Variant report

Variant	rs9596572
Chromosome Location	chr13:52343551-52343552
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr13:52306205..52308495-chr13:52341263..52344229,2	MCF-7	breast:
2	chr13:52024516..52028939-chr13:52342727..52345568,4	MCF-7	breast:
3	chr13:52337340..52339624-chr13:52341106..52343794,2	K562	blood:
4	chr13:52337387..52338953-chr13:52340888..52343879,2	MCF-7	breast:
5	chr13:52024690..52027265-chr13:52341888..52344446,2	K562	blood:

Variant related genes	Relation type
ENSG00000224892	Chromatin interaction
ENSG00000236778	Chromatin interaction
ENSG00000102786	Chromatin interaction

Extended variants
information (count: 38 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:29)

rs_ID	r²[population]
rs1058141	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.96[GIH][hapmap];1.00[JPT][hapmap];0.89[LWK][hapmap];1.00[MEX][hapmap];0.94[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.85[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1058142	0.89[LWK][hapmap];0.92[MKK][hapmap];1.00[YRI][hapmap]
rs10676	1.00[ASW][hapmap];0.96[GIH][hapmap];0.93[LWK][hapmap];0.82[MEX][hapmap];0.98[MKK][hapmap];1.00[TSI][hapmap];0.95[YRI][hapmap];0.96[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs12427805	1.00[CEU][hapmap];0.96[GIH][hapmap];0.89[LWK][hapmap];1.00[MEX][hapmap];0.87[MKK][hapmap];1.00[TSI][hapmap];0.89[YRI][hapmap];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs12428478	1.00[CEU][hapmap];0.96[GIH][hapmap];1.00[TSI][hapmap];0.88[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs12430600	1.00[CEU][hapmap];0.96[GIH][hapmap];0.86[LWK][hapmap];0.93[MEX][hapmap];0.94[MKK][hapmap];1.00[TSI][hapmap];0.95[YRI][hapmap];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs12430760	0.85[CEU][hapmap];0.86[AMR][1000 genomes]
rs17069413	0.85[CEU][hapmap];0.93[GIH][hapmap];0.89[LWK][hapmap];1.00[MEX][hapmap];0.89[MKK][hapmap];0.89[YRI][hapmap];0.96[AMR][1000 genomes]
rs17075849	0.82[CEU][hapmap];0.84[YRI][hapmap];0.96[AMR][1000 genomes]
rs17531181	0.93[GIH][hapmap];1.00[MEX][hapmap]
rs2011276	0.80[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2296027	0.91[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];0.96[LWK][hapmap];0.93[MEX][hapmap];0.94[MKK][hapmap];1.00[TSI][hapmap];0.95[YRI][hapmap];0.94[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2408491	1.00[CEU][hapmap];0.96[GIH][hapmap];0.89[LWK][hapmap];1.00[MEX][hapmap];0.89[MKK][hapmap];1.00[TSI][hapmap];0.89[YRI][hapmap];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs55910561	0.82[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs57280031	0.85[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs57837262	0.80[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs59291282	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73199739	0.88[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73199742	0.89[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73199750	0.98[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7321346	0.96[AMR][1000 genomes]
rs7329391	0.93[GIH][hapmap];0.83[LWK][hapmap];1.00[MEX][hapmap];0.93[AMR][1000 genomes]
rs74086223	0.96[AMR][1000 genomes]
rs7985214	0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs8001480	0.85[CEU][hapmap];0.81[GIH][hapmap];1.00[MEX][hapmap];0.86[AMR][1000 genomes]
rs9526795	0.89[LWK][hapmap];0.86[MKK][hapmap];1.00[YRI][hapmap]
rs9535754	0.83[LWK][hapmap];0.85[YRI][hapmap]
rs9568662	1.00[YRI][hapmap];0.90[AFR][1000 genomes];0.97[AMR][1000 genomes]
rs9596573	0.90[AMR][1000 genomes];1.00[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:9 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv832612	chr13:52176983-52362525	Weak transcription Enhancers Genic enhancers Strong transcription Flanking Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Active TSS Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
2	nsv530718	chr13:52291802-52832752	Enhancers ZNF genes & repeats Weak transcription Active TSS Bivalent Enhancer Flanking Active TSS Strong transcription Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	38 gene(s)	inside rSNPs	diseases
3	nsv933424	chr13:52293482-52507732	Enhancers Flanking Active TSS Active TSS Weak transcription Strong transcription Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	27 gene(s)	inside rSNPs	diseases
4	nsv455884	chr13:52302630-52405251	Enhancers Flanking Active TSS Strong transcription Genic enhancers Weak transcription Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	20 gene(s)	inside rSNPs	diseases
5	nsv561644	chr13:52302630-52405251	Enhancers Strong transcription Weak transcription Active TSS Flanking Active TSS Bivalent Enhancer Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	20 gene(s)	inside rSNPs	diseases
6	nsv455887	chr13:52318522-52405251	Enhancers Flanking Active TSS ZNF genes & repeats Weak transcription Strong transcription Active TSS Transcr. at gene 5' and 3' Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	20 gene(s)	inside rSNPs	diseases
7	nsv561645	chr13:52318522-52405251	Enhancers Weak transcription Strong transcription ZNF genes & repeats Flanking Active TSS Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	20 gene(s)	inside rSNPs	diseases
8	nsv1044310	chr13:52321564-52643924	Weak transcription Flanking Active TSS ZNF genes & repeats Enhancers Strong transcription Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	33 gene(s)	inside rSNPs	diseases
9	nsv1050117	chr13:52325116-52643924	Enhancers Genic enhancers Flanking Active TSS Strong transcription Active TSS Weak transcription ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	33 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:106 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr13:52330600-52355600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
2	chr13:52333000-52343600	Weak transcription	Psoas Muscle	Psoas
3	chr13:52334400-52343800	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
4	chr13:52335200-52347000	Weak transcription	Fetal Brain Male	brain
5	chr13:52335200-52348000	Weak transcription	Fetal Brain Female	brain
6	chr13:52339400-52343800	Strong transcription	Primary neutrophils fromperipheralblood	blood
7	chr13:52339400-52343800	Weak transcription	Brain Anterior Caudate	brain
8	chr13:52339400-52343800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
9	chr13:52339400-52345000	Weak transcription	Primary B cells from peripheral blood	blood
10	chr13:52339400-52347000	Weak transcription	A549	lung
11	chr13:52339400-52347600	Weak transcription	Aorta	Aorta
12	chr13:52339400-52347600	Weak transcription	Sigmoid Colon	Sigmoid Colon
13	chr13:52339400-52347800	Weak transcription	Rectal Smooth Muscle	rectum
14	chr13:52339400-52349600	Weak transcription	Placenta	Placenta
15	chr13:52339400-52352000	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
16	chr13:52339400-52356200	Weak transcription	Rectal Mucosa Donor 31	rectum
17	chr13:52339400-52357400	Weak transcription	Colonic Mucosa	Colon
18	chr13:52339600-52343600	Weak transcription	Stomach Mucosa	stomach
19	chr13:52339600-52344000	Weak transcription	Brain Cingulate Gyrus	brain
20	chr13:52339600-52344400	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
21	chr13:52339600-52356800	Weak transcription	Rectal Mucosa Donor 29	rectum
22	chr13:52339600-52361400	Weak transcription	Primary T helper naive cells from peripheral blood	blood
23	chr13:52339600-52375000	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
24	chr13:52339800-52343600	Strong transcription	Foreskin Fibroblast Primary Cells skin01	Skin
25	chr13:52339800-52345600	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
26	chr13:52339800-52345600	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
27	chr13:52339800-52346200	Strong transcription	Primary T cells from cord blood	blood
28	chr13:52339800-52359800	Weak transcription	Colon Smooth Muscle	Colon
29	chr13:52339800-52371400	Weak transcription	Primary T killer memory cells from peripheral blood	blood
30	chr13:52339800-52375200	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
31	chr13:52340000-52343600	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
32	chr13:52340400-52344000	Strong transcription	Primary T cells fromperipheralblood	blood
33	chr13:52340400-52346400	Strong transcription	Thymus	Thymus
34	chr13:52340400-52348200	Strong transcription	Fetal Stomach	stomach
35	chr13:52340600-52343600	Strong transcription	Fetal Intestine Small	intestine
36	chr13:52340800-52343800	Weak transcription	HMEC	breast
37	chr13:52340800-52352200	Weak transcription	Primary hematopoietic stem cells	blood
38	chr13:52341000-52344200	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
39	chr13:52341200-52343600	Weak transcription	HSMMtube	muscle
40	chr13:52341200-52344000	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
41	chr13:52341200-52347800	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
42	chr13:52341400-52343600	Weak transcription	Brain Hippocampus Middle	brain
43	chr13:52341400-52343600	Weak transcription	Brain Inferior Temporal Lobe	brain
44	chr13:52341400-52343800	Weak transcription	Brain Angular Gyrus	brain
45	chr13:52341400-52354600	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
46	chr13:52341400-52361200	Weak transcription	Primary T helper cells PMA-I stimulated	--
47	chr13:52341600-52343800	Weak transcription	HepG2	liver
48	chr13:52341600-52344000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
49	chr13:52341600-52345000	Weak transcription	NHLF	lung
50	chr13:52341600-52352000	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived

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