Variant report

Variant	rs2456973
Chromosome Location	chr12:56416928-56416929
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr12:56415172..56417202-chr12:56434468..56437064,2	MCF-7	breast:
2	chr12:56395480..56397433-chr12:56414863..56417335,2	MCF-7	breast:
3	chr12:56400102..56402586-chr12:56415416..56418384,2	MCF-7	breast:
4	chr12:56390677..56393462-chr12:56415719..56417706,2	K562	blood:
5	chr12:56415753..56419249-chr12:56520139..56522769,3	K562	blood:
6	chr12:56415122..56418251-chr12:56424382..56426492,3	MCF-7	breast:

Variant related genes	Relation type
ENSG00000139531	Chromatin interaction
ENSG00000123411	Chromatin interaction
ENSG00000197728	Chromatin interaction
ENSG00000257449	Chromatin interaction
ENSG00000139641	Chromatin interaction
ENSG00000258317	Chromatin interaction

Extended variants
information (count: 41 )
Associated
traits (count: 9 )

rSNPs within LD-proxies of this variant (count:37)

rs_ID	r²[population]
rs10876864	0.95[CHB][hapmap];1.00[JPT][hapmap];0.81[ASN][1000 genomes]
rs10876866	0.81[AFR][1000 genomes];0.94[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs10876870	0.83[CHB][hapmap];0.94[JPT][hapmap]
rs11171739	0.83[CHB][hapmap];0.94[JPT][hapmap]
rs1131017	1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[ASN][1000 genomes]
rs1689510	0.84[AFR][1000 genomes];0.91[AMR][1000 genomes];0.91[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs1701704	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1702877	0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs1873914	0.84[CHB][hapmap];0.82[JPT][hapmap]
rs2017445	0.96[AMR][1000 genomes];0.90[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2271194	0.94[JPT][hapmap]
rs2292239	0.86[CEU][hapmap];0.88[JPT][hapmap];0.82[EUR][1000 genomes]
rs2640562	0.96[AFR][1000 genomes];0.84[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs2640564	0.96[AFR][1000 genomes];0.88[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs34415530	0.96[AFR][1000 genomes];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs3741499	0.86[CEU][hapmap];0.83[CHB][hapmap];0.94[JPT][hapmap];0.85[EUR][1000 genomes]
rs4759229	0.86[CEU][hapmap];0.83[CHB][hapmap];0.94[JPT][hapmap];0.85[EUR][1000 genomes]
rs61938962	0.96[AFR][1000 genomes];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs61938963	0.96[AFR][1000 genomes];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs705696	0.82[EUR][1000 genomes]
rs705698	0.91[CEU][hapmap];0.82[JPT][hapmap]
rs705699	0.84[CHB][hapmap]
rs705700	0.82[JPT][hapmap]
rs705702	0.91[CEU][hapmap];0.82[JPT][hapmap];0.80[EUR][1000 genomes]
rs705704	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[YRI][hapmap];0.93[AFR][1000 genomes];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs705705	0.87[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs7302200	0.93[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs7305461	0.81[CHB][hapmap]
rs772920	0.80[EUR][1000 genomes]
rs772921	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.84[AFR][1000 genomes];0.97[AMR][1000 genomes];0.94[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs773107	0.86[CEU][hapmap]
rs773108	0.90[CEU][hapmap];0.84[CHB][hapmap];0.82[JPT][hapmap]
rs773109	0.91[CEU][hapmap];0.84[CHB][hapmap];0.88[JPT][hapmap]
rs773110	0.80[AMR][1000 genomes]
rs773114	0.84[CHB][hapmap];0.83[JPT][hapmap]
rs7971751	0.83[CHB][hapmap];0.94[JPT][hapmap]
rs877636	0.86[CEU][hapmap];0.83[CHB][hapmap];0.94[JPT][hapmap];0.82[EUR][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	nsv1051961	chr12:56262220-56629427	Weak transcription Enhancers Strong transcription Flanking Bivalent TSS/Enh Flanking Active TSS Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	284 gene(s)	inside rSNPs	diseases
2	nsv832424	chr12:56275226-56466917	Enhancers Flanking Active TSS Active TSS Weak transcription 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 target site	121 gene(s)	inside rSNPs	diseases
3	nsv1043988	chr12:56348185-56534900	Weak transcription Flanking Active TSS Enhancers Genic enhancers Active TSS Strong transcription Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	189 gene(s)	inside rSNPs	diseases
4	nsv832427	chr12:56392545-56512774	Weak transcription Strong transcription Genic enhancers Enhancers Flanking Active TSS Transcr. at gene 5' and 3' Active TSS Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	152 gene(s)	inside rSNPs	diseases

Variant related diseases (count:1)

Disease	PMID	Source
Vitiligo	22561518	GWAS catalog

mRNA abundance (count:8)

SNP	Gene	Cis/trans	Tissue	Source
rs2456973	AC034102.1	cis	Muscle Skeletal	GTEx
rs2456973	DEFB124	trans	lymphoblastoid	RTeQTL
rs2456973	LOC644166///LOC644191///LOC728937///RPS26	Cis_1M	lymphoblastoid	RTeQTL
rs2456973	SUOX	cis	Thyroid	GTEx
rs2456973	RAB5B	cis	Muscle Skeletal	GTEx
rs2456973	RPS26///RPS26L///LOC644166///LOC644191	cis	uninvolved skin	skin_eQTL
rs2456973	RPS26	cis	multi-tissue	Pritchard
rs2456973	RPS26///RPS26L///LOC644166///LOC644191	cis	lesional skin	skin_eQTL

Chromatin state (count:118 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:56402000-56418600	Weak transcription	Gastric	stomach
2	chr12:56402200-56418400	Weak transcription	Pancreas	Pancrea
3	chr12:56402200-56418400	Weak transcription	HSMMtube	muscle
4	chr12:56402200-56434800	Weak transcription	Psoas Muscle	Psoas
5	chr12:56402400-56422400	Weak transcription	Osteobl	bone
6	chr12:56402400-56423000	Weak transcription	Muscle Satellite Cultured Cells	--
7	chr12:56406000-56417000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
8	chr12:56406000-56422800	Weak transcription	HSMM	muscle
9	chr12:56409400-56435000	Weak transcription	Stomach Mucosa	stomach
10	chr12:56409800-56422600	Weak transcription	Liver	Liver
11	chr12:56414000-56418600	Weak transcription	Skeletal Muscle Male	skeletal muscle
12	chr12:56415400-56418600	Weak transcription	Left Ventricle	heart
13	chr12:56415400-56422400	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
14	chr12:56415600-56418800	Weak transcription	Lung	lung
15	chr12:56415600-56426200	Weak transcription	Aorta	Aorta
16	chr12:56415800-56420600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
17	chr12:56415800-56420600	Weak transcription	Esophagus	oesophagus
18	chr12:56415800-56422400	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
19	chr12:56415800-56422400	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
20	chr12:56416000-56418400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
21	chr12:56416000-56418600	Weak transcription	Breast Myoepithelial Primary Cells	Breast
22	chr12:56416000-56418600	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
23	chr12:56416000-56418600	Weak transcription	Fetal Muscle Trunk	muscle
24	chr12:56416000-56418600	Weak transcription	Skeletal Muscle Female	skeletal muscle
25	chr12:56416000-56419000	Weak transcription	Adipose Nuclei	Adipose
26	chr12:56416000-56419000	Weak transcription	Rectal Smooth Muscle	rectum
27	chr12:56416000-56419000	Weak transcription	Sigmoid Colon	Sigmoid Colon
28	chr12:56416000-56420600	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
29	chr12:56416000-56420600	Weak transcription	Brain Substantia Nigra	brain
30	chr12:56416000-56420600	Weak transcription	Pancreatic Islets	Pancreatic Islet
31	chr12:56416000-56420600	Weak transcription	Right Ventricle	heart
32	chr12:56416000-56421200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
33	chr12:56416000-56421200	Weak transcription	Rectal Mucosa Donor 29	rectum
34	chr12:56416000-56422800	Weak transcription	NH-A	brain
35	chr12:56416000-56426000	Weak transcription	Rectal Mucosa Donor 31	rectum
36	chr12:56416000-56434800	Weak transcription	Primary B cells from cord blood	blood
37	chr12:56416000-56434800	Weak transcription	Primary B cells from peripheral blood	blood
38	chr12:56416000-56435000	Weak transcription	Right Atrium	heart
39	chr12:56416200-56417000	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
40	chr12:56416200-56417000	Active TSS	K562	blood
41	chr12:56416200-56417200	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
42	chr12:56416200-56417200	Enhancers	Fetal Brain Male	brain
43	chr12:56416200-56417600	Weak transcription	iPS-20b Cell Line	embryonic stem cell
44	chr12:56416200-56417600	Enhancers	Fetal Stomach	stomach
45	chr12:56416200-56417800	Weak transcription	Brain Inferior Temporal Lobe	brain
46	chr12:56416200-56418000	Weak transcription	HUES6 Cell Line	embryonic stem cell
47	chr12:56416200-56418200	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
48	chr12:56416200-56418200	Weak transcription	Brain Anterior Caudate	brain
49	chr12:56416200-56418400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
50	chr12:56416200-56418400	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung

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