Variant report

Variant	rs10506869
Chromosome Location	chr12:82744981-82744982
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr12:82738205..82740436-chr12:82743409..82745352,2	MCF-7	breast:
2	chr12:82738128..82740375-chr12:82744468..82746353,2	MCF-7	breast:
3	chr12:82728460..82730073-chr12:82743111..82745513,2	K562	blood:
4	chr12:82724986..82727041-chr12:82743079..82745860,3	K562	blood:
5	chr12:82741804..82746481-chr12:82748884..82753039,9	MCF-7	breast:

Variant related genes	Relation type
ENSG00000127720	Chromatin interaction
ENSG00000133773	Chromatin interaction

Extended variants
information (count: 130 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:122)

rs_ID	r²[population]
rs10506872	1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs10506873	1.00[CHB][hapmap];1.00[GIH][hapmap];1.00[ASN][1000 genomes]
rs10735453	0.85[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[GIH][hapmap];0.93[LWK][hapmap];1.00[MEX][hapmap];0.98[MKK][hapmap];1.00[TSI][hapmap];0.95[YRI][hapmap];0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10746241	0.82[YRI][hapmap];0.89[AFR][1000 genomes]
rs10746242	0.92[CEU][hapmap];1.00[CHB][hapmap];0.89[YRI][hapmap];0.81[AFR][1000 genomes];0.89[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10746244	0.85[ASW][hapmap];0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[GIH][hapmap];0.86[LWK][hapmap];0.86[MEX][hapmap];0.89[MKK][hapmap];0.90[TSI][hapmap];0.89[YRI][hapmap];0.89[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10746245	0.92[CEU][hapmap];1.00[CHB][hapmap];0.89[YRI][hapmap];0.84[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10778888	0.89[AFR][1000 genomes];0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10778889	1.00[CHB][hapmap];0.90[LWK][hapmap];0.85[MEX][hapmap];0.97[MKK][hapmap];0.89[TSI][hapmap];0.95[YRI][hapmap];0.88[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs10778895	0.81[AFR][1000 genomes];0.89[AMR][1000 genomes];0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10778902	0.81[AFR][1000 genomes];0.89[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10778908	1.00[CHB][hapmap]
rs10862480	0.81[AFR][1000 genomes];0.89[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10862482	0.92[CEU][hapmap];1.00[CHB][hapmap];0.89[YRI][hapmap];0.82[AFR][1000 genomes];0.89[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11115234	1.00[ASN][1000 genomes]
rs11115240	1.00[ASN][1000 genomes]
rs11115241	1.00[ASN][1000 genomes]
rs11115242	1.00[ASN][1000 genomes]
rs11831879	0.80[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11835324	1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs11836773	1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs1494023	0.85[ASW][hapmap];0.92[CEU][hapmap];1.00[CHB][hapmap];0.92[GIH][hapmap];0.85[LWK][hapmap];0.86[MEX][hapmap];0.82[MKK][hapmap];0.90[TSI][hapmap];0.89[YRI][hapmap];0.84[AMR][1000 genomes];0.80[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1494024	0.92[CEU][hapmap];1.00[CHB][hapmap];0.89[YRI][hapmap];0.84[AMR][1000 genomes];0.80[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1494027	1.00[CHB][hapmap]
rs17711838	1.00[ASN][1000 genomes]
rs17712868	1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs17712927	1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs17719063	1.00[CHB][hapmap];1.00[GIH][hapmap];1.00[ASN][1000 genomes]
rs17719970	1.00[ASN][1000 genomes]
rs17720305	1.00[ASN][1000 genomes]
rs17773938	0.91[CEU][hapmap];1.00[CHB][hapmap];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17774157	1.00[CHB][hapmap];1.00[GIH][hapmap];1.00[ASN][1000 genomes]
rs17774489	1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs17774872	1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs17775025	1.00[ASN][1000 genomes]
rs17775169	1.00[CHB][hapmap];1.00[GIH][hapmap];1.00[ASN][1000 genomes]
rs17776036	1.00[ASN][1000 genomes]
rs17776290	1.00[ASN][1000 genomes]
rs17776375	1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs2401034	0.85[ASW][hapmap];0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[GIH][hapmap];0.86[LWK][hapmap];0.86[MEX][hapmap];0.81[MKK][hapmap];0.90[TSI][hapmap];0.89[YRI][hapmap];0.84[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2401035	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[GIH][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.98[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.99[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2642010	0.85[ASW][hapmap];0.92[CEU][hapmap];1.00[CHB][hapmap];0.92[GIH][hapmap];0.85[LWK][hapmap];0.86[MEX][hapmap];0.82[MKK][hapmap];0.90[TSI][hapmap];0.89[YRI][hapmap];1.00[ASN][1000 genomes]
rs2717446	0.85[ASW][hapmap];0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[GIH][hapmap];0.86[LWK][hapmap];0.86[MEX][hapmap];0.81[MKK][hapmap];0.90[TSI][hapmap];0.89[YRI][hapmap];0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2731287	0.80[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2895914	0.84[ASW][hapmap];0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[GIH][hapmap];0.83[LWK][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.89[YRI][hapmap];0.88[AFR][1000 genomes];0.92[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2896434	1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs34638401	1.00[ASN][1000 genomes]
rs34775923	1.00[ASN][1000 genomes]
rs4143188	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[GIH][hapmap];0.90[TSI][hapmap];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4143189	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[GIH][hapmap];0.90[TSI][hapmap];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4319577	0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4411333	0.91[CEU][hapmap];1.00[CHB][hapmap];0.88[YRI][hapmap];0.84[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4491327	1.00[ASN][1000 genomes]
rs4495950	0.85[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[GIH][hapmap];0.93[LWK][hapmap];0.98[MKK][hapmap];1.00[TSI][hapmap];0.90[YRI][hapmap];0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4544081	1.00[CHB][hapmap]
rs4882453	0.84[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4882526	0.89[AFR][1000 genomes];0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4882527	0.89[AFR][1000 genomes];0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4882528	0.88[AFR][1000 genomes];0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4882530	0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs57418508	0.80[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6539659	0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6539662	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[YRI][hapmap];0.90[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7138488	1.00[CHB][hapmap];1.00[GIH][hapmap];1.00[ASN][1000 genomes]
rs7294780	1.00[ASN][1000 genomes]
rs7294918	1.00[ASN][1000 genomes]
rs7295042	1.00[ASN][1000 genomes]
rs7295566	1.00[ASN][1000 genomes]
rs7304084	0.92[CEU][hapmap];1.00[CHB][hapmap];0.89[YRI][hapmap];0.84[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7311246	0.85[ASW][hapmap];0.92[CEU][hapmap];1.00[CHB][hapmap];0.92[GIH][hapmap];0.85[LWK][hapmap];0.86[MEX][hapmap];0.82[MKK][hapmap];0.90[TSI][hapmap];0.89[YRI][hapmap];0.84[AMR][1000 genomes];0.80[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73149542	1.00[ASN][1000 genomes]
rs73149557	0.81[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73149567	1.00[ASN][1000 genomes]
rs73149577	1.00[ASN][1000 genomes]
rs73149595	1.00[ASN][1000 genomes]
rs73149597	1.00[ASN][1000 genomes]
rs73151403	1.00[ASN][1000 genomes]
rs73151413	1.00[ASN][1000 genomes]
rs73151422	1.00[ASN][1000 genomes]
rs73151425	1.00[ASN][1000 genomes]
rs73151445	1.00[ASN][1000 genomes]
rs73151447	1.00[ASN][1000 genomes]
rs73151450	1.00[ASN][1000 genomes]
rs73151460	1.00[ASN][1000 genomes]
rs73151484	1.00[ASN][1000 genomes]
rs73151489	1.00[ASN][1000 genomes]
rs73151496	1.00[ASN][1000 genomes]
rs73153504	1.00[ASN][1000 genomes]
rs73153509	1.00[ASN][1000 genomes]
rs73153526	1.00[ASN][1000 genomes]
rs73153530	1.00[ASN][1000 genomes]
rs73153534	1.00[ASN][1000 genomes]
rs73153539	1.00[ASN][1000 genomes]
rs73153551	1.00[ASN][1000 genomes]
rs73153559	1.00[ASN][1000 genomes]
rs73153561	1.00[ASN][1000 genomes]
rs73153569	1.00[ASN][1000 genomes]
rs73153571	1.00[ASN][1000 genomes]
rs73153572	1.00[ASN][1000 genomes]
rs73153573	1.00[ASN][1000 genomes]
rs73153577	1.00[ASN][1000 genomes]
rs73153578	1.00[ASN][1000 genomes]
rs73153584	1.00[ASN][1000 genomes]
rs73153585	1.00[ASN][1000 genomes]
rs73153587	1.00[ASN][1000 genomes]
rs73153588	0.84[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs73153590	0.84[AMR][1000 genomes];0.80[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73153592	0.84[AMR][1000 genomes];0.80[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73153599	0.80[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73155404	0.80[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73155406	1.00[ASN][1000 genomes]
rs73155441	1.00[ASN][1000 genomes]
rs7488252	0.90[CEU][hapmap];0.88[YRI][hapmap];0.84[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7956163	0.84[AMR][1000 genomes];0.80[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7957993	1.00[ASN][1000 genomes]
rs7960966	1.00[ASN][1000 genomes]
rs7964174	1.00[ASN][1000 genomes]
rs7966041	0.80[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7967097	0.80[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7968024	0.84[AMR][1000 genomes];0.80[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7971746	0.80[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7977442	0.85[ASW][hapmap];0.92[GIH][hapmap];0.81[LWK][hapmap];0.91[MKK][hapmap];0.90[TSI][hapmap];0.84[YRI][hapmap]

Variant overlapped rSNPs/rCNVs (count:8 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv559539	chr12:82280797-82896218	Genic enhancers Enhancers Strong transcription Weak transcription Active TSS Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases
2	nsv1041954	chr12:82314981-83008609	Enhancers Active TSS Genic enhancers Weak transcription Strong transcription Bivalent Enhancer ZNF genes & repeats Flanking Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases
3	nsv541550	chr12:82314981-83008609	Enhancers Strong transcription Active TSS Weak transcription Flanking Active TSS Genic enhancers ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases
4	nsv832471	chr12:82578953-82755360	Enhancers Weak transcription Strong transcription Flanking Active TSS Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Genic enhancers ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region	5 gene(s)	inside rSNPs	diseases
5	nsv1053093	chr12:82645292-83287809	Enhancers Weak transcription Genic enhancers Flanking Active TSS Active TSS Strong transcription ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	21 gene(s)	inside rSNPs	diseases
6	nsv541551	chr12:82645292-83287809	Weak transcription Enhancers Strong transcription Active TSS ZNF genes & repeats Flanking Active TSS Transcr. at gene 5' and 3' Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	21 gene(s)	inside rSNPs	diseases
7	nsv559541	chr12:82715210-83108395	Weak transcription Flanking Active TSS Strong transcription Enhancers Active TSS Bivalent Enhancer Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	19 gene(s)	inside rSNPs	diseases
8	nsv899348	chr12:82744187-83169297	Enhancers Strong transcription Bivalent Enhancer Weak transcription Active TSS Flanking Active TSS Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	19 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs10506869	C12orf26	cis	cerebellum	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:82735400-82745200	Weak transcription	Brain Cingulate Gyrus	brain
2	chr12:82736800-82745000	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
3	chr12:82738400-82745200	Weak transcription	Primary hematopoietic stem cells	blood
4	chr12:82739600-82745000	Weak transcription	Ovary	ovary
5	chr12:82740000-82746000	Weak transcription	Fetal Lung	lung
6	chr12:82740200-82745000	Weak transcription	A549	lung
7	chr12:82740200-82745200	Weak transcription	Rectal Mucosa Donor 31	rectum
8	chr12:82740200-82745200	Weak transcription	HSMM	muscle
9	chr12:82740200-82745400	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
10	chr12:82740200-82751600	Weak transcription	Gastric	stomach
11	chr12:82740800-82745000	Weak transcription	Fetal Stomach	stomach
12	chr12:82740800-82750000	Weak transcription	Fetal Intestine Small	intestine
13	chr12:82740800-82750000	Weak transcription	Psoas Muscle	Psoas
14	chr12:82741000-82745200	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
15	chr12:82741000-82749400	Weak transcription	Fetal Brain Male	brain
16	chr12:82741200-82745000	Weak transcription	Fetal Intestine Large	intestine
17	chr12:82741200-82745000	Weak transcription	Thymus	Thymus
18	chr12:82741200-82751000	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
19	chr12:82741400-82747000	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
20	chr12:82741400-82749400	Weak transcription	Primary T killer memory cells from peripheral blood	blood
21	chr12:82741600-82749200	Strong transcription	Adipose Nuclei	Adipose
22	chr12:82741600-82749800	Strong transcription	Primary T cells from cord blood	blood
23	chr12:82741800-82745000	Weak transcription	Primary neutrophils fromperipheralblood	blood
24	chr12:82741800-82745200	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
25	chr12:82741800-82747800	Strong transcription	Brain Hippocampus Middle	brain
26	chr12:82742000-82745000	Weak transcription	Fetal Kidney	kidney
27	chr12:82742000-82745000	Weak transcription	GM12878-XiMat	blood
28	chr12:82742000-82745200	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
29	chr12:82742000-82745200	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
30	chr12:82742000-82745200	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
31	chr12:82742000-82749400	Strong transcription	Liver	Liver
32	chr12:82742000-82750000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
33	chr12:82742200-82745200	Weak transcription	HUES6 Cell Line	embryonic stem cell
34	chr12:82742200-82745400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
35	chr12:82742200-82747200	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
36	chr12:82742200-82749400	Strong transcription	Duodenum Smooth Muscle	Duodenum
37	chr12:82742400-82745000	Weak transcription	Primary monocytes fromperipheralblood	blood
38	chr12:82742400-82745200	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
39	chr12:82742400-82750000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
40	chr12:82742400-82750000	Strong transcription	Rectal Mucosa Donor 29	rectum
41	chr12:82742600-82745200	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
42	chr12:82742600-82745200	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
43	chr12:82742600-82745200	Weak transcription	Dnd41	blood
44	chr12:82742600-82745600	Weak transcription	Cortex derived primary cultured neurospheres	brain
45	chr12:82742600-82747800	Strong transcription	Stomach Smooth Muscle	stomach
46	chr12:82742600-82748600	Weak transcription	Rectal Smooth Muscle	rectum
47	chr12:82742600-82749200	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
48	chr12:82742600-82750800	Weak transcription	H9 Cell Line	embryonic stem cell
49	chr12:82742600-82751400	Weak transcription	Aorta	Aorta
50	chr12:82742600-82751600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived

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