Variant report

Variant	rs2456972
Chromosome Location	chr12:56442728-56442729
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:0)
CpG islands
(count:0)
Chromatin interactive
region (count:12)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:12 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr12:56433777..56443620-chr12:56502225..56514736,38	MCF-7	breast:
2	chr12:56431889..56443161-chr12:56494616..56500426,22	MCF-7	breast:
3	chr12:56434006..56443603-chr12:56507645..56514884,44	K562	blood:
4	chr12:56442718..56445165-chr12:56497582..56500384,2	MCF-7	breast:
5	chr12:56434544..56443137-chr12:56494029..56505252,21	K562	blood:
6	chr12:56441074..56443653-chr12:56557896..56559421,2	K562	blood:
7	chr12:56433331..56443603-chr12:56506173..56514581,35	K562	blood:
8	chr12:56439022..56443137-chr12:56446581..56450430,4	MCF-7	breast:
9	chr12:56441625..56443197-chr12:56520577..56522756,2	MCF-7	breast:
10	chr12:56386787..56388837-chr12:56442198..56444594,2	MCF-7	breast:
11	chr12:56441244..56443084-chr12:56479692..56481794,2	MCF-7	breast:
12	chr12:56433908..56446518-chr12:56506026..56517165,55	MCF-7	breast:

No data

Variant related genes	Relation type
ENSG00000139641	Chromatin interaction
ENSG00000170515	Chromatin interaction
ENSG00000257553	Chromatin interaction
ENSG00000258317	Chromatin interaction
ENSG00000135482	Chromatin interaction
ENSG00000229117	Chromatin interaction
ENSG00000257411	Chromatin interaction
ENSG00000258345	Chromatin interaction
ENSG00000065361	Chromatin interaction

Extended variants
information (count: 79 )
Associated
traits (count: 8 )

rSNPs within LD-proxies of this variant (count:74)

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];0.98[EUR][1000 genomes]
rs1274494	1.00[CHD][hapmap];0.85[MEX][hapmap]
rs12810011	0.98[EUR][1000 genomes]
rs12815302	0.93[EUR][1000 genomes]
rs12815387	1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[TSI][hapmap];0.91[EUR][1000 genomes]
rs12815488	0.98[EUR][1000 genomes]
rs12817471	0.83[EUR][1000 genomes]
rs12818756	0.98[EUR][1000 genomes]
rs12831468	0.98[EUR][1000 genomes]
rs12831884	1.00[CEU][hapmap]
rs1614219	0.90[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1626158	1.00[ASN][1000 genomes]
rs1689511	1.00[CEU][hapmap];0.91[YRI][hapmap];0.88[AFR][1000 genomes];0.89[AMR][1000 genomes];0.96[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];0.83[AFR][1000 genomes];0.94[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs1702876	0.81[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	0.98[EUR][1000 genomes]
rs2131569	0.91[EUR][1000 genomes]
rs2271192	1.00[CHD][hapmap]
rs2271193	1.00[ASN][1000 genomes]
rs2271195	1.00[ASN][1000 genomes]
rs2277340	1.00[ASN][1000 genomes]
rs2640566	1.00[ASN][1000 genomes]
rs2658479	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]
rs2661728	1.00[ASN][1000 genomes]
rs2661729	1.00[ASN][1000 genomes]
rs2934152	1.00[ASN][1000 genomes]
rs34228181	0.98[EUR][1000 genomes]
rs34303864	0.98[EUR][1000 genomes]
rs34406511	0.98[EUR][1000 genomes]
rs34485293	0.89[EUR][1000 genomes]
rs34507011	0.89[EUR][1000 genomes]
rs34602183	0.94[EUR][1000 genomes]
rs34650555	0.98[EUR][1000 genomes]
rs34921584	0.98[EUR][1000 genomes]
rs35485002	0.94[EUR][1000 genomes]
rs35662491	0.84[EUR][1000 genomes]
rs35666826	0.87[EUR][1000 genomes]
rs35961650	0.96[EUR][1000 genomes]
rs4759022	1.00[CEU][hapmap];0.98[EUR][1000 genomes]
rs4759218	1.00[CHD][hapmap];0.85[MEX][hapmap]
rs4759239	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs71459334	0.98[EUR][1000 genomes]
rs71459336	0.96[EUR][1000 genomes]
rs71459339	0.98[EUR][1000 genomes]
rs71459342	0.87[EUR][1000 genomes]
rs7298818	0.92[EUR][1000 genomes]
rs7300292	1.00[ASN][1000 genomes]
rs7300772	0.96[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7304690	1.00[ASN][1000 genomes]
rs7311008	1.00[CHD][hapmap]
rs73338377	1.00[ASN][1000 genomes]
rs73338385	1.00[ASN][1000 genomes]
rs73338396	0.87[ASN][1000 genomes]
rs772919	0.92[AFR][1000 genomes];0.91[EUR][1000 genomes]
rs772922	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHD][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];0.88[AFR][1000 genomes];0.94[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs772923	1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[TSI][hapmap];0.91[EUR][1000 genomes]
rs773115	0.87[AFR][1000 genomes];0.94[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7963590	0.87[EUR][1000 genomes]
rs7970035	1.00[ASN][1000 genomes]
rs7977537	0.93[EUR][1000 genomes]
rs9738143	1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 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
5	nsv1067906	chr12:56424828-56445284	Enhancers Genic enhancers Strong transcription Flanking Active TSS Transcr. at gene 5' and 3' Weak transcription ZNF genes & repeats Active TSS Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	57 gene(s)	inside rSNPs	diseases

mRNA abundance (count:8)

SNP	Gene	Cis/trans	Tissue	Source
rs2456972	LOC644934	trans	multi-tissue	Pritchard
rs2456972	RPS26	cis	lymphoblastoid	seeQTL
rs2456972	RPS26P10	trans	multi-tissue	Pritchard
rs2456972	RDH5	cis	lymphoblastoid	seeQTL
rs2456972	LOC441502	trans	multi-tissue	Pritchard
rs2456972	RPS26	cis	multi-tissue	Pritchard
rs2456972	CCDC4	trans	multi-tissue	Pritchard
rs2456972	LOC441377	trans	multi-tissue	Pritchard

Chromatin state (count:31 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:56437000-56447200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
2	chr12:56437000-56472800	Weak transcription	Right Atrium	heart
3	chr12:56437800-56450000	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
4	chr12:56439600-56443600	Weak transcription	Adipose Nuclei	Adipose
5	chr12:56439600-56443800	Weak transcription	NHDF-Ad	bronchial
6	chr12:56439600-56447200	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
7	chr12:56439600-56448800	Weak transcription	HSMMtube	muscle
8	chr12:56439600-56449600	Weak transcription	Placenta Amnion	Placenta Amnion
9	chr12:56439800-56448600	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
10	chr12:56440000-56445400	Weak transcription	Placenta	Placenta
11	chr12:56440000-56448600	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
12	chr12:56440200-56446000	Weak transcription	HSMM	muscle
13	chr12:56440400-56443000	Weak transcription	Brain Germinal Matrix	brain
14	chr12:56440400-56443600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
15	chr12:56440400-56445600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
16	chr12:56440400-56448600	Weak transcription	HMEC	breast
17	chr12:56440600-56448400	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
18	chr12:56440600-56448600	Weak transcription	A549	lung
19	chr12:56440800-56442800	Weak transcription	Fetal Stomach	stomach
20	chr12:56440800-56444400	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
21	chr12:56440800-56454000	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
22	chr12:56440800-56455600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
23	chr12:56441000-56443200	Weak transcription	GM12878-XiMat	blood
24	chr12:56441000-56443800	Weak transcription	Fetal Intestine Small	intestine
25	chr12:56441000-56445000	Weak transcription	Primary T helper cells PMA-I stimulated	--
26	chr12:56441000-56446400	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
27	chr12:56441000-56448400	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
28	chr12:56441200-56442800	Enhancers	HepG2	liver
29	chr12:56441200-56444200	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
30	chr12:56441200-56448600	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
31	chr12:56442600-56442800	Active TSS	Brain Inferior Temporal Lobe	brain

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