Variant report

Variant	rs2279464
Chromosome Location	chr12:48690409-48690410
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr12:48688262..48692290-chr12:48702214..48707293,5	K562	blood:
2	chr12:48593487..48595723-chr12:48689162..48691231,3	K562	blood:
3	chr12:48689964..48692021-chr12:48694764..48697453,3	MCF-7	breast:
4	chr12:48682061..48686479-chr12:48688143..48691883,6	K562	blood:
5	chr12:48689650..48692193-chr12:48742789..48745705,2	K562	blood:
6	chr12:48680562..48682797-chr12:48688715..48691085,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000257735	Chromatin interaction
ENSG00000167528	Chromatin interaction

Extended variants
information (count: 117 )
Associated
traits (count: 6 )

rSNPs within LD-proxies of this variant (count:99)

rs_ID	r²[population]
rs10082861	0.84[JPT][hapmap]
rs1021313	0.82[AMR][1000 genomes];0.91[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs10219623	0.87[JPT][hapmap]
rs10431526	0.83[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10437919	0.93[ASN][1000 genomes]
rs10437920	0.93[ASN][1000 genomes]
rs10467101	0.93[CHB][hapmap];0.85[JPT][hapmap];0.81[AMR][1000 genomes];0.90[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs10875745	0.82[CHB][hapmap];0.87[JPT][hapmap]
rs10875746	0.87[JPT][hapmap]
rs10875750	0.82[CHB][hapmap];0.87[JPT][hapmap]
rs10875767	0.93[CHB][hapmap];0.94[JPT][hapmap];0.85[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs10875768	0.84[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs10875769	0.82[ASN][1000 genomes]
rs10875770	0.94[CHB][hapmap];0.93[JPT][hapmap];0.86[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs10875772	0.94[CHB][hapmap];0.93[JPT][hapmap];0.85[YRI][hapmap];0.96[AMR][1000 genomes];0.90[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs10875777	0.82[AMR][1000 genomes];0.91[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs10875778	0.98[AMR][1000 genomes];0.91[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs10875779	0.98[AMR][1000 genomes];0.91[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs10875782	0.90[ASN][1000 genomes]
rs10875792	0.93[CHB][hapmap];1.00[JPT][hapmap];0.82[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10875793	0.94[CHB][hapmap];1.00[JPT][hapmap];0.82[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10875799	0.89[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs11168413	0.87[JPT][hapmap]
rs11168414	0.82[CHB][hapmap];0.87[JPT][hapmap]
rs11168418	0.82[CHB][hapmap];0.87[JPT][hapmap]
rs11168420	0.87[JPT][hapmap]
rs11168421	0.87[JPT][hapmap]
rs11168425	0.87[JPT][hapmap]
rs11168427	0.82[CHB][hapmap];0.87[JPT][hapmap]
rs11168433	0.82[CHB][hapmap];0.87[JPT][hapmap]
rs11168450	0.87[JPT][hapmap]
rs11168459	0.94[CHB][hapmap];0.93[JPT][hapmap];0.83[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs11168483	0.90[ASN][1000 genomes]
rs11168487	0.98[AMR][1000 genomes];0.91[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs11168493	0.95[ASN][1000 genomes]
rs11168508	0.84[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11168510	0.84[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11168514	0.82[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11168516	0.94[CHB][hapmap];1.00[JPT][hapmap];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11168520	0.86[ASN][1000 genomes]
rs11168536	0.90[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs12227601	0.83[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12297470	0.82[CHB][hapmap];0.86[JPT][hapmap]
rs12300647	0.90[ASN][1000 genomes]
rs12305511	0.82[CHB][hapmap];0.87[JPT][hapmap];0.82[ASN][1000 genomes]
rs12305647	0.82[ASN][1000 genomes]
rs12310813	0.82[CHB][hapmap];0.87[JPT][hapmap]
rs12312134	0.81[JPT][hapmap]
rs12313745	0.85[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs12317751	0.93[ASN][1000 genomes]
rs12318705	0.90[ASN][1000 genomes]
rs12322347	0.85[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs12322348	0.84[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs1471997	0.94[CHB][hapmap];1.00[JPT][hapmap];0.92[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs17122666	0.87[JPT][hapmap]
rs17122812	0.94[CHB][hapmap];0.94[JPT][hapmap];1.00[YRI][hapmap];0.83[AMR][1000 genomes];0.83[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs1859445	0.87[CHB][hapmap];0.87[JPT][hapmap]
rs2012773	0.87[JPT][hapmap]
rs2054903	0.94[CHB][hapmap];0.93[JPT][hapmap];0.85[YRI][hapmap];0.93[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2054904	0.93[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2107638	0.87[JPT][hapmap]
rs2171642	0.90[ASN][1000 genomes]
rs2228500	0.82[CHB][hapmap];0.87[JPT][hapmap]
rs2269933	0.86[JPT][hapmap]
rs2269935	0.82[CHB][hapmap];0.87[JPT][hapmap]
rs2409005	0.87[ASN][1000 genomes]
rs2450992	0.81[ASN][1000 genomes]
rs2634675	0.88[CHB][hapmap];1.00[JPT][hapmap];0.83[ASN][1000 genomes]
rs2732439	0.94[CHB][hapmap];1.00[JPT][hapmap];0.83[ASN][1000 genomes]
rs2732465	0.94[CHB][hapmap];1.00[JPT][hapmap];0.83[ASN][1000 genomes]
rs2898065	0.82[AMR][1000 genomes];0.93[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2898066	0.88[ASN][1000 genomes]
rs3185921	0.94[CHB][hapmap];1.00[JPT][hapmap];0.89[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs3751273	0.94[CHB][hapmap];1.00[JPT][hapmap];0.90[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs4760619	0.87[CHB][hapmap];0.87[JPT][hapmap]
rs4760622	0.82[CHB][hapmap];0.87[JPT][hapmap];0.82[ASN][1000 genomes]
rs4760625	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4760681	0.82[CHB][hapmap];0.86[JPT][hapmap]
rs4760687	0.87[JPT][hapmap]
rs4760695	0.82[CHB][hapmap];0.87[JPT][hapmap];0.82[ASN][1000 genomes]
rs4760696	0.87[JPT][hapmap]
rs4760697	0.87[JPT][hapmap]
rs4760699	0.86[ASN][1000 genomes]
rs61940962	0.83[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs61941003	0.98[AMR][1000 genomes];0.91[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs61941006	0.82[AMR][1000 genomes];0.91[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6580659	0.85[JPT][hapmap]
rs7135779	0.86[JPT][hapmap]
rs716553	0.93[ASN][1000 genomes]
rs725454	0.87[JPT][hapmap]
rs7297298	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7302466	0.90[ASN][1000 genomes]
rs7303055	0.93[ASN][1000 genomes]
rs7486008	0.93[ASN][1000 genomes]
rs7486424	0.87[JPT][hapmap]
rs7975956	0.90[ASN][1000 genomes]
rs8804	0.82[CHB][hapmap];0.87[JPT][hapmap]
rs9634261	1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9788082	0.83[AMR][1000 genomes];0.88[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:18 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv2758307	chr12:48429702-48825499	Weak transcription Enhancers Active TSS Strong transcription Flanking Active TSS Flanking Bivalent TSS/Enh Genic enhancers Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	57 gene(s)	inside rSNPs	diseases
2	esv2759898	chr12:48429702-48825499	Weak transcription Strong transcription ZNF genes & repeats Genic enhancers Enhancers Active TSS Flanking Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	57 gene(s)	inside rSNPs	diseases
3	nsv8971	chr12:48536526-48758501	Flanking Active TSS Enhancers Weak transcription Bivalent Enhancer Strong transcription Bivalent/Poised TSS Genic enhancers Active TSS 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	39 gene(s)	inside rSNPs	diseases
4	esv34439	chr12:48541757-48779562	Bivalent/Poised TSS Flanking Active TSS Weak transcription Active TSS Enhancers Strong transcription Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	39 gene(s)	inside rSNPs	diseases
5	esv2757502	chr12:48547128-48779562	Genic enhancers Flanking Active TSS Enhancers Bivalent Enhancer Weak transcription Flanking Bivalent TSS/Enh Active TSS Bivalent/Poised TSS ZNF genes & repeats Strong transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	39 gene(s)	inside rSNPs	diseases
6	nsv899062	chr12:48658212-48711867	Enhancers Active TSS Flanking Active TSS Weak transcription ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region	4 gene(s)	inside rSNPs	diseases
7	nsv899063	chr12:48664989-48713768	Flanking Active TSS Enhancers Active TSS Flanking Bivalent TSS/Enh Weak transcription Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region	4 gene(s)	inside rSNPs	diseases
8	nsv899064	chr12:48664989-48721832	Bivalent Enhancer Active TSS Flanking Active TSS Enhancers Weak transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region	5 gene(s)	inside rSNPs	diseases
9	nsv899065	chr12:48667019-48711867	Enhancers Flanking Active TSS Active TSS Weak transcription Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region	4 gene(s)	inside rSNPs	diseases
10	nsv899066	chr12:48667019-48713768	Active TSS Enhancers Bivalent Enhancer Weak transcription Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region	4 gene(s)	inside rSNPs	diseases
11	nsv427911	chr12:48670336-48979396	Weak transcription Strong transcription Flanking Active TSS Flanking Bivalent TSS/Enh Active TSS Enhancers Bivalent Enhancer ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	35 gene(s)	inside rSNPs	diseases
12	esv34952	chr12:48672333-48703533	Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Enhancers Weak transcription Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region	4 gene(s)	inside rSNPs	diseases
13	nsv469369	chr12:48675783-48711867	Enhancers Bivalent/Poised TSS Bivalent Enhancer Flanking Active TSS Active TSS Weak transcription Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region	4 gene(s)	inside rSNPs	diseases
14	nsv469370	chr12:48675783-48711867	Bivalent Enhancer Weak transcription Enhancers Active TSS Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region	4 gene(s)	inside rSNPs	diseases
15	nsv469372	chr12:48675783-48711867	Enhancers Flanking Active TSS Active TSS Bivalent/Poised TSS Weak transcription Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region	4 gene(s)	inside rSNPs	diseases
16	nsv470290	chr12:48675783-48711867	Weak transcription Active TSS Bivalent Enhancer Flanking Active TSS Enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region	4 gene(s)	inside rSNPs	diseases
17	nsv558791	chr12:48675783-48711867	Flanking Bivalent TSS/Enh Active TSS Weak transcription Enhancers Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region	4 gene(s)	inside rSNPs	diseases
18	nsv832402	chr12:48686761-48851020	Enhancers Weak transcription Flanking Active TSS Active TSS Strong transcription 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	26 gene(s)	inside rSNPs	diseases

mRNA abundance (count:6)

SNP	Gene	Cis/trans	Tissue	Source
rs2279464	RP1-228P16.1	cis	Skin Sun Exposed Lower leg	GTEx
rs2279464	RP1-228P16.1	cis	Artery Tibial	GTEx
rs2279464	RP1-228P16.1	cis	Thyroid	GTEx
rs2279464	ZNF641	cis	Muscle Skeletal	GTEx
rs2279464	RP1-228P16.1	cis	Adipose Subcutaneous	GTEx
rs2279464	RP1-228P16.1	cis	Heart Left Ventricle	GTEx

Chromatin state (count:116 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:48686000-48690800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
2	chr12:48688400-48690600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
3	chr12:48689800-48690600	Weak transcription	Placenta Amnion	Placenta Amnion
4	chr12:48689800-48691000	Active TSS	Primary hematopoietic stem cells short term culture	blood
5	chr12:48690000-48691200	Active TSS	Brain Hippocampus Middle	brain
6	chr12:48690000-48691200	Flanking Active TSS	K562	blood
7	chr12:48690200-48690600	Flanking Active TSS	Primary hematopoietic stem cells	blood
8	chr12:48690200-48690600	Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
9	chr12:48690200-48690600	Active TSS	Rectal Mucosa Donor 29	rectum
10	chr12:48690200-48690600	Active TSS	Right Atrium	heart
11	chr12:48690200-48690600	Enhancers	Stomach Mucosa	stomach
12	chr12:48690200-48690800	Active TSS	iPS-20b Cell Line	embryonic stem cell
13	chr12:48690200-48690800	Flanking Active TSS	Thymus	Thymus
14	chr12:48690200-48691000	Active TSS	HUES64 Cell Line	embryonic stem cell
15	chr12:48690200-48691000	Bivalent/Poised TSS	iPS-15b Cell Line	embryonic stem cell
16	chr12:48690200-48691000	Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
17	chr12:48690200-48691000	Flanking Active TSS	Primary neutrophils fromperipheralblood	blood
18	chr12:48690200-48691000	Flanking Active TSS	Primary T helper naive cells fromperipheralblood	blood
19	chr12:48690200-48691000	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
20	chr12:48690200-48691000	Active TSS	Primary T helper cells PMA-I stimulated	--
21	chr12:48690200-48691000	Flanking Bivalent TSS/Enh	Cortex derived primary cultured neurospheres	brain
22	chr12:48690200-48691000	Active TSS	Foreskin Melanocyte Primary Cells skin03	Skin
23	chr12:48690200-48691000	Active TSS	Fetal Heart	heart
24	chr12:48690200-48691000	Active TSS	Fetal Stomach	stomach
25	chr12:48690200-48691000	Active TSS	A549	lung
26	chr12:48690200-48691000	Bivalent/Poised TSS	HSMM	muscle
27	chr12:48690200-48691000	Active TSS	NHEK	skin
28	chr12:48690200-48691000	Bivalent/Poised TSS	NHLF	lung
29	chr12:48690200-48691200	Active TSS	ES-I3 Cell Line	embryonic stem cell
30	chr12:48690200-48691200	Bivalent/Poised TSS	HUES48 Cell Line	embryonic stem cell
31	chr12:48690200-48691200	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
32	chr12:48690200-48691200	Active TSS	Breast Myoepithelial Primary Cells	Breast
33	chr12:48690200-48691200	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
34	chr12:48690200-48691200	Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
35	chr12:48690200-48691200	Active TSS	Brain Angular Gyrus	brain
36	chr12:48690200-48691200	Active TSS	Brain Cingulate Gyrus	brain
37	chr12:48690200-48691200	Active TSS	Duodenum Mucosa	Duodenum
38	chr12:48690200-48691200	Active TSS	Duodenum Smooth Muscle	Duodenum
39	chr12:48690200-48691200	Active TSS	Fetal Intestine Small	intestine
40	chr12:48690200-48691200	Active TSS	Fetal Lung	lung
41	chr12:48690200-48691200	Active TSS	Psoas Muscle	Psoas
42	chr12:48690200-48691200	Active TSS	Rectal Smooth Muscle	rectum
43	chr12:48690200-48691200	Active TSS	Stomach Smooth Muscle	stomach
44	chr12:48690200-48691400	Active TSS	Brain Anterior Caudate	brain
45	chr12:48690200-48691400	Active TSS	Brain Inferior Temporal Lobe	brain
46	chr12:48690200-48691400	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
47	chr12:48690200-48691400	Active TSS	Brain Substantia Nigra	brain
48	chr12:48690200-48691400	Active TSS	Fetal Brain Female	brain
49	chr12:48690200-48691400	Active TSS	Fetal Kidney	kidney
50	chr12:48690200-48691400	Active TSS	Pancreatic Islets	Pancreatic Islet

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