Variant report

Variant	rs10746245
Chromosome Location	chr12:82800847-82800848
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr12:82750490..82752640-chr12:82799108..82801602,2	MCF-7	breast:
2	chr12:82795159..82796748-chr12:82799968..82802561,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000133773	Chromatin interaction
ENSG00000127720	Chromatin interaction

Extended variants
information (count: 141 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:133)

rs_ID	r²[population]
rs10506869	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]
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];0.85[AFR][1000 genomes];0.84[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10735454	0.84[YRI][hapmap]
rs10746242	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]
rs10746244	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	0.84[AFR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10778889	1.00[CHB][hapmap];0.95[YRI][hapmap];0.83[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs10778895	0.94[AFR][1000 genomes];0.94[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10778902	0.94[AFR][1000 genomes];0.94[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10778908	1.00[CHB][hapmap]
rs10862480	0.94[AFR][1000 genomes];0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10862482	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[YRI][hapmap];0.91[AFR][1000 genomes];0.94[AMR][1000 genomes];0.95[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]
rs11115308	1.00[ASN][1000 genomes]
rs11831879	0.94[AMR][1000 genomes];0.89[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];1.00[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1494024	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[YRI][hapmap];1.00[AMR][1000 genomes];0.89[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];0.85[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];0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2401035	0.92[CEU][hapmap];1.00[CHB][hapmap];0.90[YRI][hapmap];0.86[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2642010	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[YRI][hapmap];0.94[AMR][1000 genomes];0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2642018	0.83[YRI][hapmap]
rs2642019	0.83[YRI][hapmap]
rs2642023	0.82[YRI][hapmap]
rs2717446	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[YRI][hapmap];0.81[AFR][1000 genomes];0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2731287	0.94[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2731289	0.91[YRI][hapmap]
rs2731290	0.80[YRI][hapmap]
rs2731291	0.80[YRI][hapmap]
rs2731292	0.82[YRI][hapmap]
rs2895914	0.84[CEU][hapmap];1.00[CHB][hapmap];0.85[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];0.85[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4143189	1.00[CEU][hapmap];1.00[CHB][hapmap];0.85[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4319577	0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4411333	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[YRI][hapmap];0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[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];0.85[AFR][1000 genomes];0.84[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4544081	1.00[CHB][hapmap]
rs4882453	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4882526	0.84[AFR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4882527	0.84[AFR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4882528	0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4882530	0.86[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs57418508	0.94[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6539659	1.00[ASN][1000 genomes]
rs6539662	0.92[CEU][hapmap];1.00[CHB][hapmap];0.96[YRI][hapmap];0.85[AFR][1000 genomes];0.86[AMR][1000 genomes];0.91[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]
rs7304084	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7306421	1.00[ASN][1000 genomes]
rs7311246	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[YRI][hapmap];1.00[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73149542	1.00[ASN][1000 genomes]
rs73149557	0.85[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	1.00[AMR][1000 genomes];0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73153590	1.00[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73153592	1.00[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73153599	0.94[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73155404	0.94[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73155406	1.00[ASN][1000 genomes]
rs73155441	0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7488252	1.00[CEU][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7956163	1.00[AMR][1000 genomes];0.89[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	0.94[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7967097	0.94[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7968024	1.00[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7971746	0.94[AMR][1000 genomes];0.89[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	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
5	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
6	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
7	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
8	esv1841396	chr12:82768717-82881082	Strong transcription Flanking Active TSS Enhancers ZNF genes & repeats Weak transcription Active TSS Genic enhancers	TF binding region Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs10746245	RP11-263K4.3	cis	Thyroid	GTEx

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:82753600-82805200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
2	chr12:82753800-82804800	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
3	chr12:82754000-82804600	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
4	chr12:82754200-82803600	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
5	chr12:82754400-82804000	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
6	chr12:82755600-82802200	Weak transcription	Pancreas	Pancrea
7	chr12:82758400-82835600	Weak transcription	Psoas Muscle	Psoas
8	chr12:82764000-82801400	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
9	chr12:82768400-82811600	Weak transcription	Fetal Stomach	stomach
10	chr12:82769200-82804400	Weak transcription	Skeletal Muscle Female	skeletal muscle
11	chr12:82769200-82809200	Weak transcription	Lung	lung
12	chr12:82779800-82808000	Weak transcription	Brain Hippocampus Middle	brain
13	chr12:82780000-82801000	Weak transcription	Fetal Heart	heart
14	chr12:82780200-82802000	Weak transcription	Brain Inferior Temporal Lobe	brain
15	chr12:82780400-82810800	Weak transcription	Fetal Brain Male	brain
16	chr12:82780800-82803200	Weak transcription	GM12878-XiMat	blood
17	chr12:82782200-82806200	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
18	chr12:82782400-82805400	Weak transcription	HSMM	muscle
19	chr12:82783000-82801000	Weak transcription	Duodenum Mucosa	Duodenum
20	chr12:82783000-82805000	Weak transcription	Primary hematopoietic stem cells	blood
21	chr12:82783000-82813200	Weak transcription	Gastric	stomach
22	chr12:82783000-82838000	Weak transcription	Sigmoid Colon	Sigmoid Colon
23	chr12:82783200-82811800	Weak transcription	Fetal Lung	lung
24	chr12:82785000-82801000	Weak transcription	Left Ventricle	heart
25	chr12:82785000-82803200	Weak transcription	Primary hematopoietic stem cells short term culture	blood
26	chr12:82785000-82805600	Weak transcription	Stomach Smooth Muscle	stomach
27	chr12:82786600-82803000	Weak transcription	Fetal Intestine Large	intestine
28	chr12:82787400-82805400	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
29	chr12:82789200-82833800	Weak transcription	Primary T helper cells PMA-I stimulated	--
30	chr12:82789400-82801000	Weak transcription	Primary T cells from cord blood	blood
31	chr12:82789600-82801400	Weak transcription	Breast Myoepithelial Primary Cells	Breast
32	chr12:82791000-82806400	Weak transcription	Brain Anterior Caudate	brain
33	chr12:82791200-82852000	Weak transcription	Duodenum Smooth Muscle	Duodenum
34	chr12:82793400-82812800	Weak transcription	Rectal Mucosa Donor 31	rectum
35	chr12:82793400-82834400	Weak transcription	Liver	Liver
36	chr12:82793600-82802600	Weak transcription	Rectal Mucosa Donor 29	rectum
37	chr12:82793600-82804600	Weak transcription	Primary monocytes fromperipheralblood	blood
38	chr12:82793600-82805200	Weak transcription	Primary T cells fromperipheralblood	blood
39	chr12:82793600-82813200	Weak transcription	Primary B cells from peripheral blood	blood
40	chr12:82793600-82833000	Weak transcription	Primary T helper cells fromperipheralblood	blood
41	chr12:82793600-82833200	Weak transcription	Primary B cells from cord blood	blood
42	chr12:82793800-82809000	Weak transcription	Adipose Nuclei	Adipose
43	chr12:82797800-82801400	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
44	chr12:82799000-82812600	Weak transcription	Fetal Intestine Small	intestine
45	chr12:82799800-82801200	Enhancers	HUVEC	blood vessel
46	chr12:82800400-82802200	Enhancers	Aorta	Aorta
47	chr12:82800400-82802200	Enhancers	Ovary	ovary
48	chr12:82800400-82802800	Enhancers	Hela-S3	cervix
49	chr12:82800400-82802800	Strong transcription	Monocytes-CD14+_RO01746	blood
50	chr12:82800600-82801200	Enhancers	Stomach Mucosa	stomach

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