Variant report

Variant	rs278155
Chromosome Location	chr12:120121569-120121570
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr12:120119326..120121851-chr12:120158588..120161443,2	MCF-7	breast:
2	chr12:120105122..120114412-chr12:120115205..120125435,13	MCF-7	breast:
3	chr12:120120248..120122666-chr12:120276652..120278749,2	K562	blood:
4	chr12:120121421..120124457-chr12:120131383..120133507,3	K562	blood:

Variant related genes	Relation type
ENSG00000111725	Chromatin interaction
ENSG00000248636	Chromatin interaction

Extended variants
information (count: 38 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:36)

rs_ID	r²[population]
rs10774503	0.88[CEU][hapmap]
rs10849688	0.86[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10849690	0.86[AMR][1000 genomes];0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11064873	0.83[CEU][hapmap];0.93[GIH][hapmap];0.88[MEX][hapmap];0.95[TSI][hapmap];0.80[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs175878	1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];0.88[TSI][hapmap];0.89[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1978107	0.83[CEU][hapmap];0.93[GIH][hapmap];0.93[MEX][hapmap];0.93[TSI][hapmap];0.94[AMR][1000 genomes];0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1978108	0.83[CEU][hapmap];0.83[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs202983	0.87[MEX][hapmap]
rs278102	0.87[MEX][hapmap]
rs278123	1.00[CEU][hapmap];0.96[GIH][hapmap];0.94[MEX][hapmap];0.86[TSI][hapmap];0.83[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs278126	0.81[ASW][hapmap];0.83[CEU][hapmap];0.87[MEX][hapmap];0.86[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs278143	1.00[CEU][hapmap];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs278144	1.00[CEU][hapmap];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs278145	1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];0.90[TSI][hapmap];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs278147	1.00[CEU][hapmap];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs278148	1.00[CEU][hapmap];0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs278149	1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];0.93[TSI][hapmap];0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs278151	1.00[CEU][hapmap];1.00[GIH][hapmap];0.94[MEX][hapmap];0.93[TSI][hapmap];0.86[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs278152	1.00[CEU][hapmap];1.00[GIH][hapmap];0.94[MEX][hapmap];0.95[TSI][hapmap];0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs278154	0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3930004	0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4213	1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];0.93[TSI][hapmap];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6490266	0.94[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6490267	0.92[CEU][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];0.90[TSI][hapmap];0.92[AMR][1000 genomes];0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7301592	0.88[CEU][hapmap]
rs7304996	0.95[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7310266	0.83[CEU][hapmap];0.93[GIH][hapmap];0.88[MEX][hapmap];0.93[TSI][hapmap];0.83[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7311779	0.88[CEU][hapmap]
rs7312321	0.88[CEU][hapmap]
rs7960723	0.89[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7963248	0.85[AMR][1000 genomes];0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7967558	0.89[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7972600	0.83[CEU][hapmap];0.86[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7973772	0.81[AMR][1000 genomes]
rs7979627	0.95[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs804667	0.83[CEU][hapmap];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1052595	chr12:119992580-120132038	Strong transcription Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Flanking Active TSS Weak transcription Enhancers Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	diseases
2	nsv541616	chr12:119992580-120132038	Weak transcription Enhancers Bivalent/Poised TSS Strong transcription Genic enhancers Flanking Active TSS Transcr. at gene 5' and 3' Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs278155	COQ5	cis	parietal	SCAN
rs278155	PXN	cis	cerebellum	SCAN
rs278155	WSB2	cis	cerebellum	SCAN

Chromatin state (count:115 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:120108200-120122000	Strong transcription	A549	lung
2	chr12:120108200-120161000	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
3	chr12:120112600-120130400	Weak transcription	Right Atrium	heart
4	chr12:120116400-120121600	Genic enhancers	Fetal Intestine Small	intestine
5	chr12:120116800-120122400	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
6	chr12:120116800-120201800	Weak transcription	Fetal Heart	heart
7	chr12:120117000-120123200	Weak transcription	Fetal Brain Male	brain
8	chr12:120117000-120145800	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
9	chr12:120118800-120124600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
10	chr12:120119200-120122000	Weak transcription	Fetal Lung	lung
11	chr12:120119200-120123600	Enhancers	Stomach Mucosa	stomach
12	chr12:120119200-120125800	Enhancers	Fetal Kidney	kidney
13	chr12:120119200-120130200	Weak transcription	Brain Angular Gyrus	brain
14	chr12:120119200-120135400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
15	chr12:120119200-120141200	Weak transcription	Rectal Smooth Muscle	rectum
16	chr12:120119400-120124600	Weak transcription	NHEK	skin
17	chr12:120119400-120124800	Weak transcription	Brain Inferior Temporal Lobe	brain
18	chr12:120119400-120125200	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
19	chr12:120119600-120123200	Weak transcription	iPS-18 Cell Line	embryonic stem cell
20	chr12:120119600-120124200	Weak transcription	HUES48 Cell Line	embryonic stem cell
21	chr12:120119600-120130200	Weak transcription	Colon Smooth Muscle	Colon
22	chr12:120119600-120147000	Weak transcription	Brain Substantia Nigra	brain
23	chr12:120119800-120121800	Weak transcription	Aorta	Aorta
24	chr12:120119800-120122200	Weak transcription	Ovary	ovary
25	chr12:120119800-120123400	Weak transcription	Lung	lung
26	chr12:120119800-120124000	Weak transcription	Fetal Thymus	thymus
27	chr12:120119800-120125400	Weak transcription	Hela-S3	cervix
28	chr12:120119800-120149800	Weak transcription	Placenta	Placenta
29	chr12:120120000-120121600	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
30	chr12:120120000-120121800	Enhancers	Adipose Nuclei	Adipose
31	chr12:120120000-120124200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
32	chr12:120120000-120124200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
33	chr12:120120000-120124400	Weak transcription	Fetal Brain Female	brain
34	chr12:120120000-120124400	Weak transcription	Right Ventricle	heart
35	chr12:120120000-120124800	Weak transcription	HMEC	breast
36	chr12:120120000-120129600	Weak transcription	Brain Hippocampus Middle	brain
37	chr12:120120000-120135000	Weak transcription	Esophagus	oesophagus
38	chr12:120120000-120135200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
39	chr12:120120200-120122000	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
40	chr12:120120200-120122000	Weak transcription	Duodenum Smooth Muscle	Duodenum
41	chr12:120120200-120122000	Weak transcription	Thymus	Thymus
42	chr12:120120200-120122400	Enhancers	Rectal Mucosa Donor 29	rectum
43	chr12:120120200-120123200	Weak transcription	Skeletal Muscle Female	skeletal muscle
44	chr12:120120200-120123400	Weak transcription	Dnd41	blood
45	chr12:120120200-120124200	Weak transcription	H9 Cell Line	embryonic stem cell
46	chr12:120120200-120124200	Weak transcription	iPS-15b Cell Line	embryonic stem cell
47	chr12:120120200-120124200	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
48	chr12:120120200-120124200	Weak transcription	Colonic Mucosa	Colon
49	chr12:120120200-120124200	Weak transcription	Gastric	stomach
50	chr12:120120200-120124200	Weak transcription	Stomach Smooth Muscle	stomach

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