Variant report

Variant	rs4760355
Chromosome Location	chr12:57725197-57725198
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr12:57724680..57727062-chr12:57736580..57739037,2	MCF-7	breast:
2	chr12:57719319..57720904-chr12:57724408..57726293,2	K562	blood:

Extended variants
information (count: 27 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:25)

rs_ID	r²[population]
rs1106766	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];0.88[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];0.85[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs11172134	0.82[CEU][hapmap];1.00[CHB][hapmap];0.81[AMR][1000 genomes]
rs11172147	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];0.88[AMR][1000 genomes];0.82[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs11172181	0.97[AMR][1000 genomes];0.89[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs11609805	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11612551	0.83[MEX][hapmap]
rs11613352	1.00[CEU][hapmap];0.82[AMR][1000 genomes];0.87[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs11614506	0.95[CEU][hapmap];0.89[CHB][hapmap];1.00[JPT][hapmap];0.96[MEX][hapmap];0.83[EUR][1000 genomes]
rs12313306	0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12313762	0.88[AMR][1000 genomes];0.81[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs12315434	0.82[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs2122982	0.83[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs2229357	1.00[JPT][hapmap]
rs3741414	1.00[CEU][hapmap];0.89[CHB][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap]
rs4760254	0.95[CEU][hapmap];1.00[CHB][hapmap];0.90[CHD][hapmap];0.88[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.89[MKK][hapmap];0.95[TSI][hapmap];0.93[AMR][1000 genomes];0.86[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs4760278	0.95[CEU][hapmap];0.89[CHB][hapmap];1.00[CHD][hapmap];0.88[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.90[AMR][1000 genomes];0.83[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs540730	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.88[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.95[TSI][hapmap]
rs56205943	0.88[AMR][1000 genomes];0.82[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs61352607	0.81[EUR][1000 genomes]
rs7397189	0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7484541	0.83[AMR][1000 genomes];0.88[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs7485577	0.83[MEX][hapmap]
rs7964492	1.00[CEU][hapmap];0.89[CHB][hapmap];1.00[JPT][hapmap];0.81[EUR][1000 genomes]
rs7971133	0.95[AMR][1000 genomes];0.88[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs7974833	0.82[AMR][1000 genomes];0.87[EUR][1000 genomes];0.81[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1046013	chr12:57714676-57895167	Active TSS Enhancers Bivalent Enhancer Genic enhancers Weak transcription Flanking Bivalent TSS/Enh Strong transcription Flanking Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	56 gene(s)	inside rSNPs	diseases
2	nsv541502	chr12:57714676-57895167	Weak transcription Flanking Bivalent TSS/Enh Strong transcription Flanking Active TSS Active TSS Genic enhancers Bivalent Enhancer Enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	56 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs4760355	IL23A	cis	parietal	SCAN
rs4760355	KRT2	cis	parietal	SCAN
rs4760355	NDUFA4L2	cis	parietal	SCAN
rs4760355	HOXC6	cis	parietal	SCAN

Chromatin state (count:91 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:57691000-57736200	Weak transcription	Right Atrium	heart
2	chr12:57693600-57743800	Weak transcription	Primary T killer memory cells from peripheral blood	blood
3	chr12:57694000-57780000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
4	chr12:57694200-57734000	Weak transcription	Rectal Smooth Muscle	rectum
5	chr12:57694400-57732400	Weak transcription	Ovary	ovary
6	chr12:57694400-57735000	Weak transcription	Psoas Muscle	Psoas
7	chr12:57695200-57794600	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
8	chr12:57697000-57726000	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
9	chr12:57697000-57735400	Weak transcription	Right Ventricle	heart
10	chr12:57697200-57734000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
11	chr12:57697200-57745000	Weak transcription	Lung	lung
12	chr12:57699800-57762400	Weak transcription	Left Ventricle	heart
13	chr12:57700000-57733800	Weak transcription	Skeletal Muscle Female	skeletal muscle
14	chr12:57700000-57736000	Weak transcription	Fetal Brain Male	brain
15	chr12:57703400-57733800	Weak transcription	Primary hematopoietic stem cells	blood
16	chr12:57703400-57734600	Weak transcription	Stomach Smooth Muscle	stomach
17	chr12:57703400-57742000	Weak transcription	Sigmoid Colon	Sigmoid Colon
18	chr12:57703800-57726600	Weak transcription	Colon Smooth Muscle	Colon
19	chr12:57704000-57726400	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
20	chr12:57704200-57725400	Weak transcription	Thymus	Thymus
21	chr12:57704200-57728200	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
22	chr12:57704200-57728800	Weak transcription	Rectal Mucosa Donor 29	rectum
23	chr12:57704200-57733600	Weak transcription	HSMM	muscle
24	chr12:57704200-57743200	Weak transcription	Duodenum Mucosa	Duodenum
25	chr12:57704400-57725800	Weak transcription	Duodenum Smooth Muscle	Duodenum
26	chr12:57704400-57733800	Weak transcription	Primary T helper cells PMA-I stimulated	--
27	chr12:57704400-57789200	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
28	chr12:57706400-57732200	Weak transcription	Primary T cells fromperipheralblood	blood
29	chr12:57709800-57746800	Weak transcription	Rectal Mucosa Donor 31	rectum
30	chr12:57712800-57735400	Weak transcription	NHLF	lung
31	chr12:57713600-57733000	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
32	chr12:57713600-57733800	Weak transcription	Skeletal Muscle Male	skeletal muscle
33	chr12:57713800-57726200	Weak transcription	NHEK	skin
34	chr12:57713800-57726200	Weak transcription	Osteobl	bone
35	chr12:57713800-57726400	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
36	chr12:57713800-57727000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
37	chr12:57713800-57745800	Weak transcription	Stomach Mucosa	stomach
38	chr12:57714400-57726200	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
39	chr12:57714400-57733600	Weak transcription	Adipose Nuclei	Adipose
40	chr12:57714400-57736200	Weak transcription	Fetal Lung	lung
41	chr12:57714600-57726400	Weak transcription	A549	lung
42	chr12:57714600-57734000	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
43	chr12:57717600-57733800	Weak transcription	Pancreatic Islets	Pancreatic Islet
44	chr12:57717800-57733600	Weak transcription	Brain Angular Gyrus	brain
45	chr12:57718800-57725400	Strong transcription	Primary T cells from cord blood	blood
46	chr12:57719800-57725200	Strong transcription	Liver	Liver
47	chr12:57720200-57730200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
48	chr12:57720400-57733800	Weak transcription	Fetal Kidney	kidney
49	chr12:57721000-57734000	Weak transcription	Cortex derived primary cultured neurospheres	brain
50	chr12:57721200-57735600	Weak transcription	Brain Germinal Matrix	brain

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