Variant report

Variant	rs10519333
Chromosome Location	chr5:112200011-112200012
allele	A/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	POLR2A	chr5:112199585-112201114	K562	blood:	n/a	n/a
2	POLR2A	chr5:112199905-112200052	HepG2	liver:	n/a	n/a
3	POLR2A	chr5:112199920-112200235	MCF10A-Er-Src	breast:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr5:112194408..112196977-chr5:112198175..112200544,3	MCF-7	breast:
2	chr5:112195906..112198557-chr5:112198644..112200582,4	MCF-7	breast:
3	chr5:112195239..112200315-chr5:112255126..112261929,8	MCF-7	breast:
4	chr5:112195408..112199487-chr5:112199566..112202603,4	K562	blood:

Variant related genes	Relation type
SRP19	TF binding region
ENSG00000272869	Chromatin interaction
ENSG00000153037	Chromatin interaction
ENSG00000129625	Chromatin interaction

Extended variants
information (count: 43 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:35)

rs_ID	r²[population]
rs10058561	0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10515449	0.90[JPT][hapmap]
rs11555908	1.00[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs13360640	1.00[EUR][1000 genomes]
rs17135066	1.00[AFR][1000 genomes];1.00[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs17135070	0.90[CHB][hapmap];1.00[JPT][hapmap];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs17135100	0.90[CHB][hapmap];1.00[JPT][hapmap];1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs17135108	0.81[CHB][hapmap];1.00[JPT][hapmap];1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs17135117	0.92[JPT][hapmap];0.91[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs17135149	0.90[CHB][hapmap];1.00[JPT][hapmap];0.82[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs17135155	0.90[CHB][hapmap];1.00[JPT][hapmap];0.82[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs17135193	0.81[CHB][hapmap]
rs2900065	1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs3733963	0.90[CHB][hapmap];1.00[JPT][hapmap];1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs3822652	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs3822654	0.90[CHB][hapmap];1.00[JPT][hapmap];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs3892986	1.00[EUR][1000 genomes]
rs57726881	0.91[AFR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs57749964	1.00[EUR][1000 genomes]
rs58625991	1.00[EUR][1000 genomes]
rs58865195	0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs59349522	1.00[EUR][1000 genomes]
rs6594652	0.91[CHB][hapmap];1.00[JPT][hapmap];0.82[AMR][1000 genomes];1.00[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs6864403	0.91[CHB][hapmap];1.00[JPT][hapmap];0.82[AMR][1000 genomes];1.00[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs6864647	0.81[CHB][hapmap]
rs728344	1.00[EUR][1000 genomes]
rs73227382	1.00[EUR][1000 genomes]
rs73227383	1.00[EUR][1000 genomes]
rs7701868	0.85[ASN][1000 genomes]
rs7728109	0.82[CHB][hapmap];1.00[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs7728481	0.88[CHB][hapmap];1.00[JPT][hapmap];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7728766	0.97[ASN][1000 genomes]
rs7730241	1.00[EUR][1000 genomes]
rs7735121	0.91[CHB][hapmap];1.00[JPT][hapmap];0.82[AMR][1000 genomes];1.00[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs9687790	0.82[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[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	esv33290	chr5:112110808-112238295	Weak transcription Strong transcription Flanking Active TSS Enhancers Genic enhancers Transcr. at gene 5' and 3' Active TSS ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	19 gene(s)	inside rSNPs	diseases
2	nsv1029271	chr5:112113308-112325943	Strong transcription Bivalent Enhancer Weak transcription Enhancers Flanking Active TSS Genic enhancers Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	30 gene(s)	inside rSNPs	diseases
3	nsv529536	chr5:112174106-112269758	Genic enhancers Strong transcription Weak transcription Flanking Active TSS Enhancers Flanking Bivalent TSS/Enh Active TSS Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	19 gene(s)	inside rSNPs	diseases
4	nsv599394	chr5:112185491-112446323	Weak transcription Active TSS Strong transcription Genic enhancers Enhancers Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	31 gene(s)	inside rSNPs	diseases
5	nsv870231	chr5:112192379-112247084	Strong transcription Weak transcription Genic enhancers Flanking Active TSS Enhancers Transcr. at gene 5' and 3' Active TSS Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	14 gene(s)	inside rSNPs	diseases
6	nsv1029595	chr5:112197662-112242375	Strong transcription Weak transcription Flanking Active TSS Active TSS Transcr. at gene 5' and 3' Genic enhancers Enhancers Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	10 gene(s)	inside rSNPs	diseases
7	nsv1030103	chr5:112197662-112255712	Weak transcription Genic enhancers Enhancers Strong transcription Flanking Active TSS Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	10 gene(s)	inside rSNPs	diseases
8	nsv537863	chr5:112197662-112255712	Weak transcription Strong transcription Genic enhancers Active TSS Enhancers Flanking Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	10 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:126 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:112197800-112211800	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
2	chr5:112198000-112205000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
3	chr5:112198200-112200200	Transcr. at gene 5' and 3'	GM12878-XiMat	blood
4	chr5:112198200-112202200	Weak transcription	Fetal Kidney	kidney
5	chr5:112198400-112200200	Genic enhancers	Primary T helper memory cells from peripheral blood 2	blood
6	chr5:112198400-112200200	Genic enhancers	Primary T helper 17 cells PMA-I stimulated	--
7	chr5:112198400-112200400	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
8	chr5:112198400-112200800	Weak transcription	Primary hematopoietic stem cells	blood
9	chr5:112198400-112211200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
10	chr5:112198400-112220600	Weak transcription	Placenta Amnion	Placenta Amnion
11	chr5:112198600-112200600	Genic enhancers	Primary T helper cells PMA-I stimulated	--
12	chr5:112198600-112201000	Genic enhancers	Osteobl	bone
13	chr5:112198600-112201200	Strong transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
14	chr5:112198600-112205600	Weak transcription	Fetal Brain Male	brain
15	chr5:112198600-112206600	Strong transcription	iPS-18 Cell Line	embryonic stem cell
16	chr5:112198600-112206800	Strong transcription	H9 Cell Line	embryonic stem cell
17	chr5:112198600-112206800	Strong transcription	HUES48 Cell Line	embryonic stem cell
18	chr5:112198600-112206800	Strong transcription	Rectal Mucosa Donor 29	rectum
19	chr5:112198600-112207000	Strong transcription	H1 Cell Line	embryonic stem cell
20	chr5:112198600-112207000	Strong transcription	HUES6 Cell Line	embryonic stem cell
21	chr5:112198600-112207400	Strong transcription	Rectal Mucosa Donor 31	rectum
22	chr5:112198600-112208800	Strong transcription	Fetal Thymus	thymus
23	chr5:112198800-112206800	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
24	chr5:112198800-112206800	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
25	chr5:112198800-112207200	Strong transcription	Fetal Muscle Trunk	muscle
26	chr5:112198800-112208800	Strong transcription	iPS-20b Cell Line	embryonic stem cell
27	chr5:112199000-112200200	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
28	chr5:112199000-112200600	Strong transcription	Thymus	Thymus
29	chr5:112199000-112200800	Strong transcription	Ovary	ovary
30	chr5:112199000-112201200	Strong transcription	ES-I3 Cell Line	embryonic stem cell
31	chr5:112199000-112201200	Strong transcription	Rectal Smooth Muscle	rectum
32	chr5:112199000-112206800	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
33	chr5:112199000-112207000	Strong transcription	Placenta	Placenta
34	chr5:112199000-112207200	Strong transcription	HUES64 Cell Line	embryonic stem cell
35	chr5:112199000-112208000	Strong transcription	Primary B cells from peripheral blood	blood
36	chr5:112199000-112226000	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
37	chr5:112199200-112201000	Strong transcription	NHDF-Ad	bronchial
38	chr5:112199200-112203400	Weak transcription	Stomach Mucosa	stomach
39	chr5:112199200-112206200	Strong transcription	Primary monocytes fromperipheralblood	blood
40	chr5:112199200-112206400	Strong transcription	Monocytes-CD14+_RO01746	blood
41	chr5:112199200-112207200	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
42	chr5:112199200-112210200	Weak transcription	Psoas Muscle	Psoas
43	chr5:112199200-112213200	Weak transcription	Fetal Heart	heart
44	chr5:112199200-112213400	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
45	chr5:112199400-112200200	Enhancers	Brain Angular Gyrus	brain
46	chr5:112199400-112200200	Weak transcription	Colon Smooth Muscle	Colon
47	chr5:112199400-112200400	Weak transcription	Skeletal Muscle Female	skeletal muscle
48	chr5:112199400-112200600	Strong transcription	Sigmoid Colon	Sigmoid Colon
49	chr5:112199400-112200600	Strong transcription	HMEC	breast
50	chr5:112199400-112200600	Strong transcription	K562	blood

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