Variant report

Variant	rs12430600
Chromosome Location	chr13:52329758-52329759
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr13:52025304..52027492-chr13:52329692..52332817,3	MCF-7	breast:
2	chr13:52282244..52284170-chr13:52327994..52329848,2	K562	blood:
3	chr13:52025517..52028130-chr13:52327623..52331582,3	MCF-7	breast:

Variant related genes	Relation type
ENSG00000102786	Chromatin interaction
ENSG00000236778	Chromatin interaction

Extended variants
information (count: 42 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:33)

rs_ID	r²[population]
rs1058141	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[GIH][hapmap];0.96[LWK][hapmap];0.93[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];0.95[YRI][hapmap];0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs1058142	0.93[ASW][hapmap];0.96[LWK][hapmap];0.98[MKK][hapmap];0.95[YRI][hapmap];0.85[AFR][1000 genomes]
rs1060562	0.86[AFR][1000 genomes]
rs10676	0.92[GIH][hapmap];0.92[MKK][hapmap];1.00[TSI][hapmap];0.90[YRI][hapmap];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs12146894	0.86[ASW][hapmap];0.85[MKK][hapmap]
rs12427805	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[GIH][hapmap];0.96[LWK][hapmap];0.93[MEX][hapmap];0.94[MKK][hapmap];1.00[TSI][hapmap];0.94[YRI][hapmap];0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs12428478	1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[TSI][hapmap];0.90[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs12430760	0.85[CEU][hapmap];0.88[AMR][1000 genomes]
rs17069413	1.00[ASW][hapmap];0.85[CEU][hapmap];0.96[GIH][hapmap];0.96[LWK][hapmap];0.93[MEX][hapmap];0.96[MKK][hapmap];0.94[YRI][hapmap];0.89[AFR][1000 genomes];0.98[AMR][1000 genomes]
rs17075849	0.82[CEU][hapmap];0.89[YRI][hapmap];0.87[AFR][1000 genomes];0.98[AMR][1000 genomes]
rs17531181	0.96[GIH][hapmap];0.93[MEX][hapmap]
rs2011276	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2296027	1.00[CEU][hapmap];0.96[GIH][hapmap];0.89[LWK][hapmap];0.86[MEX][hapmap];0.88[MKK][hapmap];1.00[TSI][hapmap];0.90[YRI][hapmap];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs2408491	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[GIH][hapmap];0.96[LWK][hapmap];0.93[MEX][hapmap];0.96[MKK][hapmap];1.00[TSI][hapmap];0.94[YRI][hapmap];0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2897944	0.81[ASW][hapmap]
rs4399447	0.81[AMR][1000 genomes]
rs55910561	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs57280031	0.84[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs57837262	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs59291282	0.82[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73199739	0.90[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73199742	0.91[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73199750	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7321346	0.89[AFR][1000 genomes];0.98[AMR][1000 genomes]
rs7329391	0.93[ASW][hapmap];0.96[GIH][hapmap];0.90[LWK][hapmap];0.93[MEX][hapmap];0.84[MKK][hapmap];0.95[AMR][1000 genomes]
rs74086223	0.87[AFR][1000 genomes];0.98[AMR][1000 genomes]
rs7985214	0.88[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs8001480	0.85[CEU][hapmap];0.85[GIH][hapmap];0.93[MEX][hapmap];0.88[AMR][1000 genomes]
rs9526795	0.93[ASW][hapmap];0.96[LWK][hapmap];0.92[MKK][hapmap];0.95[YRI][hapmap];0.89[AFR][1000 genomes]
rs9535754	0.86[ASW][hapmap];0.90[LWK][hapmap];0.80[MKK][hapmap];0.81[YRI][hapmap];0.87[AFR][1000 genomes]
rs9568662	0.95[YRI][hapmap];0.95[AMR][1000 genomes]
rs9596572	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]
rs9596573	0.88[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

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs12430600	FLJ13639	cis	multi-tissue	Pritchard

Chromatin state (count:122 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr13:52305000-52338200	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
2	chr13:52306200-52339000	Weak transcription	Fetal Kidney	kidney
3	chr13:52308200-52342800	Weak transcription	Placenta Amnion	Placenta Amnion
4	chr13:52315600-52332200	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
5	chr13:52316200-52332200	Weak transcription	Rectal Smooth Muscle	rectum
6	chr13:52318400-52334200	Weak transcription	Fetal Brain Male	brain
7	chr13:52322000-52334400	Weak transcription	Colonic Mucosa	Colon
8	chr13:52322600-52330000	Weak transcription	Ovary	ovary
9	chr13:52322600-52330400	Weak transcription	Right Ventricle	heart
10	chr13:52322600-52332400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
11	chr13:52322600-52334400	Weak transcription	Skeletal Muscle Female	skeletal muscle
12	chr13:52322600-52337000	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
13	chr13:52322600-52338200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
14	chr13:52322600-52338200	Weak transcription	Stomach Mucosa	stomach
15	chr13:52322600-52342200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
16	chr13:52322600-52342200	Strong transcription	Primary monocytes fromperipheralblood	blood
17	chr13:52322800-52337600	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
18	chr13:52322800-52338200	Weak transcription	HUVEC	blood vessel
19	chr13:52323000-52330200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
20	chr13:52323000-52330400	Weak transcription	Fetal Intestine Small	intestine
21	chr13:52323000-52330600	Weak transcription	Rectal Mucosa Donor 31	rectum
22	chr13:52323000-52333600	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
23	chr13:52323000-52336400	Weak transcription	K562	blood
24	chr13:52323000-52336600	Strong transcription	Primary T helper cells fromperipheralblood	blood
25	chr13:52323000-52337200	Strong transcription	Primary B cells from cord blood	blood
26	chr13:52323000-52343400	Strong transcription	Monocytes-CD14+_RO01746	blood
27	chr13:52323200-52330400	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
28	chr13:52323200-52330400	Weak transcription	Colon Smooth Muscle	Colon
29	chr13:52323200-52332200	Weak transcription	A549	lung
30	chr13:52323200-52334600	Strong transcription	HSMM	muscle
31	chr13:52323200-52335000	Strong transcription	HUES64 Cell Line	embryonic stem cell
32	chr13:52323200-52335400	Strong transcription	HUES48 Cell Line	embryonic stem cell
33	chr13:52323200-52336800	Strong transcription	Primary hematopoietic stem cells	blood
34	chr13:52323200-52337600	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
35	chr13:52323200-52338200	Weak transcription	Pancreatic Islets	Pancreatic Islet
36	chr13:52323200-52341600	Weak transcription	iPS-15b Cell Line	embryonic stem cell
37	chr13:52323600-52330800	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
38	chr13:52323600-52332200	Weak transcription	Psoas Muscle	Psoas
39	chr13:52323800-52330600	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
40	chr13:52324200-52335400	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
41	chr13:52324400-52335800	Strong transcription	Muscle Satellite Cultured Cells	--
42	chr13:52324400-52337000	Strong transcription	HepG2	liver
43	chr13:52324400-52337200	Strong transcription	Primary hematopoietic stem cells short term culture	blood
44	chr13:52324600-52336600	Strong transcription	Primary B cells from peripheral blood	blood
45	chr13:52324600-52336800	Strong transcription	Primary T cells from cord blood	blood
46	chr13:52324600-52337400	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
47	chr13:52324800-52332800	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
48	chr13:52324800-52333600	Strong transcription	Fetal Muscle Leg	muscle
49	chr13:52324800-52333600	Strong transcription	Left Ventricle	heart
50	chr13:52324800-52335600	Strong transcription	Primary T cells fromperipheralblood	blood

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