Variant report

Variant	rs6760222
Chromosome Location	chr2:86526127-86526128
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:0)
CpG islands
(count:0)
Chromatin interactive
region (count:8)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:8 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr2:86525502..86526465-chr2:86599763..86600646,3	MCF-7	breast:
2	chr2:86525895..86526398-chr2:86597345..86598331,2	MCF-7	breast:
3	chr2:86519380..86521878-chr2:86524185..86527077,2	K562	blood:
4	chr2:86525581..86526450-chr2:86595097..86596076,7	MCF-7	breast:
5	chr2:86447692..86448797-chr2:86525346..86526631,6	MCF-7	breast:
6	chr2:86525475..86526402-chr2:86594830..86595950,4	MCF-7	breast:
7	chr2:86525418..86526527-chr2:86599676..86600615,4	MCF-7	breast:
8	chr2:86447857..86448893-chr2:86525541..86526483,3	MCF-7	breast:

No data

Extended variants
information (count: 66 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:65)

rs_ID	r²[population]
rs10451631	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10451665	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10451666	1.00[CEU][hapmap];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10451668	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11127018	0.81[JPT][hapmap]
rs17027263	1.00[CEU][hapmap]
rs1863062	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28527367	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35807694	1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs35943273	1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs3731815	0.90[JPT][hapmap]
rs3731816	0.90[JPT][hapmap]
rs3821015	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs3827551	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap]
rs56657747	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs56742104	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs57006782	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs57137376	1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs57279476	0.85[EUR][1000 genomes]
rs57412282	0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs57743711	1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs57786125	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs57924251	0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs58029983	1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs58141172	0.89[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs58210919	0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs58287226	0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs58728311	0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs58996019	1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs59149450	0.88[ASN][1000 genomes]
rs59300790	1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs59409236	0.89[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs59523869	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs59567456	1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs59697218	0.82[ASN][1000 genomes]
rs60032974	1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs60067772	0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs60237707	0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs60295664	1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs60345058	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs60427833	0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs60474859	0.89[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs60484746	1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs60791163	0.89[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs60840060	1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs61392096	1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs61636758	1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs61669204	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61700819	1.00[EUR][1000 genomes]
rs6704826	0.86[ASW][hapmap]
rs6716825	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[TSI][hapmap];0.84[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6728494	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6734431	0.85[ASW][hapmap];0.90[LWK][hapmap]
rs6748079	1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs72938375	0.89[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs72940115	1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs72940124	1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs72940126	1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs72940131	1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs72940149	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72940152	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72940160	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs753918	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7593666	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.94[GIH][hapmap];1.00[JPT][hapmap];1.00[TSI][hapmap];0.84[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7606682	1.00[CEU][hapmap]

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

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv3412938	chr2:86370969-86867936	Strong transcription Enhancers Genic enhancers Weak transcription Flanking Bivalent TSS/Enh Active TSS Flanking Active TSS ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	77 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs6760222	POLR1A	cis	lymphoblastoid	seeQTL
rs6760222	POLR1A	cis	multi-tissue	Pritchard

Chromatin state (count:48 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:86514000-86529200	Weak transcription	Pancreas	Pancrea
2	chr2:86518400-86527600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
3	chr2:86521600-86528600	Weak transcription	Pancreatic Islets	Pancreatic Islet
4	chr2:86522600-86529000	Weak transcription	Small Intestine	intestine
5	chr2:86524000-86526400	Enhancers	Rectal Smooth Muscle	rectum
6	chr2:86524000-86526400	Enhancers	Right Atrium	heart
7	chr2:86524000-86526800	Enhancers	Left Ventricle	heart
8	chr2:86524000-86527600	Enhancers	Psoas Muscle	Psoas
9	chr2:86524000-86527800	Enhancers	Right Ventricle	heart
10	chr2:86524000-86529600	Enhancers	Skeletal Muscle Female	skeletal muscle
11	chr2:86524200-86527200	Enhancers	Duodenum Smooth Muscle	Duodenum
12	chr2:86524200-86530000	Enhancers	Brain Hippocampus Middle	brain
13	chr2:86524200-86530200	Enhancers	Colon Smooth Muscle	Colon
14	chr2:86524200-86533600	Enhancers	Fetal Lung	lung
15	chr2:86524400-86526800	Enhancers	Fetal Heart	heart
16	chr2:86524600-86533400	Enhancers	Fetal Muscle Leg	muscle
17	chr2:86524800-86530200	Enhancers	Brain Angular Gyrus	brain
18	chr2:86525000-86529200	Enhancers	Fetal Muscle Trunk	muscle
19	chr2:86525000-86530200	Enhancers	HSMMtube	muscle
20	chr2:86525200-86529600	Enhancers	Brain Anterior Caudate	brain
21	chr2:86525200-86530200	Enhancers	Brain Germinal Matrix	brain
22	chr2:86525400-86526200	Weak transcription	Spleen	Spleen
23	chr2:86525400-86526600	Enhancers	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
24	chr2:86525600-86526400	Enhancers	Adipose Nuclei	Adipose
25	chr2:86525600-86526400	Flanking Active TSS	Brain Inferior Temporal Lobe	brain
26	chr2:86525600-86526400	Enhancers	Esophagus	oesophagus
27	chr2:86525600-86526400	Enhancers	Lung	lung
28	chr2:86525600-86526600	Enhancers	Cortex derived primary cultured neurospheres	brain
29	chr2:86525600-86526600	Enhancers	Fetal Intestine Large	intestine
30	chr2:86525600-86526600	Enhancers	Fetal Intestine Small	intestine
31	chr2:86525600-86529600	Enhancers	Brain Dorsolateral Prefrontal Cortex	brain
32	chr2:86525600-86530200	Enhancers	Fetal Adrenal Gland	Adrenal Gland
33	chr2:86525800-86526200	Bivalent Enhancer	HUVEC	blood vessel
34	chr2:86525800-86526400	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
35	chr2:86525800-86526400	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
36	chr2:86525800-86526400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
37	chr2:86525800-86526400	Flanking Active TSS	Brain Cingulate Gyrus	brain
38	chr2:86525800-86526400	Enhancers	Fetal Brain Male	brain
39	chr2:86525800-86526600	Enhancers	Fetal Stomach	stomach
40	chr2:86525800-86527400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
41	chr2:86525800-86530000	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
42	chr2:86525800-86530200	Enhancers	Fetal Brain Female	brain
43	chr2:86525800-86540800	Weak transcription	Aorta	Aorta
44	chr2:86526000-86526200	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
45	chr2:86526000-86526200	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
46	chr2:86526000-86526200	Enhancers	Brain Substantia Nigra	brain
47	chr2:86526000-86526200	Flanking Active TSS	Skeletal Muscle Male	skeletal muscle
48	chr2:86526000-86526400	Flanking Active TSS	Stomach Smooth Muscle	stomach

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