Variant report

Variant	rs2679722
Chromosome Location	chr2:86135154-86135155
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr2:86111166..86115659-chr2:86134509..86137457,4	MCF-7	breast:
2	chr2:86127269..86128951-chr2:86134327..86136016,2	K562	blood:

Variant related genes	Relation type
ENSG00000115525	Chromatin interaction

Extended variants
information (count: 83 )
Associated
traits (count: 7 )

rSNPs within LD-proxies of this variant (count:83)

rs_ID	r²[population]
rs10181978	0.81[AMR][1000 genomes]
rs10185207	0.82[AMR][1000 genomes]
rs10192998	0.82[AMR][1000 genomes]
rs10193207	0.82[AMR][1000 genomes]
rs1025704	0.82[AMR][1000 genomes]
rs1025705	0.82[AMR][1000 genomes]
rs1025706	0.82[AMR][1000 genomes]
rs1025707	0.82[AMR][1000 genomes]
rs1025708	0.82[AMR][1000 genomes]
rs11682312	0.82[AMR][1000 genomes]
rs11693421	0.82[AMR][1000 genomes]
rs11693423	0.82[AMR][1000 genomes]
rs11693435	0.82[AMR][1000 genomes]
rs12616165	0.85[AMR][1000 genomes];0.91[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs12714154	0.80[TSI][hapmap]
rs12714157	0.82[AMR][1000 genomes]
rs12714158	0.82[AMR][1000 genomes]
rs1401383	0.90[MKK][hapmap];0.82[TSI][hapmap]
rs1401385	0.82[TSI][hapmap]
rs1438156	0.87[AMR][1000 genomes];0.92[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs1518983	0.84[EUR][1000 genomes]
rs1533605	0.83[ASW][hapmap];0.89[LWK][hapmap];0.86[YRI][hapmap]
rs1543972	0.96[CEU][hapmap]
rs17026750	0.95[CEU][hapmap];0.90[CHB][hapmap];0.95[JPT][hapmap];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs17026756	0.82[AMR][1000 genomes]
rs1866244	0.82[AMR][1000 genomes]
rs1878898	0.96[CEU][hapmap];0.91[GIH][hapmap]
rs1878904	0.96[CEU][hapmap];0.91[GIH][hapmap]
rs2008559	0.86[AMR][1000 genomes];0.90[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2083170	0.88[AMR][1000 genomes]
rs2164878	0.86[AMR][1000 genomes];0.91[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2366950	0.89[AMR][1000 genomes]
rs2577768	0.96[CEU][hapmap]
rs2577769	0.96[CEU][hapmap]
rs2577777	0.84[EUR][1000 genomes]
rs2577778	0.84[EUR][1000 genomes]
rs2577779	0.84[EUR][1000 genomes]
rs2577780	0.84[EUR][1000 genomes]
rs2577785	0.89[AMR][1000 genomes];0.89[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2577786	0.83[EUR][1000 genomes]
rs2679710	0.96[CEU][hapmap]
rs2679711	0.96[CEU][hapmap]
rs2679712	0.96[CEU][hapmap];0.91[GIH][hapmap]
rs2679713	0.96[CEU][hapmap]
rs2679720	0.84[EUR][1000 genomes]
rs2679721	0.84[EUR][1000 genomes]
rs2679725	0.84[EUR][1000 genomes]
rs2918014	0.84[EUR][1000 genomes]
rs2918015	0.82[EUR][1000 genomes]
rs2918016	0.83[EUR][1000 genomes]
rs2945823	0.84[EUR][1000 genomes]
rs2945824	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2945825	0.84[EUR][1000 genomes]
rs2945826	0.83[EUR][1000 genomes]
rs35153287	0.83[EUR][1000 genomes]
rs4331504	0.92[AMR][1000 genomes]
rs4553826	0.83[ASW][hapmap];0.89[LWK][hapmap];0.86[YRI][hapmap]
rs4832015	0.83[ASW][hapmap];0.89[LWK][hapmap];0.86[YRI][hapmap]
rs4832016	0.85[CEU][hapmap]
rs4832210	0.85[CEU][hapmap]
rs4832217	0.96[CEU][hapmap];0.91[GIH][hapmap]
rs4832219	0.84[TSI][hapmap]
rs4832222	0.82[AMR][1000 genomes]
rs4832226	0.82[AMR][1000 genomes]
rs6547636	0.85[CEU][hapmap];0.83[GIH][hapmap]
rs6547647	0.87[AMR][1000 genomes];0.91[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs6718537	0.84[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs6720161	0.85[CEU][hapmap];0.83[GIH][hapmap]
rs6735629	0.96[CEU][hapmap]
rs6750686	0.83[CEU][hapmap]
rs71411844	0.82[AMR][1000 genomes]
rs7576135	0.85[AMR][1000 genomes];0.90[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs7593080	0.87[ASN][1000 genomes]
rs764471	0.96[CEU][hapmap]
rs893445	0.88[AMR][1000 genomes]
rs893447	0.82[AMR][1000 genomes]
rs893448	0.82[AMR][1000 genomes]
rs893449	0.82[AMR][1000 genomes]
rs9309626	0.82[AMR][1000 genomes]
rs9309627	0.82[AMR][1000 genomes]
rs934828	0.82[AMR][1000 genomes]
rs954176	0.96[CEU][hapmap]
rs959313	0.96[CEU][hapmap]

mRNA abundance (count:7)

SNP	Gene	Cis/trans	Tissue	Source
rs2679722	POLR1A	cis	lymphoblastoid	seeQTL
rs2679722	KCMF1	cis	cerebellum	SCAN
rs2679722	POLR1A	cis	cerebellum	SCAN
rs2679722	IMMT	cis	cerebellum	SCAN
rs2679722	PTCD3	cis	parietal	SCAN
rs2679722	ST3GAL5	cis	cerebellum	SCAN
rs2679722	PTCD3	cis	cerebellum	SCAN

Chromatin state (count:56 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:86128600-86141200	Weak transcription	Primary T cells from cord blood	blood
2	chr2:86129800-86137800	Weak transcription	NHDF-Ad	bronchial
3	chr2:86129800-86138000	Weak transcription	Fetal Thymus	thymus
4	chr2:86129800-86141400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
5	chr2:86130600-86138000	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
6	chr2:86131400-86137800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
7	chr2:86131400-86142400	Weak transcription	Esophagus	oesophagus
8	chr2:86131600-86135400	Enhancers	Brain Hippocampus Middle	brain
9	chr2:86131800-86141600	Weak transcription	Primary B cells from peripheral blood	blood
10	chr2:86132000-86135200	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
11	chr2:86133200-86137600	Weak transcription	Brain Inferior Temporal Lobe	brain
12	chr2:86133200-86137800	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
13	chr2:86133200-86137800	Weak transcription	Brain Cingulate Gyrus	brain
14	chr2:86133200-86137800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
15	chr2:86133200-86139200	Weak transcription	Skeletal Muscle Male	skeletal muscle
16	chr2:86133200-86142800	Weak transcription	Colon Smooth Muscle	Colon
17	chr2:86133200-86149200	Weak transcription	Stomach Smooth Muscle	stomach
18	chr2:86133200-86152000	Weak transcription	Skeletal Muscle Female	skeletal muscle
19	chr2:86133800-86135400	Enhancers	Placenta	Placenta
20	chr2:86133800-86136800	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
21	chr2:86133800-86139000	Weak transcription	Cortex derived primary cultured neurospheres	brain
22	chr2:86134000-86135400	Enhancers	Lung	lung
23	chr2:86134000-86135800	Enhancers	K562	blood
24	chr2:86134000-86136800	Enhancers	HMEC	breast
25	chr2:86134000-86136800	Enhancers	NHEK	skin
26	chr2:86134200-86135400	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
27	chr2:86134200-86136000	Enhancers	A549	lung
28	chr2:86134400-86135200	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
29	chr2:86134400-86135400	Enhancers	Osteobl	bone
30	chr2:86134400-86136400	Weak transcription	Brain Anterior Caudate	brain
31	chr2:86134400-86136600	Enhancers	HepG2	liver
32	chr2:86134400-86137200	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
33	chr2:86134400-86148000	Weak transcription	Thymus	Thymus
34	chr2:86134600-86137800	Weak transcription	Brain Substantia Nigra	brain
35	chr2:86134800-86135200	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
36	chr2:86134800-86135400	Enhancers	Adipose Nuclei	Adipose
37	chr2:86134800-86135600	Enhancers	Breast Myoepithelial Primary Cells	Breast
38	chr2:86134800-86135800	Enhancers	Muscle Satellite Cultured Cells	--
39	chr2:86135000-86135200	Enhancers	Fetal Muscle Leg	muscle
40	chr2:86135000-86135200	Enhancers	Fetal Stomach	stomach
41	chr2:86135000-86135200	Enhancers	Right Atrium	heart
42	chr2:86135000-86135200	Enhancers	Stomach Mucosa	stomach
43	chr2:86135000-86135200	Enhancers	NH-A	brain
44	chr2:86135000-86135400	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
45	chr2:86135000-86135400	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
46	chr2:86135000-86135400	Enhancers	Brain Angular Gyrus	brain
47	chr2:86135000-86135400	Enhancers	Fetal Muscle Trunk	muscle
48	chr2:86135000-86135400	Enhancers	Ovary	ovary
49	chr2:86135000-86135400	Enhancers	Pancreas	Pancrea
50	chr2:86135000-86135400	Enhancers	Right Ventricle	heart

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