Variant report

Variant	rs1029453
Chromosome Location	chr4:110571210-110571211
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-CASP6-3	chr4:110570571-110571385	ucscGeneNc_uc003hzj_2

Extended variants
information (count: 29 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:26)

rs_ID	r²[population]
rs10017480	1.00[CEU][hapmap];0.94[EUR][1000 genomes]
rs10032195	1.00[CEU][hapmap];0.94[EUR][1000 genomes]
rs1029452	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10488884	1.00[CEU][hapmap];0.94[EUR][1000 genomes]
rs12331696	0.92[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs13101299	1.00[CEU][hapmap];1.00[YRI][hapmap];0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs13103963	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13133957	0.94[EUR][1000 genomes]
rs13144711	1.00[JPT][hapmap];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13145412	1.00[CEU][hapmap];0.92[EUR][1000 genomes]
rs28369312	0.88[EUR][1000 genomes]
rs28462209	0.94[EUR][1000 genomes]
rs3181345	0.89[CEU][hapmap]
rs34682042	0.92[EUR][1000 genomes]
rs5030543	1.00[JPT][hapmap]
rs5030545	1.00[JPT][hapmap]
rs56077978	0.82[AFR][1000 genomes];0.82[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs58110408	0.90[ASN][1000 genomes]
rs59467404	0.83[ASN][1000 genomes]
rs60422601	0.94[EUR][1000 genomes]
rs61236558	0.93[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs6830801	1.00[CEU][hapmap];0.94[EUR][1000 genomes]
rs6858600	0.89[CEU][hapmap];0.90[EUR][1000 genomes]
rs7669692	0.83[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs9993884	1.00[CEU][hapmap];0.94[EUR][1000 genomes]
rs9999288	1.00[CEU][hapmap];0.96[YRI][hapmap];0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv461613	chr4:109922064-110593460	Enhancers Flanking Active TSS Weak transcription Bivalent/Poised TSS Bivalent Enhancer Strong transcription Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	43 gene(s)	inside rSNPs	diseases
2	nsv595129	chr4:109922064-110593460	Strong transcription Weak transcription Active TSS Bivalent/Poised TSS Flanking Active TSS Enhancers Flanking Bivalent TSS/Enh Genic enhancers Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	43 gene(s)	inside rSNPs	diseases
3	esv3349784	chr4:110348873-110723163	Enhancers Flanking Active TSS Weak transcription ZNF genes & repeats Active TSS Strong transcription Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	35 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:28 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:110533000-110573000	Weak transcription	Monocytes-CD14+_RO01746	blood
2	chr4:110546600-110580600	Weak transcription	Thymus	Thymus
3	chr4:110565800-110576600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
4	chr4:110568400-110573600	Weak transcription	Sigmoid Colon	Sigmoid Colon
5	chr4:110569600-110572200	Weak transcription	Primary B cells from cord blood	blood
6	chr4:110569800-110571400	ZNF genes & repeats	Dnd41	blood
7	chr4:110569800-110573200	Enhancers	Primary T killer naive cells fromperipheralblood	blood
8	chr4:110569800-110573200	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
9	chr4:110570000-110571400	Strong transcription	Fetal Thymus	thymus
10	chr4:110570000-110571600	Flanking Active TSS	Primary T helper naive cells from peripheral blood	blood
11	chr4:110570000-110572600	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
12	chr4:110570400-110571400	Enhancers	Primary T cells fromperipheralblood	blood
13	chr4:110570400-110573200	Enhancers	Primary T helper cells fromperipheralblood	blood
14	chr4:110570400-110582000	Weak transcription	HSMM	muscle
15	chr4:110570600-110572200	Weak transcription	Primary B cells from peripheral blood	blood
16	chr4:110570600-110572400	Enhancers	Primary T cells effector/memory enriched fromperipheralblood	blood
17	chr4:110570600-110573000	Enhancers	Primary T regulatory cells fromperipheralblood	blood
18	chr4:110570800-110572200	Weak transcription	Primary hematopoietic stem cells	blood
19	chr4:110570800-110572400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
20	chr4:110570800-110573600	Enhancers	Primary T helper naive cells fromperipheralblood	blood
21	chr4:110571000-110571400	Flanking Active TSS	Primary T helper cells PMA-I stimulated	--
22	chr4:110571000-110605400	Weak transcription	Left Ventricle	heart
23	chr4:110571200-110571400	Enhancers	GM12878-XiMat	blood
24	chr4:110571200-110573400	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
25	chr4:110571200-110573400	Enhancers	Primary T killer memory cells from peripheral blood	blood
26	chr4:110571200-110573600	Enhancers	Primary T cells from cord blood	blood
27	chr4:110571200-110573600	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
28	chr4:110571200-110573800	Enhancers	Primary T helper memory cells from peripheral blood 2	blood

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