Variant report

Variant	rs12278842
Chromosome Location	chr11:5703558-5703559
allele	C/G
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	POLR2A	chr11:5703536-5706824	IMR90	lung:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	11:5033143-5038367..11:5700314-5707362	K562	blood:
2	11:4801044-4820112..11:5700314-5707362	H1-hESC	embryonic stem cell:	embryo
3	11:4988858-5002113..11:5700314-5707362	Hela-S3	cervix:

Variant related genes	Relation type
TRIM5	TF binding region
ENSG00000231070	Chromatin interaction
ENSG00000224300	Chromatin interaction
ENSG00000176951	Chromatin interaction
ENSG00000225003	Chromatin interaction

Extended variants
information (count: 48 )
Associated
traits (count: 9 )

rSNPs within LD-proxies of this variant (count:38)

rs_ID	r²[population]
rs11038702	0.89[EUR][1000 genomes]
rs12164821	0.84[ASN][1000 genomes]
rs12285766	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12287199	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.95[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.97[MKK][hapmap];1.00[TSI][hapmap];0.92[YRI][hapmap];0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12799127	0.88[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs12799329	0.83[AFR][1000 genomes];0.89[AMR][1000 genomes];0.84[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12800585	0.81[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs12801311	0.86[AFR][1000 genomes];0.87[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1498553	0.95[CHB][hapmap];0.89[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.96[MEX][hapmap];0.92[MKK][hapmap];0.95[TSI][hapmap];0.89[AMR][1000 genomes];0.88[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1498555	0.95[CHB][hapmap];0.82[CHD][hapmap];0.84[GIH][hapmap];0.95[JPT][hapmap];0.92[ASN][1000 genomes]
rs1814722	0.96[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2133256	0.96[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2343227	0.97[AFR][1000 genomes];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2343229	0.97[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2880576	0.91[AFR][1000 genomes];0.85[AMR][1000 genomes];0.86[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs3207178	0.82[AMR][1000 genomes];0.83[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs34506684	0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34720081	0.87[AMR][1000 genomes];0.85[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs3802980	0.88[ASW][hapmap];0.82[CEU][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.96[LWK][hapmap];1.00[MEX][hapmap];0.94[MKK][hapmap];0.95[TSI][hapmap];0.89[YRI][hapmap];0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs3802981	0.94[ASW][hapmap];0.95[CHB][hapmap];0.89[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.91[LWK][hapmap];1.00[MEX][hapmap];0.99[MKK][hapmap];0.95[TSI][hapmap];0.89[YRI][hapmap];0.95[AMR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4514451	0.97[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4564369	0.94[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4575305	0.97[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4992797	0.89[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4992798	0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4992799	0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4992801	0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4992802	0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs61363160	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6578674	0.85[AFR][1000 genomes];0.86[AMR][1000 genomes];0.82[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6578675	0.97[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6578676	0.97[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6578677	0.97[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs67656732	0.90[AMR][1000 genomes];0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7122886	0.82[AFR][1000 genomes];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7123417	0.94[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7127617	0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7127767	0.96[CEU][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap];0.95[TSI][hapmap];0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:10 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1046068	chr11:5335943-6063742	Strong transcription Weak transcription Active TSS ZNF genes & repeats Flanking Active TSS Enhancers Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	89 gene(s)	inside rSNPs	diseases
2	nsv896939	chr11:5497799-5809548	Enhancers Active TSS Weak transcription Strong transcription Flanking Active TSS Genic enhancers Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	48 gene(s)	inside rSNPs	diseases
3	nsv553241	chr11:5506034-6203685	Genic enhancers Strong transcription Enhancers Weak transcription Flanking Active TSS Active TSS Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	74 gene(s)	inside rSNPs	diseases
4	nsv1041568	chr11:5585716-5765688	Strong transcription Enhancers Weak transcription Active TSS Genic enhancers Bivalent Enhancer Flanking Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	34 gene(s)	inside rSNPs	diseases
5	nsv1053414	chr11:5612989-6030212	Flanking Active TSS Active TSS Enhancers Bivalent/Poised TSS Strong transcription Weak transcription Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	50 gene(s)	inside rSNPs	diseases
6	nsv530216	chr11:5614439-6468232	Transcr. at gene 5' and 3' Flanking Active TSS Active TSS Enhancers Bivalent Enhancer Weak transcription Strong transcription Bivalent/Poised TSS Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	90 gene(s)	inside rSNPs	diseases
7	nsv553273	chr11:5639873-5871831	Strong transcription Weak transcription Active TSS Flanking Active TSS Enhancers Genic enhancers Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	37 gene(s)	inside rSNPs	diseases
8	nsv1036389	chr11:5695451-6177680	Weak transcription Bivalent Enhancer Genic enhancers Flanking Active TSS Active TSS Enhancers Bivalent/Poised TSS Strong transcription ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	55 gene(s)	inside rSNPs	diseases
9	nsv540943	chr11:5695451-6177680	Strong transcription Flanking Active TSS Enhancers Weak transcription Active TSS Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	55 gene(s)	inside rSNPs	diseases
10	nsv896948	chr11:5701281-5719667	Weak transcription Enhancers Active TSS Flanking Active TSS Strong transcription Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases

mRNA abundance (count:9)

SNP	Gene	Cis/trans	Tissue	Source
rs12278842	DNHD1	cis	cerebellum	SCAN
rs12278842	OR56A3	cis	cerebellum	SCAN
rs12278842	OR51B4	cis	cerebellum	SCAN
rs12278842	CNGA4	cis	cerebellum	SCAN
rs12278842	OR52I2	cis	cerebellum	SCAN
rs12278842	OR52M1	cis	cerebellum	SCAN
rs12278842	OR51I2	cis	cerebellum	SCAN
rs12278842	ILK	cis	cerebellum	SCAN
rs12278842	OR52W1	cis	cerebellum	SCAN

Chromatin state (count:121 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:5674800-5705400	Weak transcription	Psoas Muscle	Psoas
2	chr11:5684000-5705400	Weak transcription	Brain Substantia Nigra	brain
3	chr11:5684200-5705400	Weak transcription	Skeletal Muscle Male	skeletal muscle
4	chr11:5684600-5703600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
5	chr11:5685400-5705400	Weak transcription	Stomach Mucosa	stomach
6	chr11:5688000-5705600	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
7	chr11:5691000-5705000	Weak transcription	Hela-S3	cervix
8	chr11:5691000-5705400	Weak transcription	Fetal Brain Male	brain
9	chr11:5694200-5705400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
10	chr11:5696000-5705200	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
11	chr11:5697000-5705600	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
12	chr11:5698200-5705400	Weak transcription	Brain Cingulate Gyrus	brain
13	chr11:5698800-5703800	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
14	chr11:5698800-5704000	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
15	chr11:5700000-5705200	Weak transcription	Skeletal Muscle Female	skeletal muscle
16	chr11:5700200-5703600	Weak transcription	Primary T killer memory cells from peripheral blood	blood
17	chr11:5700200-5704000	Strong transcription	Primary hematopoietic stem cells short term culture	blood
18	chr11:5700200-5705400	Weak transcription	Brain Anterior Caudate	brain
19	chr11:5700200-5705400	Weak transcription	HepG2	liver
20	chr11:5700400-5704400	Weak transcription	Colonic Mucosa	Colon
21	chr11:5700400-5705200	Weak transcription	Fetal Kidney	kidney
22	chr11:5700400-5705200	Weak transcription	K562	blood
23	chr11:5700400-5705400	Weak transcription	Brain Hippocampus Middle	brain
24	chr11:5700600-5705400	Weak transcription	HUES48 Cell Line	embryonic stem cell
25	chr11:5700600-5705400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
26	chr11:5700600-5705600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
27	chr11:5700800-5703600	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
28	chr11:5700800-5705200	Weak transcription	Small Intestine	intestine
29	chr11:5701000-5705400	Weak transcription	NHDF-Ad	bronchial
30	chr11:5701200-5703600	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
31	chr11:5701200-5703600	Weak transcription	Colon Smooth Muscle	Colon
32	chr11:5701200-5704800	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
33	chr11:5701200-5705200	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
34	chr11:5701200-5705200	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
35	chr11:5701200-5705400	Weak transcription	iPS-18 Cell Line	embryonic stem cell
36	chr11:5701400-5703600	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
37	chr11:5701400-5703800	Weak transcription	Duodenum Smooth Muscle	Duodenum
38	chr11:5701400-5703800	Weak transcription	Gastric	stomach
39	chr11:5701400-5703800	Weak transcription	Stomach Smooth Muscle	stomach
40	chr11:5701400-5704000	Weak transcription	Esophagus	oesophagus
41	chr11:5701400-5704000	Weak transcription	Lung	lung
42	chr11:5701400-5704200	Weak transcription	Left Ventricle	heart
43	chr11:5701400-5704200	Weak transcription	Spleen	Spleen
44	chr11:5701400-5704400	Weak transcription	Aorta	Aorta
45	chr11:5701400-5704800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
46	chr11:5701400-5704800	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
47	chr11:5701400-5705000	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
48	chr11:5701400-5705000	Weak transcription	Primary neutrophils fromperipheralblood	blood
49	chr11:5701400-5705000	Weak transcription	Cortex derived primary cultured neurospheres	brain
50	chr11:5701400-5705000	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin

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