Variant report

Variant	rs7302422
Chromosome Location	chr12:50645471-50645472
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	IKZF1	chr12:50645471-50645714	GM12878	blood:	n/a	n/a
2	ZNF384	chr12:50645419-50645619	GM12878	blood:	n/a	n/a
3	NFIC	chr12:50645314-50645834	GM12878	blood:	n/a	n/a
4	RUNX3	chr12:50645324-50646069	GM12878	blood:	n/a	n/a
5	BATF	chr12:50645434-50645778	GM12878	blood:	n/a	chr12:50645621-50645632
6	MEF2A	chr12:50645343-50645793	GM12878	blood:	n/a	chr12:50645429-50645450
7	RUNX3	chr12:50645390-50645973	GM12878	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr12:50640930..50642693-chr12:50644330..50646038,2	MCF-7	breast:
2	chr12:50614825..50617496-chr12:50643116..50645944,3	K562	blood:
3	chr12:50643519..50647012-chr12:50649051..50651928,4	K562	blood:
4	chr12:50610860..50612440-chr12:50643733..50646467,2	MCF-7	breast:

Variant related genes	Relation type
LIMA1	TF binding region
ENSG00000050405	Chromatin interaction
ENSG00000212496	Chromatin interaction
ENSG00000257531	Chromatin interaction

Extended variants
information (count: 15 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:11)

rs_ID	r²[population]
rs10450773	0.83[EUR][1000 genomes]
rs10747572	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs10783346	0.89[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10783347	0.85[AMR][1000 genomes];0.99[ASN][1000 genomes]
rs12423130	0.90[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28364704	0.87[AMR][1000 genomes];0.99[ASN][1000 genomes]
rs3815671	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs61928280	0.89[EUR][1000 genomes]
rs736167	0.88[AFR][1000 genomes];0.88[AMR][1000 genomes];0.87[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7974834	0.89[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs8181651	0.89[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];0.97[GIH][hapmap];0.95[JPT][hapmap];0.85[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];0.95[YRI][hapmap];0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv530671	chr12:50233858-50708991	Flanking Active TSS Active TSS Enhancers Weak transcription Genic enhancers Bivalent/Poised TSS Strong transcription 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 miRNA target site	117 gene(s)	inside rSNPs	diseases
2	nsv899075	chr12:50594947-50835060	Flanking Active TSS Weak transcription Enhancers Active TSS Strong transcription Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA	56 gene(s)	inside rSNPs	diseases
3	esv2761738	chr12:50627292-50836427	Weak transcription Enhancers Flanking Active TSS Active TSS Strong transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA	50 gene(s)	inside rSNPs	diseases
4	nsv1035796	chr12:50634342-50784312	Weak transcription Flanking Active TSS Enhancers Strong transcription Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	35 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:74 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:50616800-50651800	Weak transcription	Brain Anterior Caudate	brain
2	chr12:50633200-50651200	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
3	chr12:50634600-50648200	Weak transcription	Spleen	Spleen
4	chr12:50635600-50646600	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
5	chr12:50636200-50651200	Weak transcription	Fetal Kidney	kidney
6	chr12:50636600-50651400	Weak transcription	Gastric	stomach
7	chr12:50636600-50651800	Weak transcription	Stomach Smooth Muscle	stomach
8	chr12:50636800-50648200	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
9	chr12:50637200-50645600	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
10	chr12:50637200-50648200	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
11	chr12:50639000-50651600	Weak transcription	Fetal Lung	lung
12	chr12:50640400-50651200	Weak transcription	Breast Myoepithelial Primary Cells	Breast
13	chr12:50640800-50647400	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
14	chr12:50641000-50662000	Weak transcription	Brain Germinal Matrix	brain
15	chr12:50641200-50653200	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
16	chr12:50641400-50647800	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
17	chr12:50641400-50659600	Weak transcription	Esophagus	oesophagus
18	chr12:50641800-50648400	Weak transcription	Lung	lung
19	chr12:50641800-50651200	Weak transcription	Brain Cingulate Gyrus	brain
20	chr12:50641800-50651200	Weak transcription	Left Ventricle	heart
21	chr12:50641800-50651200	Weak transcription	Rectal Smooth Muscle	rectum
22	chr12:50641800-50651800	Weak transcription	Fetal Stomach	stomach
23	chr12:50641800-50651800	Weak transcription	Right Ventricle	heart
24	chr12:50641800-50652000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
25	chr12:50642000-50645600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
26	chr12:50642600-50651200	Weak transcription	Brain Inferior Temporal Lobe	brain
27	chr12:50642600-50652000	Weak transcription	Fetal Muscle Trunk	muscle
28	chr12:50642800-50649000	Weak transcription	Aorta	Aorta
29	chr12:50642800-50651200	Weak transcription	Brain Angular Gyrus	brain
30	chr12:50643000-50645600	Weak transcription	HMEC	breast
31	chr12:50643000-50645600	Weak transcription	NHLF	lung
32	chr12:50643000-50646200	Enhancers	Duodenum Mucosa	Duodenum
33	chr12:50643000-50647400	Enhancers	Rectal Mucosa Donor 31	rectum
34	chr12:50643000-50648600	Weak transcription	Pancreas	Pancrea
35	chr12:50643000-50649400	Enhancers	Fetal Intestine Large	intestine
36	chr12:50643000-50651000	Weak transcription	Muscle Satellite Cultured Cells	--
37	chr12:50643000-50651200	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
38	chr12:50643200-50651000	Weak transcription	Adipose Nuclei	Adipose
39	chr12:50643400-50648000	Weak transcription	NHDF-Ad	bronchial
40	chr12:50643600-50645600	Weak transcription	HSMM	muscle
41	chr12:50643600-50646200	Enhancers	Placenta	Placenta
42	chr12:50643600-50648000	Weak transcription	NH-A	brain
43	chr12:50643600-50649200	Enhancers	Stomach Mucosa	stomach
44	chr12:50643800-50645600	Enhancers	GM12878-XiMat	blood
45	chr12:50643800-50646800	Weak transcription	A549	lung
46	chr12:50643800-50651000	Weak transcription	Pancreatic Islets	Pancreatic Islet
47	chr12:50643800-50651200	Weak transcription	Cortex derived primary cultured neurospheres	brain
48	chr12:50643800-50651400	Weak transcription	Colon Smooth Muscle	Colon
49	chr12:50644000-50645600	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
50	chr12:50644000-50645600	Weak transcription	Skeletal Muscle Female	skeletal muscle

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