Variant report

Variant	rs2658479
Chromosome Location	chr12:56417403-56417404
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr12:56417053..56422414-chr12:56432550..56437155,7	K562	blood:
2	chr12:56400102..56402586-chr12:56415416..56418384,2	MCF-7	breast:
3	chr12:56390677..56393462-chr12:56415719..56417706,2	K562	blood:
4	chr12:56415753..56419249-chr12:56520139..56522769,3	K562	blood:
5	chr12:56415122..56418251-chr12:56424382..56426492,3	MCF-7	breast:

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

Extended variants
information (count: 74 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:70)

rs_ID	r²[population]
rs1045435	1.00[ASN][1000 genomes]
rs10783777	1.00[ASN][1000 genomes]
rs10783778	1.00[ASN][1000 genomes]
rs10876867	1.00[ASN][1000 genomes]
rs1091527	1.00[ASN][1000 genomes]
rs11171713	0.88[CEU][hapmap]
rs11550558	0.88[CEU][hapmap];0.90[GIH][hapmap];0.91[TSI][hapmap];1.00[ASN][1000 genomes]
rs11835310	1.00[ASN][1000 genomes]
rs11837075	0.87[ASN][1000 genomes]
rs12099979	0.88[CEU][hapmap];0.94[EUR][1000 genomes]
rs12810011	0.94[EUR][1000 genomes]
rs12815302	0.89[EUR][1000 genomes]
rs12815387	1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[TSI][hapmap];0.94[EUR][1000 genomes]
rs12815488	0.94[EUR][1000 genomes]
rs12818756	0.94[EUR][1000 genomes]
rs12831468	0.94[EUR][1000 genomes]
rs12831884	1.00[CEU][hapmap]
rs1614219	0.85[AFR][1000 genomes];0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1626158	1.00[ASN][1000 genomes]
rs1689511	1.00[CEU][hapmap];0.91[YRI][hapmap];0.85[AFR][1000 genomes];0.89[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1689517	1.00[ASN][1000 genomes]
rs1689518	1.00[ASN][1000 genomes]
rs1701706	0.88[ASW][hapmap];1.00[CEU][hapmap];1.00[GIH][hapmap];0.89[LWK][hapmap];1.00[MEX][hapmap];0.98[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.89[AFR][1000 genomes];0.94[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs1702876	0.86[AFR][1000 genomes]
rs17118206	0.88[CEU][hapmap];0.90[GIH][hapmap];0.91[TSI][hapmap]
rs17118208	0.88[CEU][hapmap];0.90[GIH][hapmap];0.91[TSI][hapmap]
rs17118262	0.94[EUR][1000 genomes]
rs2131569	0.94[EUR][1000 genomes]
rs2271193	1.00[ASN][1000 genomes]
rs2271195	1.00[ASN][1000 genomes]
rs2277340	1.00[ASN][1000 genomes]
rs2456972	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2640566	1.00[ASN][1000 genomes]
rs2661728	1.00[ASN][1000 genomes]
rs2661729	1.00[ASN][1000 genomes]
rs2934152	1.00[ASN][1000 genomes]
rs34228181	0.94[EUR][1000 genomes]
rs34303864	0.94[EUR][1000 genomes]
rs34406511	0.94[EUR][1000 genomes]
rs34485293	0.93[EUR][1000 genomes]
rs34507011	0.93[EUR][1000 genomes]
rs34602183	0.91[EUR][1000 genomes]
rs34650555	0.94[EUR][1000 genomes]
rs34921584	0.94[EUR][1000 genomes]
rs35485002	0.98[EUR][1000 genomes]
rs35662491	0.80[EUR][1000 genomes]
rs35666826	0.83[EUR][1000 genomes]
rs35961650	1.00[EUR][1000 genomes]
rs4759022	1.00[CEU][hapmap];0.94[EUR][1000 genomes]
rs4759218	0.85[MEX][hapmap]
rs4759239	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs71459334	0.94[EUR][1000 genomes]
rs71459336	0.93[EUR][1000 genomes]
rs71459339	0.94[EUR][1000 genomes]
rs71459342	0.83[EUR][1000 genomes]
rs7298818	0.89[EUR][1000 genomes]
rs7300292	1.00[ASN][1000 genomes]
rs7300772	0.90[AFR][1000 genomes];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs7304690	1.00[ASN][1000 genomes]
rs73338377	1.00[ASN][1000 genomes]
rs73338385	1.00[ASN][1000 genomes]
rs73338396	0.87[ASN][1000 genomes]
rs772919	0.90[AFR][1000 genomes];0.95[EUR][1000 genomes]
rs772922	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];0.94[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs772923	1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[TSI][hapmap];0.94[EUR][1000 genomes]
rs773115	0.93[AFR][1000 genomes];0.94[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7963590	0.83[EUR][1000 genomes]
rs7970035	1.00[ASN][1000 genomes]
rs7977537	0.89[EUR][1000 genomes]
rs9738143	1.00[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	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

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs2658479	RPS26	cis	lymphoblastoid	seeQTL
rs2658479	RDH5	cis	lymphoblastoid	seeQTL
rs2658479	LOC644166///LOC644191///LOC728937///RPS26	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:117 , 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	chr12:56406000-56422800	Weak transcription	HSMM	muscle
8	chr12:56409400-56435000	Weak transcription	Stomach Mucosa	stomach
9	chr12:56409800-56422600	Weak transcription	Liver	Liver
10	chr12:56414000-56418600	Weak transcription	Skeletal Muscle Male	skeletal muscle
11	chr12:56415400-56418600	Weak transcription	Left Ventricle	heart
12	chr12:56415400-56422400	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
13	chr12:56415600-56418800	Weak transcription	Lung	lung
14	chr12:56415600-56426200	Weak transcription	Aorta	Aorta
15	chr12:56415800-56420600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
16	chr12:56415800-56420600	Weak transcription	Esophagus	oesophagus
17	chr12:56415800-56422400	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
18	chr12:56415800-56422400	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
19	chr12:56416000-56418400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
20	chr12:56416000-56418600	Weak transcription	Breast Myoepithelial Primary Cells	Breast
21	chr12:56416000-56418600	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
22	chr12:56416000-56418600	Weak transcription	Fetal Muscle Trunk	muscle
23	chr12:56416000-56418600	Weak transcription	Skeletal Muscle Female	skeletal muscle
24	chr12:56416000-56419000	Weak transcription	Adipose Nuclei	Adipose
25	chr12:56416000-56419000	Weak transcription	Rectal Smooth Muscle	rectum
26	chr12:56416000-56419000	Weak transcription	Sigmoid Colon	Sigmoid Colon
27	chr12:56416000-56420600	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
28	chr12:56416000-56420600	Weak transcription	Brain Substantia Nigra	brain
29	chr12:56416000-56420600	Weak transcription	Pancreatic Islets	Pancreatic Islet
30	chr12:56416000-56420600	Weak transcription	Right Ventricle	heart
31	chr12:56416000-56421200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
32	chr12:56416000-56421200	Weak transcription	Rectal Mucosa Donor 29	rectum
33	chr12:56416000-56422800	Weak transcription	NH-A	brain
34	chr12:56416000-56426000	Weak transcription	Rectal Mucosa Donor 31	rectum
35	chr12:56416000-56434800	Weak transcription	Primary B cells from cord blood	blood
36	chr12:56416000-56434800	Weak transcription	Primary B cells from peripheral blood	blood
37	chr12:56416000-56435000	Weak transcription	Right Atrium	heart
38	chr12:56416200-56417600	Weak transcription	iPS-20b Cell Line	embryonic stem cell
39	chr12:56416200-56417600	Enhancers	Fetal Stomach	stomach
40	chr12:56416200-56417800	Weak transcription	Brain Inferior Temporal Lobe	brain
41	chr12:56416200-56418000	Weak transcription	HUES6 Cell Line	embryonic stem cell
42	chr12:56416200-56418200	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
43	chr12:56416200-56418200	Weak transcription	Brain Anterior Caudate	brain
44	chr12:56416200-56418400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
45	chr12:56416200-56418400	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
46	chr12:56416200-56418400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
47	chr12:56416200-56418400	Weak transcription	Ovary	ovary
48	chr12:56416200-56418600	Weak transcription	Brain Hippocampus Middle	brain
49	chr12:56416200-56418600	Weak transcription	Colon Smooth Muscle	Colon
50	chr12:56416200-56418600	Weak transcription	Placenta Amnion	Placenta Amnion

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