Variant report

Variant	rs3901991
Chromosome Location	chr19:42128922-42128923
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr19:42122210..42124944-chr19:42127760..42129362,2	K562	blood:
2	chr19:42128745..42130555-chr19:42132891..42134764,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000105352	Chromatin interaction

Extended variants
information (count: 50 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:42)

rs_ID	r²[population]
rs1029804	0.85[CHB][hapmap]
rs10420203	0.94[ASN][1000 genomes]
rs11671442	0.96[ASN][1000 genomes]
rs12463151	0.86[ASN][1000 genomes]
rs12972738	0.91[ASN][1000 genomes]
rs12983687	0.93[ASN][1000 genomes]
rs12983719	0.93[ASN][1000 genomes]
rs12984811	0.93[ASN][1000 genomes]
rs17724333	0.91[AFR][1000 genomes];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2019253	0.85[AFR][1000 genomes];0.85[AMR][1000 genomes];0.99[ASN][1000 genomes]
rs2019254	0.85[AFR][1000 genomes];0.85[AMR][1000 genomes];0.99[ASN][1000 genomes]
rs2109245	1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2159442	1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2159443	0.99[ASN][1000 genomes]
rs2215324	0.93[ASN][1000 genomes]
rs2317315	0.95[CHB][hapmap];0.85[JPT][hapmap];0.81[YRI][hapmap];0.80[AFR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs28617711	0.85[AFR][1000 genomes];0.85[AMR][1000 genomes];0.99[ASN][1000 genomes]
rs3745931	0.85[AFR][1000 genomes];0.85[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs3745932	0.96[ASN][1000 genomes]
rs3745933	1.00[CHB][hapmap];0.94[JPT][hapmap];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs3848567	0.85[AFR][1000 genomes];0.85[AMR][1000 genomes];0.98[ASN][1000 genomes]
rs3890967	0.85[AFR][1000 genomes];0.85[AMR][1000 genomes];0.99[ASN][1000 genomes]
rs3890968	0.84[AFR][1000 genomes];0.85[AMR][1000 genomes];0.99[ASN][1000 genomes]
rs3909375	0.88[ASN][1000 genomes]
rs3909376	0.88[ASN][1000 genomes]
rs4405658	0.90[CHB][hapmap]
rs4803487	0.93[ASN][1000 genomes]
rs59581960	0.92[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs61491423	1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6508984	0.91[ASN][1000 genomes]
rs6508985	0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6508986	0.85[ASN][1000 genomes]
rs6508987	0.84[ASN][1000 genomes]
rs73035509	1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs73035517	0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs73043189	1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs73045005	1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs73931731	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs8104928	0.84[CHB][hapmap];0.89[JPT][hapmap];1.00[EUR][1000 genomes]
rs8111279	0.91[ASN][1000 genomes]
rs929501	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs929503	0.87[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:8 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1057624	chr19:42057334-42152828	Transcr. at gene 5' and 3' Weak transcription Enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers Strong transcription Flanking Active TSS Bivalent/Poised TSS ZNF genes & repeats Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases
2	nsv1058847	chr19:42057334-42172442	Bivalent/Poised TSS Genic enhancers Flanking Active TSS Enhancers Bivalent Enhancer Weak transcription ZNF genes & repeats Strong transcription Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases
3	nsv1063241	chr19:42057334-42175160	Bivalent Enhancer Flanking Active TSS Weak transcription Enhancers Genic enhancers Active TSS Strong transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases
4	nsv519408	chr19:42066279-42171906	Bivalent Enhancer Enhancers Weak transcription ZNF genes & repeats Genic enhancers Strong transcription Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases
5	esv3319146	chr19:42082639-42212929	Weak transcription Enhancers Flanking Active TSS Strong transcription Bivalent/Poised TSS Bivalent Enhancer 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	11 gene(s)	inside rSNPs	diseases
6	esv3319147	chr19:42082742-42212770	Enhancers ZNF genes & repeats Weak transcription Flanking Active TSS Bivalent Enhancer Active TSS Genic enhancers Bivalent/Poised TSS Strong transcription 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	esv3422975	chr19:42106166-42212774	Weak transcription Bivalent Enhancer Flanking Active TSS Enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Genic enhancers Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
8	nsv522854	chr19:42120283-42931004	Weak transcription Bivalent/Poised TSS Genic enhancers Bivalent Enhancer Flanking Active TSS Enhancers Flanking Bivalent TSS/Enh Active TSS Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	104 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:13 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr19:42118200-42131600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
2	chr19:42122000-42130600	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
3	chr19:42125200-42129200	Enhancers	Primary hematopoietic stem cells	blood
4	chr19:42127200-42129200	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
5	chr19:42127600-42130600	Flanking Active TSS	Primary neutrophils fromperipheralblood	blood
6	chr19:42127800-42130000	Active TSS	Primary B cells from cord blood	blood
7	chr19:42128400-42130200	Enhancers	Primary monocytes fromperipheralblood	blood
8	chr19:42128400-42131400	Weak transcription	Spleen	Spleen
9	chr19:42128400-42132600	Enhancers	Primary hematopoietic stem cells short term culture	blood
10	chr19:42128400-42132800	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
11	chr19:42128600-42129400	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
12	chr19:42128600-42129800	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
13	chr19:42128600-42130200	Enhancers	Primary T regulatory cells fromperipheralblood	blood

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