomes]
rs9568253	0.88[CEU][hapmap];0.82[JPT][hapmap];0.87[EUR][1000 genomes]
rs9568254	0.82[JPT][hapmap];0.86[EUR][1000 genomes]
rs9568255	0.87[EUR][1000 genomes]
rs9568256	0.89[CEU][hapmap];0.83[JPT][hapmap];0.87[EUR][1000 genomes]
rs9568257	0.88[CEU][hapmap];0.81[JPT][hapmap];0.87[EUR][1000 genomes]
rs9568258	0.88[CEU][hapmap];0.81[JPT][hapmap];0.87[EUR][1000 genomes]
rs9568259	0.87[EUR][1000 genomes]
rs9568260	0.87[EUR][1000 genomes]
rs9568265	0.87[EUR][1000 genomes]
rs9568266	0.85[EUR][1000 genomes]
rs9568270	0.84[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9568272	0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9568274	0.88[JPT][hapmap]
rs9568275	0.94[AFR][1000 genomes];0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9568276	0.94[AFR][1000 genomes];0.90[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9568277	0.94[AFR][1000 genomes];0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9568279	0.98[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9568280	0.98[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9568282	0.98[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9568283	0.98[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9568288	0.92[EUR][1000 genomes]
rs9568289	0.90[EUR][1000 genomes]
rs9596139	0.87[EUR][1000 genomes]
rs9596140	0.87[EUR][1000 genomes]
rs9596141	0.87[EUR][1000 genomes]
rs9596142	0.89[CEU][hapmap];0.83[JPT][hapmap];0.87[EUR][1000 genomes]
rs9596143	0.87[EUR][1000 genomes]
rs9596144	0.87[EUR][1000 genomes]
rs9596145	0.87[EUR][1000 genomes]
rs9596148	0.88[CEU][hapmap];0.81[JPT][hapmap];0.87[EUR][1000 genomes]
rs9596150	0.89[CEU][hapmap];0.83[JPT][hapmap];0.87[EUR][1000 genomes]
rs9596151	0.89[CEU][hapmap];0.82[JPT][hapmap];0.87[EUR][1000 genomes]
rs9596152	0.87[EUR][1000 genomes]
rs9596159	0.98[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9596160	0.98[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:15 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1047311	chr13:49895019-50224227	Enhancers Flanking Active TSS Weak transcription ZNF genes & repeats Strong transcription Active TSS Flanking Bivalent TSS/Enh Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	27 gene(s)	inside rSNPs	diseases
2	nsv916093	chr13:50050919-50290245	Strong transcription Enhancers Weak transcription ZNF genes & repeats Active TSS Flanking Active TSS Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	29 gene(s)	inside rSNPs	diseases
3	nsv1054965	chr13:50102730-50251347	Enhancers Weak transcription Strong transcription Flanking Active TSS Active TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	23 gene(s)	inside rSNPs	diseases
4	nsv541771	chr13:50102730-50251347	Enhancers Active TSS Genic enhancers Strong transcription Weak transcription Flanking Active TSS Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	23 gene(s)	inside rSNPs	diseases
5	esv2763020	chr13:50105055-50192259	Weak transcription Flanking Active TSS Enhancers Genic enhancers Strong transcription Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	10 gene(s)	inside rSNPs	diseases
6	nsv900071	chr13:50107289-50286218	Weak transcription Strong transcription Enhancers Active TSS Transcr. at gene 5' and 3' Genic enhancers Flanking Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	29 gene(s)	inside rSNPs	diseases
7	nsv561616	chr13:50120435-50190246	Weak transcription Enhancers Strong transcription Flanking Active TSS Genic enhancers Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region	9 gene(s)	inside rSNPs	diseases
8	nsv949162	chr13:50120985-50195882	Flanking Active TSS Active TSS Weak transcription Enhancers Strong transcription Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
9	nsv1046912	chr13:50122840-50189313	Bivalent Enhancer Strong transcription Flanking Active TSS Weak transcription Enhancers Active TSS ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region	8 gene(s)	inside rSNPs	diseases
10	nsv1043902	chr13:50122840-50189999	Strong transcription Flanking Active TSS Weak transcription Active TSS Enhancers Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region	9 gene(s)	inside rSNPs	diseases
11	esv2761789	chr13:50122852-50185910	Strong transcription Enhancers Flanking Active TSS Weak transcription Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region	8 gene(s)	inside rSNPs	diseases
12	nsv455883	chr13:50124621-50185204	Flanking Active TSS Weak transcription Strong transcription Genic enhancers Enhancers Active TSS ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region	8 gene(s)	inside rSNPs	diseases
13	nsv561617	chr13:50124621-50185204	Genic enhancers Enhancers Weak transcription Flanking Active TSS Strong transcription Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region	8 gene(s)	inside rSNPs	diseases
14	nsv1043697	chr13:50129199-50249241	Weak transcription Strong transcription Active TSS Enhancers Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	22 gene(s)	inside rSNPs	diseases
15	esv2752657	chr13:50144995-50244150	Active TSS Enhancers Flanking Active TSS Weak transcription Strong transcription Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	20 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs2407794	RCBTB1	cis	Whole Blood	GTEx
rs2407794	KPNA3	Cis_1M	lymphoblastoid	RTeQTL

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr13:50181000-50185800	Enhancers	Fetal Heart	heart
2	chr13:50181200-50192000	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
3	chr13:50181400-50185400	Weak transcription	HepG2	liver
4	chr13:50181400-50194400	Weak transcription	Right Ventricle	heart
5	chr13:50183800-50190200	Weak transcription	Primary hematopoietic stem cells short term culture	blood
6	chr13:50184200-50185600	Enhancers	Fetal Muscle Leg	muscle

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