Variant report

Variant	rs12809473
Chromosome Location	chr12:124476599-124476600
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr12:124457604..124459142-chr12:124475055..124476708,2	MCF-7	breast:
2	chr12:124469541..124471956-chr12:124474758..124478951,5	K562	blood:
3	chr12:124433267..124435422-chr12:124476091..124477918,2	K562	blood:
4	chr12:124455649..124457478-chr12:124476003..124477748,2	K562	blood:
5	chr12:124474945..124477651-chr12:124481965..124484404,2	K562	blood:

Variant related genes	Relation type
ENSG00000270095	Chromatin interaction
ENSG00000178882	Chromatin interaction
ENSG00000119242	Chromatin interaction
ENSG00000179195	Chromatin interaction

Extended variants
information (count: 99 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:95)

rs_ID	r²[population]
rs1054852	0.80[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[ASN][1000 genomes]
rs10773048	0.88[CHB][hapmap]
rs10846579	0.96[CEU][hapmap];0.93[EUR][1000 genomes]
rs10846580	1.00[CEU][hapmap];0.95[EUR][1000 genomes]
rs11057393	0.90[EUR][1000 genomes]
rs11057394	0.96[CEU][hapmap];0.93[EUR][1000 genomes]
rs11057396	1.00[CEU][hapmap];0.85[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs11057397	1.00[CEU][hapmap];0.85[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs11057399	0.90[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs11057400	0.85[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs11057401	0.92[CEU][hapmap];1.00[CHB][hapmap];0.86[AMR][1000 genomes];0.89[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs11057407	1.00[CHB][hapmap];0.86[AMR][1000 genomes];0.89[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs11057408	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[YRI][hapmap];0.93[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11057409	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11057412	0.96[CEU][hapmap];0.85[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11057413	0.90[AFR][1000 genomes];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11831913	0.88[CEU][hapmap];1.00[CHB][hapmap];0.80[JPT][hapmap];0.86[AMR][1000 genomes];0.87[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs11833002	0.84[AMR][1000 genomes];0.96[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs11835839	0.81[AMR][1000 genomes];0.95[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs11837287	1.00[CEU][hapmap];0.89[CHB][hapmap];0.85[JPT][hapmap];0.81[YRI][hapmap];0.95[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1187415	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12296259	0.85[AMR][1000 genomes];0.95[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs12298484	1.00[CEU][hapmap];0.85[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs12301673	0.80[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs12303671	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12303933	0.90[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12310367	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[YRI][hapmap];0.93[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12311114	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.80[YRI][hapmap];0.88[AMR][1000 genomes];0.90[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12311848	0.93[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12316080	0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs12317176	0.96[CEU][hapmap];0.91[EUR][1000 genomes]
rs12809125	0.96[CEU][hapmap];0.93[EUR][1000 genomes]
rs12823740	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs12824567	0.88[CEU][hapmap];1.00[CHB][hapmap];0.91[JPT][hapmap];0.81[YRI][hapmap];0.86[AMR][1000 genomes];0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12827409	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][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]
rs12829951	0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs12833624	0.88[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1882491	0.88[AMR][1000 genomes];0.87[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2130382	0.92[CEU][hapmap];0.82[YRI][hapmap];0.90[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2178663	0.92[CEU][hapmap];1.00[CHB][hapmap];0.88[AMR][1000 genomes];0.88[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs3186071	0.85[AMR][1000 genomes];0.89[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs34102591	0.98[ASN][1000 genomes]
rs34114498	0.85[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34180676	0.84[AMR][1000 genomes];0.87[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs34854841	0.86[AMR][1000 genomes];0.90[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs34878139	0.84[AMR][1000 genomes];0.96[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs35099862	0.94[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35825716	0.85[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs3789967	0.83[AMR][1000 genomes];0.94[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs3802999	1.00[CEU][hapmap];0.85[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs4405410	0.96[CEU][hapmap];1.00[CHB][hapmap];0.80[JPT][hapmap];0.85[YRI][hapmap];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs4575361	0.86[EUR][1000 genomes]
rs4765127	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[YRI][hapmap];0.92[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4765148	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[YRI][hapmap];0.84[AFR][1000 genomes];0.91[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4765219	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs4765305	0.80[AMR][1000 genomes];0.95[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs4765335	0.87[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs4765528	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4765541	0.85[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4765562	0.87[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4765568	1.00[CHB][hapmap];1.00[JPT][hapmap];0.98[ASN][1000 genomes]
rs4930721	0.87[CEU][hapmap];0.88[EUR][1000 genomes]
rs4930722	0.85[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs4930723	1.00[CEU][hapmap];1.00[CHB][hapmap];0.91[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs4930724	0.92[CEU][hapmap];1.00[CHB][hapmap];0.90[EUR][1000 genomes]
rs4930725	0.88[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs4930726	1.00[CEU][hapmap];1.00[CHB][hapmap];0.80[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs55990776	0.90[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs56041971	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6488912	0.83[AMR][1000 genomes];0.96[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs6488913	1.00[CEU][hapmap];0.96[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs6488914	0.92[CEU][hapmap];1.00[CHB][hapmap];0.88[AMR][1000 genomes];0.89[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs7131882	0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs7132655	1.00[CEU][hapmap];1.00[CHB][hapmap];0.80[JPT][hapmap];0.89[YRI][hapmap];0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs7133378	0.92[CEU][hapmap];0.83[EUR][1000 genomes]
rs7134121	0.81[AFR][1000 genomes];0.94[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs7135314	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs71458830	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7301953	0.88[CEU][hapmap];0.85[EUR][1000 genomes]
rs7305864	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs7307053	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[AMR][1000 genomes];0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7307277	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.99[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7311233	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[YRI][hapmap];0.85[AFR][1000 genomes];0.91[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7311969	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7312404	1.00[CEU][hapmap];1.00[CHB][hapmap];0.84[YRI][hapmap];0.81[AFR][1000 genomes];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs7955815	0.86[AMR][1000 genomes];0.88[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs7958691	1.00[CEU][hapmap];0.85[AMR][1000 genomes];0.95[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs7961449	0.96[CEU][hapmap];1.00[CHB][hapmap];0.95[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs7966192	0.80[AMR][1000 genomes];0.95[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs7973683	1.00[CEU][hapmap];1.00[CHB][hapmap];0.85[AMR][1000 genomes];0.96[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs7975482	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[YRI][hapmap];0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7978610	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[YRI][hapmap];0.94[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs952632	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[YRI][hapmap];0.95[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9863	0.80[CEU][hapmap];0.83[EUR][1000 genomes]
rs9971695	1.00[CEU][hapmap];0.94[EUR][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	esv3493374	chr12:124458433-124496012	Strong transcription Enhancers Weak transcription Flanking Active TSS Active TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases
2	esv3493363	chr12:124458497-124495976	Strong transcription Genic enhancers Weak transcription Active TSS Enhancers Flanking Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases
3	esv3493385	chr12:124458565-124495928	Enhancers Flanking Active TSS Strong transcription Weak transcription Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases
4	esv1818097	chr12:124465667-124488972	Enhancers Weak transcription Genic enhancers Strong transcription Flanking Active TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs12809473	RP11-380L11.4	cis	Esophagus Muscularis	GTEx
rs12809473	CCDC92	cis	Heart Left Ventricle	GTEx

Chromatin state (count:124 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:124459200-124477000	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
2	chr12:124459200-124477200	Weak transcription	Placenta Amnion	Placenta Amnion
3	chr12:124460400-124479800	Weak transcription	Primary T killer memory cells from peripheral blood	blood
4	chr12:124461200-124496800	Weak transcription	H1 Cell Line	embryonic stem cell
5	chr12:124466000-124477800	Strong transcription	Fetal Stomach	stomach
6	chr12:124469000-124483000	Weak transcription	Ovary	ovary
7	chr12:124469000-124492600	Weak transcription	iPS-15b Cell Line	embryonic stem cell
8	chr12:124469400-124479600	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
9	chr12:124470000-124478800	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
10	chr12:124470200-124478400	Strong transcription	Hela-S3	cervix
11	chr12:124470800-124490200	Weak transcription	Primary T helper naive cells from peripheral blood	blood
12	chr12:124471000-124478200	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
13	chr12:124471000-124478600	Strong transcription	Primary T cells from cord blood	blood
14	chr12:124471600-124478400	Strong transcription	Primary T helper cells fromperipheralblood	blood
15	chr12:124471600-124478600	Strong transcription	Dnd41	blood
16	chr12:124471800-124477800	Strong transcription	Brain Germinal Matrix	brain
17	chr12:124471800-124480400	Weak transcription	Fetal Brain Male	brain
18	chr12:124472000-124478000	Strong transcription	Primary T helper cells PMA-I stimulated	--
19	chr12:124472000-124478200	Strong transcription	Fetal Muscle Trunk	muscle
20	chr12:124472000-124478200	Strong transcription	Stomach Smooth Muscle	stomach
21	chr12:124472000-124478400	Strong transcription	Primary monocytes fromperipheralblood	blood
22	chr12:124472200-124477200	Strong transcription	GM12878-XiMat	blood
23	chr12:124472200-124478200	Strong transcription	Primary T cells fromperipheralblood	blood
24	chr12:124472200-124478200	Strong transcription	A549	lung
25	chr12:124472200-124478800	Strong transcription	Primary B cells from peripheral blood	blood
26	chr12:124472400-124477400	Strong transcription	Primary T helper naive cells fromperipheralblood	blood
27	chr12:124472600-124477800	Strong transcription	Duodenum Smooth Muscle	Duodenum
28	chr12:124472600-124478600	Strong transcription	Fetal Brain Female	brain
29	chr12:124472600-124478600	Strong transcription	Thymus	Thymus
30	chr12:124472800-124477800	Strong transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
31	chr12:124473400-124477800	Strong transcription	Brain Dorsolateral Prefrontal Cortex	brain
32	chr12:124473400-124477800	Enhancers	Right Ventricle	heart
33	chr12:124473600-124478400	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
34	chr12:124473800-124476800	Weak transcription	HUES6 Cell Line	embryonic stem cell
35	chr12:124473800-124478600	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
36	chr12:124474000-124476600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
37	chr12:124474000-124476800	Enhancers	Fetal Intestine Small	intestine
38	chr12:124474000-124479800	Weak transcription	Esophagus	oesophagus
39	chr12:124474200-124476600	Genic enhancers	K562	blood
40	chr12:124474200-124477000	Enhancers	Adipose Nuclei	Adipose
41	chr12:124474200-124480400	Weak transcription	HUES64 Cell Line	embryonic stem cell
42	chr12:124474400-124476600	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
43	chr12:124474400-124477400	Weak transcription	iPS-20b Cell Line	embryonic stem cell
44	chr12:124474400-124477400	Enhancers	Osteobl	bone
45	chr12:124474400-124478600	Genic enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
46	chr12:124474400-124480200	Weak transcription	iPS-18 Cell Line	embryonic stem cell
47	chr12:124474400-124490400	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
48	chr12:124474600-124478400	Genic enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
49	chr12:124474600-124479400	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
50	chr12:124474600-124484800	Weak transcription	Fetal Kidney	kidney

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