Variant report

Variant	rs2042313
Chromosome Location	chr5:53212417-53212418
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	GATA3	chr5:53212337-53213530	SK-N-SH	brain:	n/a	chr5:53213199-53213206 chr5:53212503-53212519 chr5:53213199-53213206 chr5:53212506-53212515 chr5:53212959-53212975 chr5:53213192-53213213 chr5:53212962-53212971 chr5:53213197-53213206 chr5:53212964-53212971 chr5:53213199-53213206 chr5:53212506-53212516 chr5:53212961-53212973 chr5:53212508-53212515 chr5:53212501-53212522 chr5:53212962-53212972
2	GATA3	chr5:53212173-53213991	SK-N-SH	brain:	n/a	chr5:53213199-53213206 chr5:53212503-53212519 chr5:53213199-53213206 chr5:53212506-53212515 chr5:53212959-53212975 chr5:53213192-53213213 chr5:53212962-53212971 chr5:53213197-53213206 chr5:53212964-53212971 chr5:53213199-53213206 chr5:53212506-53212516 chr5:53212961-53212973 chr5:53212508-53212515 chr5:53212501-53212522 chr5:53212962-53212972
3	POLR2A	chr5:53212401-53212637	K562	blood:	n/a	n/a

Variant related genes	Relation type
RNU6-272P	TF binding region

Extended variants
information (count: 34 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:27)

rs_ID	r²[population]
rs1021390	0.88[ASN][1000 genomes]
rs1027210	1.00[ASW][hapmap];0.95[CHB][hapmap];0.95[CHD][hapmap];0.97[GIH][hapmap];0.90[JPT][hapmap];0.90[LWK][hapmap];0.83[YRI][hapmap];0.90[AFR][1000 genomes];0.89[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs12189288	0.86[ASN][1000 genomes]
rs175248	0.88[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs1979646	0.82[CHB][hapmap];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs1979647	0.84[GIH][hapmap];0.89[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs1981842	0.90[CHB][hapmap];0.94[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2035771	0.95[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs271207	0.94[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs271208	0.82[ASW][hapmap];0.91[GIH][hapmap];0.88[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs271243	0.85[GIH][hapmap];1.00[EUR][1000 genomes]
rs271245	0.85[GIH][hapmap];1.00[EUR][1000 genomes]
rs271250	1.00[EUR][1000 genomes]
rs271257	1.00[EUR][1000 genomes]
rs271261	1.00[EUR][1000 genomes]
rs37539	1.00[EUR][1000 genomes]
rs37540	1.00[EUR][1000 genomes]
rs3776740	1.00[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs3797287	0.98[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs3797290	0.95[CHB][hapmap];0.95[JPT][hapmap];0.94[YRI][hapmap];0.89[AFR][1000 genomes];0.89[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs3822502	0.95[CHB][hapmap];0.92[CHD][hapmap];1.00[JPT][hapmap];0.95[ASN][1000 genomes]
rs40211	0.85[GIH][hapmap];1.00[EUR][1000 genomes]
rs40212	1.00[EUR][1000 genomes]
rs4865559	0.95[CHB][hapmap];0.95[JPT][hapmap];0.93[ASN][1000 genomes]
rs6450173	0.94[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs6899160	0.84[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs7733347	1.00[ASW][hapmap];0.95[CHB][hapmap];0.92[CHD][hapmap];0.97[GIH][hapmap];0.89[JPT][hapmap];0.93[YRI][hapmap];0.89[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:7 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv2752745	chr5:52422063-53343529	Transcr. at gene 5' and 3' ZNF genes & repeats Weak transcription Enhancers Flanking Active TSS Bivalent Enhancer Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Genic enhancers Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	22 gene(s)	inside rSNPs	diseases
2	nsv1032632	chr5:52667145-53655624	Weak transcription Enhancers Flanking Active TSS Active TSS Strong transcription ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	29 gene(s)	inside rSNPs	diseases
3	nsv1032504	chr5:52908394-53398435	Weak transcription Enhancers Strong transcription ZNF genes & repeats Flanking Active TSS Active TSS Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	13 gene(s)	inside rSNPs	diseases
4	nsv537763	chr5:52908394-53398435	Weak transcription Genic enhancers Enhancers Strong transcription Flanking Active TSS ZNF genes & repeats Active TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	13 gene(s)	inside rSNPs	diseases
5	nsv533778	chr5:53092696-53284566	ZNF genes & repeats Enhancers Weak transcription Active TSS Flanking Active TSS Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	6 gene(s)	inside rSNPs	diseases
6	nsv880713	chr5:53198059-53906103	Flanking Active TSS Weak transcription Enhancers ZNF genes & repeats Active TSS Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Strong transcription Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	20 gene(s)	inside rSNPs	diseases
7	nsv830299	chr5:53207020-53386600	Weak transcription Enhancers Flanking Active TSS ZNF genes & repeats Strong transcription Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	6 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:11 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:53173800-53227800	Weak transcription	Breast Myoepithelial Primary Cells	Breast
2	chr5:53177000-53212800	Weak transcription	Fetal Intestine Small	intestine
3	chr5:53187600-53232800	Weak transcription	Primary T cells from cord blood	blood
4	chr5:53189800-53216600	Weak transcription	Left Ventricle	heart
5	chr5:53200800-53251600	Weak transcription	Primary B cells from cord blood	blood
6	chr5:53206800-53236600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
7	chr5:53208000-53213200	Weak transcription	Fetal Stomach	stomach
8	chr5:53208200-53215000	Weak transcription	Fetal Brain Female	brain
9	chr5:53210600-53213000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
10	chr5:53211800-53212800	Weak transcription	K562	blood
11	chr5:53212400-53213600	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin

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