Variant report

Variant	rs10746242
Chromosome Location	chr12:82754100-82754101
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	CTCF	chr12:82750976-82754265	A549	lung:	n/a	chr12:82752664-82752682 chr12:82752667-82752677 chr12:82752861-82752869 chr12:82752670-82752679 chr12:82753648-82753656 chr12:82752666-82752679 chr12:82753645-82753666

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr12:82742903..82744608-chr12:82753963..82756367,2	K562	blood:
2	chr12:82753358..82755104-chr12:82772991..82774509,2	K562	blood:

Variant related genes	Relation type
CCDC59	TF binding region

Extended variants
information (count: 139 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:131)

rs_ID	r²[population]
rs10506869	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]
rs10506872	1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs10506873	1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs10735453	0.92[CEU][hapmap];1.00[CHB][hapmap];0.95[YRI][hapmap];0.91[AFR][1000 genomes];0.89[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10735454	0.84[YRI][hapmap]
rs10746244	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10746245	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10778888	0.90[AFR][1000 genomes];0.81[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10778889	1.00[CHB][hapmap];0.95[YRI][hapmap];0.89[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs10778895	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10778898	0.85[AMR][1000 genomes]
rs10778902	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10778908	1.00[CHB][hapmap]
rs10862480	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10862482	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[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	0.89[AMR][1000 genomes];0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11832758	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	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[YRI][hapmap];0.94[AMR][1000 genomes];0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1494024	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[YRI][hapmap];0.94[AMR][1000 genomes];0.84[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[ASN][1000 genomes]
rs17719970	1.00[ASN][1000 genomes]
rs17720305	1.00[ASN][1000 genomes]
rs17773938	0.84[CEU][hapmap];1.00[CHB][hapmap];0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17774157	1.00[CHB][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[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]
rs17776885	1.00[ASN][1000 genomes]
rs2254688	0.86[YRI][hapmap]
rs2401034	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[YRI][hapmap];0.92[AFR][1000 genomes];0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2401035	0.92[CEU][hapmap];1.00[CHB][hapmap];0.90[YRI][hapmap];0.81[AFR][1000 genomes];0.92[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2642010	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[YRI][hapmap];0.89[AMR][1000 genomes];0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2642018	0.82[YRI][hapmap]
rs2642019	0.82[YRI][hapmap]
rs2642023	0.81[YRI][hapmap]
rs2717446	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[YRI][hapmap];0.83[AFR][1000 genomes];0.89[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2731287	0.89[AMR][1000 genomes];0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2731289	0.91[YRI][hapmap]
rs2731292	0.81[YRI][hapmap]
rs2895914	0.84[CEU][hapmap];1.00[CHB][hapmap];0.81[AMR][1000 genomes];0.87[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	1.00[CEU][hapmap];1.00[CHB][hapmap];0.81[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4143189	1.00[CEU][hapmap];1.00[CHB][hapmap];0.81[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4319577	0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4411333	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[YRI][hapmap];0.88[AFR][1000 genomes];0.94[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4491327	1.00[ASN][1000 genomes]
rs4495950	0.92[CEU][hapmap];1.00[CHB][hapmap];0.90[YRI][hapmap];0.91[AFR][1000 genomes];0.89[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4544081	1.00[CHB][hapmap]
rs4882453	0.94[AFR][1000 genomes];0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4882526	0.90[AFR][1000 genomes];0.81[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4882527	0.90[AFR][1000 genomes];0.81[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4882528	0.81[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4882530	0.92[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs57418508	0.89[AMR][1000 genomes];0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6539659	0.80[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6539662	0.92[CEU][hapmap];1.00[CHB][hapmap];0.95[YRI][hapmap];0.91[AFR][1000 genomes];0.92[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7138488	1.00[CHB][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	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[YRI][hapmap];0.92[AFR][1000 genomes];0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7311246	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[YRI][hapmap];0.94[AMR][1000 genomes];0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73149542	1.00[ASN][1000 genomes]
rs73149557	0.87[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	0.94[AMR][1000 genomes];0.82[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73153590	0.94[AMR][1000 genomes];0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73153592	0.94[AMR][1000 genomes];0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73153599	0.89[AMR][1000 genomes];0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73155404	0.89[AMR][1000 genomes];0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73155406	1.00[ASN][1000 genomes]
rs73155441	0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7488252	1.00[CEU][hapmap];1.00[YRI][hapmap];0.92[AFR][1000 genomes];0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7956163	0.94[AMR][1000 genomes];0.84[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	0.89[AMR][1000 genomes];0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7967097	0.89[AMR][1000 genomes];0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7968024	0.94[AMR][1000 genomes];0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7971746	0.89[AMR][1000 genomes];0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7977442	0.95[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
rs10746242	RP11-263K4.3	cis	Thyroid	GTEx

Chromatin state (count:92 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:82751200-82754600	Active TSS	GM12878-XiMat	blood
2	chr12:82753200-82754200	Enhancers	Primary neutrophils fromperipheralblood	blood
3	chr12:82753200-82754400	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
4	chr12:82753200-82754600	Enhancers	Primary T helper naive cells fromperipheralblood	blood
5	chr12:82753200-82754800	Weak transcription	Pancreas	Pancrea
6	chr12:82753200-82755400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
7	chr12:82753200-82755400	Weak transcription	Gastric	stomach
8	chr12:82753200-82755400	Weak transcription	Spleen	Spleen
9	chr12:82753200-82756000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
10	chr12:82753200-82767200	Weak transcription	Aorta	Aorta
11	chr12:82753200-82767800	Weak transcription	Esophagus	oesophagus
12	chr12:82753200-82767800	Weak transcription	Lung	lung
13	chr12:82753400-82754200	Enhancers	Primary T helper cells PMA-I stimulated	--
14	chr12:82753400-82754200	Enhancers	Cortex derived primary cultured neurospheres	brain
15	chr12:82753400-82754400	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
16	chr12:82753400-82754400	Enhancers	Primary T helper cells fromperipheralblood	blood
17	chr12:82753400-82754400	Enhancers	Primary T killer memory cells from peripheral blood	blood
18	chr12:82753400-82754600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
19	chr12:82753400-82754600	Weak transcription	Ovary	ovary
20	chr12:82753400-82755400	Weak transcription	Hela-S3	cervix
21	chr12:82753400-82755800	Weak transcription	iPS-15b Cell Line	embryonic stem cell
22	chr12:82753400-82756800	Weak transcription	H1 Cell Line	embryonic stem cell
23	chr12:82753400-82756800	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
24	chr12:82753400-82756800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
25	chr12:82753400-82761400	Weak transcription	Brain Anterior Caudate	brain
26	chr12:82753400-82763000	Weak transcription	Primary hematopoietic stem cells	blood
27	chr12:82753400-82763200	Weak transcription	Placenta	Placenta
28	chr12:82753400-82763800	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
29	chr12:82753400-82765200	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
30	chr12:82753400-82765400	Weak transcription	Primary T cells fromperipheralblood	blood
31	chr12:82753400-82767400	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
32	chr12:82753400-82767800	Weak transcription	Sigmoid Colon	Sigmoid Colon
33	chr12:82753400-82767800	Weak transcription	Thymus	Thymus
34	chr12:82753400-82768600	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
35	chr12:82753400-82786200	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
36	chr12:82753600-82754200	Enhancers	Breast Myoepithelial Primary Cells	Breast
37	chr12:82753600-82754200	Enhancers	Brain Inferior Temporal Lobe	brain
38	chr12:82753600-82754200	Enhancers	HUVEC	blood vessel
39	chr12:82753600-82754400	Enhancers	Liver	Liver
40	chr12:82753600-82754400	Enhancers	Brain Cingulate Gyrus	brain
41	chr12:82753600-82754400	Enhancers	Brain Dorsolateral Prefrontal Cortex	brain
42	chr12:82753600-82754600	Enhancers	Brain Angular Gyrus	brain
43	chr12:82753600-82754600	Enhancers	Brain Substantia Nigra	brain
44	chr12:82753600-82754600	Enhancers	Colon Smooth Muscle	Colon
45	chr12:82753600-82754600	Enhancers	Duodenum Smooth Muscle	Duodenum
46	chr12:82753600-82755200	Weak transcription	Fetal Stomach	stomach
47	chr12:82753600-82755200	Weak transcription	Right Ventricle	heart
48	chr12:82753600-82756800	Weak transcription	iPS-20b Cell Line	embryonic stem cell
49	chr12:82753600-82758000	Weak transcription	Left Ventricle	heart
50	chr12:82753600-82758000	Weak transcription	Psoas Muscle	Psoas

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