Variant report

Variant	rs2173525
Chromosome Location	chr5:52070084-52070085
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr5:52069827..52072246-chr5:52094290..52096328,2	MCF-7	breast:

Extended variants
information (count: 33 )
Associated
traits (count: 0)

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

rs_ID	r²[population]
rs1363958	1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1363959	0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1363960	0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1363961	1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs16880238	1.00[CHB][hapmap];0.85[ASN][1000 genomes]
rs16880266	1.00[CHB][hapmap];0.87[JPT][hapmap];0.88[ASN][1000 genomes]
rs17209816	1.00[CEU][hapmap]
rs1833883	0.93[ASN][1000 genomes]
rs1833884	0.91[ASN][1000 genomes]
rs193438	0.89[ASN][1000 genomes]
rs2133476	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2245991	1.00[CEU][hapmap];1.00[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];0.96[ASN][1000 genomes]
rs2245997	1.00[CEU][hapmap];1.00[CHB][hapmap];0.87[JPT][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs244485	0.89[ASN][1000 genomes]
rs244488	0.84[ASN][1000 genomes]
rs2548503	0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2548504	0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2548505	0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2548506	1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2548507	1.00[CEU][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2648732	0.90[ASN][1000 genomes]
rs2648733	1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2648734	1.00[CEU][hapmap];0.93[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];0.95[ASN][1000 genomes]
rs2648735	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];0.83[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2648737	1.00[CEU][hapmap];0.81[EUR][1000 genomes]
rs3096173	0.88[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	esv2754787	chr5:51688543-52193243	Enhancers Active TSS Genic enhancers Weak transcription Flanking Active TSS Strong transcription Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	28 gene(s)	inside rSNPs	diseases
2	nsv462187	chr5:51758804-52333420	Enhancers Weak transcription Strong transcription Flanking Active TSS Bivalent/Poised TSS Active TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	43 gene(s)	inside rSNPs	diseases
3	nsv598163	chr5:51758804-52333420	Strong transcription Weak transcription Enhancers Active TSS Genic enhancers Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	43 gene(s)	inside rSNPs	diseases
4	nsv471013	chr5:51779197-52339114	Weak transcription Enhancers Flanking Active TSS Active TSS Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer Strong transcription Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	43 gene(s)	inside rSNPs	diseases
5	nsv1027410	chr5:52022713-52103360	Flanking Active TSS Flanking Bivalent TSS/Enh Enhancers Weak transcription Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS Strong transcription Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	18 gene(s)	inside rSNPs	diseases
6	nsv1024123	chr5:52052104-52089545	Enhancers Flanking Active TSS Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh Weak transcription Bivalent/Poised TSS Strong transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
7	nsv1020640	chr5:52058830-52120858	Enhancers Active TSS Weak transcription Flanking Active TSS Bivalent/Poised TSS Strong transcription Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	18 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:33 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:52066000-52070400	Enhancers	Dnd41	blood
2	chr5:52066800-52072600	Enhancers	Primary T helper cells fromperipheralblood	blood
3	chr5:52067000-52070400	Enhancers	Primary T killer memory cells from peripheral blood	blood
4	chr5:52067000-52070800	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
5	chr5:52067000-52070800	Enhancers	Primary T helper naive cells from peripheral blood	blood
6	chr5:52067000-52073200	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
7	chr5:52068000-52073200	Enhancers	Primary T helper cells PMA-I stimulated	--
8	chr5:52068400-52071200	Weak transcription	GM12878-XiMat	blood
9	chr5:52068400-52074000	Enhancers	Primary T cells from cord blood	blood
10	chr5:52068600-52070400	Enhancers	Liver	Liver
11	chr5:52068600-52070600	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
12	chr5:52068600-52070800	Enhancers	Fetal Adrenal Gland	Adrenal Gland
13	chr5:52069200-52070200	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
14	chr5:52069400-52070400	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
15	chr5:52069400-52070400	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
16	chr5:52069400-52070800	Enhancers	Primary T helper naive cells fromperipheralblood	blood
17	chr5:52069600-52070200	Enhancers	Adipose Nuclei	Adipose
18	chr5:52069600-52070200	Enhancers	Right Atrium	heart
19	chr5:52069600-52070400	Enhancers	HUES64 Cell Line	embryonic stem cell
20	chr5:52069800-52070200	Enhancers	iPS-15b Cell Line	embryonic stem cell
21	chr5:52069800-52070200	Enhancers	iPS DF 6.9 Cell Line	embryonic stem cell
22	chr5:52069800-52070200	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
23	chr5:52069800-52070200	Enhancers	Small Intestine	intestine
24	chr5:52069800-52070400	Enhancers	ES-WA7 Cell Line	embryonic stem cell
25	chr5:52069800-52070400	Enhancers	HUES48 Cell Line	embryonic stem cell
26	chr5:52069800-52070400	Enhancers	HUES6 Cell Line	embryonic stem cell
27	chr5:52069800-52070400	Enhancers	Primary T cells effector/memory enriched fromperipheralblood	blood
28	chr5:52069800-52070600	Enhancers	Primary T cells fromperipheralblood	blood
29	chr5:52069800-52070800	Enhancers	Fetal Thymus	thymus
30	chr5:52070000-52070200	Enhancers	HepG2	liver
31	chr5:52070000-52070400	Flanking Active TSS	iPS-18 Cell Line	embryonic stem cell
32	chr5:52070000-52070400	Enhancers	iPS-20b Cell Line	embryonic stem cell
33	chr5:52070000-52070600	Enhancers	Primary T killer naive cells fromperipheralblood	blood

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