Variant report

Variant	rs12297814
Chromosome Location	chr12:50093214-50093215
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr12:50021570..50023423-chr12:50090979..50093576,2	K562	blood:
2	chr12:50091504..50093605-chr12:50134186..50136244,2	MCF-7	breast:
3	chr12:50092701..50095008-chr12:50097299..50100800,3	K562	blood:

Variant related genes	Relation type
ENSG00000139644	Chromatin interaction

Extended variants
information (count: 33 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:31)

rs_ID	r²[population]
rs10128824	0.85[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs11169110	1.00[ASW][hapmap];0.93[LWK][hapmap];1.00[MKK][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs11169114	1.00[ASW][hapmap];1.00[LWK][hapmap];1.00[MKK][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs11169115	1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs11169120	1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs11169123	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs12299477	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs12299666	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs12299743	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs12299751	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs12300919	0.83[AFR][1000 genomes]
rs12300962	0.83[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs12306951	1.00[AMR][1000 genomes]
rs12310046	1.00[CEU][hapmap]
rs12310580	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs12312112	1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs12313657	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs12313681	1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs12314036	1.00[ASW][hapmap];0.93[LWK][hapmap];1.00[MKK][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs12315508	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs12317162	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs12319527	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs12320895	1.00[ASW][hapmap];1.00[LWK][hapmap];1.00[MKK][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs1317263	1.00[AMR][1000 genomes]
rs17119738	1.00[AMR][1000 genomes]
rs17123787	1.00[AMR][1000 genomes]
rs17123827	1.00[AMR][1000 genomes]
rs17123879	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs17123924	1.00[ASW][hapmap];0.93[LWK][hapmap];1.00[MKK][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs9804867	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs9805090	0.96[AFR][1000 genomes];1.00[AMR][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	nsv1045327	chr12:49975040-50551375	Strong transcription Weak transcription Enhancers Genic enhancers Flanking Active TSS Active TSS Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	170 gene(s)	inside rSNPs	diseases
2	nsv541490	chr12:49975040-50551375	Weak transcription Transcr. at gene 5' and 3' Enhancers Genic enhancers Active TSS Strong transcription Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	170 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:113 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:50079000-50096200	Weak transcription	Brain Inferior Temporal Lobe	brain
2	chr12:50089200-50093400	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
3	chr12:50090600-50093400	Enhancers	Psoas Muscle	Psoas
4	chr12:50090800-50093400	Enhancers	Brain Substantia Nigra	brain
5	chr12:50090800-50093400	Flanking Active TSS	GM12878-XiMat	blood
6	chr12:50091000-50094000	Enhancers	Brain Anterior Caudate	brain
7	chr12:50091200-50093800	Enhancers	Cortex derived primary cultured neurospheres	brain
8	chr12:50091200-50094000	Enhancers	Primary hematopoietic stem cells	blood
9	chr12:50091200-50096400	Weak transcription	Sigmoid Colon	Sigmoid Colon
10	chr12:50092000-50093400	Flanking Active TSS	HUES6 Cell Line	embryonic stem cell
11	chr12:50092000-50093400	Flanking Active TSS	HUES64 Cell Line	embryonic stem cell
12	chr12:50092000-50093400	Flanking Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
13	chr12:50092000-50093400	Enhancers	Fetal Adrenal Gland	Adrenal Gland
14	chr12:50092000-50093400	Enhancers	Placenta	Placenta
15	chr12:50092000-50093400	Enhancers	Fetal Thymus	thymus
16	chr12:50092000-50093400	Enhancers	Spleen	Spleen
17	chr12:50092000-50093400	Enhancers	HMEC	breast
18	chr12:50092200-50093400	Flanking Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
19	chr12:50092200-50093400	Enhancers	Colon Smooth Muscle	Colon
20	chr12:50092200-50093400	Enhancers	Fetal Lung	lung
21	chr12:50092200-50093400	Enhancers	Thymus	Thymus
22	chr12:50092200-50093400	Flanking Active TSS	HSMMtube	muscle
23	chr12:50092200-50093400	Flanking Active TSS	Osteobl	bone
24	chr12:50092200-50093600	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
25	chr12:50092200-50093800	Enhancers	Liver	Liver
26	chr12:50092400-50093400	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
27	chr12:50092400-50093400	Enhancers	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
28	chr12:50092400-50093400	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
29	chr12:50092400-50093400	Flanking Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
30	chr12:50092400-50093400	Flanking Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
31	chr12:50092400-50093400	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
32	chr12:50092400-50093400	Flanking Active TSS	Primary T cells from cord blood	blood
33	chr12:50092400-50093400	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
34	chr12:50092400-50093400	Flanking Active TSS	Muscle Satellite Cultured Cells	--
35	chr12:50092400-50093400	Enhancers	Brain Dorsolateral Prefrontal Cortex	brain
36	chr12:50092400-50093400	Enhancers	Placenta Amnion	Placenta Amnion
37	chr12:50092400-50093400	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
38	chr12:50092400-50093400	Flanking Active TSS	NH-A	brain
39	chr12:50092400-50093600	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
40	chr12:50092400-50093800	Flanking Active TSS	Primary B cells from cord blood	blood
41	chr12:50092400-50093800	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
42	chr12:50092400-50093800	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
43	chr12:50092400-50093800	Enhancers	Fetal Kidney	kidney
44	chr12:50092400-50093800	Enhancers	NHLF	lung
45	chr12:50092400-50094000	Genic enhancers	Fetal Stomach	stomach
46	chr12:50092600-50093400	Enhancers	ES-WA7 Cell Line	embryonic stem cell
47	chr12:50092600-50093400	Flanking Active TSS	Primary hematopoietic stem cells short term culture	blood
48	chr12:50092600-50093400	Flanking Active TSS	Primary T helper cells PMA-I stimulated	--
49	chr12:50092600-50093400	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
50	chr12:50092600-50093400	Flanking Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin

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