Variant report

Variant	rs2577786
Chromosome Location	chr2:86143143-86143144
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr2:86140957..86144673-chr2:86146213..86150354,4	K562	blood:
2	chr2:86140957..86144482-chr2:86147122..86150354,4	K562	blood:

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-ATOH8-2	chr2:86141408-86144322	XLOC_001558

Extended variants
information (count: 69 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:69)

rs_ID	r²[population]
rs10496320	0.84[JPT][hapmap]
rs11127006	0.84[JPT][hapmap]
rs1135603	0.80[AMR][1000 genomes];0.87[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs12614498	0.82[CHB][hapmap]
rs12622987	0.84[JPT][hapmap]
rs13008291	0.83[ASN][1000 genomes]
rs13014421	0.84[JPT][hapmap]
rs1401384	0.86[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs1518983	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1518991	0.85[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs1543972	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs17026675	0.83[JPT][hapmap]
rs17026750	0.91[CEU][hapmap];0.84[EUR][1000 genomes]
rs1878898	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];0.92[MEX][hapmap];0.82[MKK][hapmap];1.00[TSI][hapmap];0.86[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs1878899	0.87[ASN][1000 genomes]
rs1878904	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];0.87[MEX][hapmap];0.98[TSI][hapmap];0.85[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2577768	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2577769	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2577770	0.87[ASN][1000 genomes]
rs2577771	0.87[ASN][1000 genomes]
rs2577772	0.86[ASN][1000 genomes]
rs2577774	0.80[AMR][1000 genomes];0.86[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2577775	0.80[AMR][1000 genomes];0.87[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2577777	0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2577778	0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2577779	0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2577780	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2679710	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2679711	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2679712	1.00[CEU][hapmap];1.00[CHB][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];0.92[MEX][hapmap];0.82[MKK][hapmap];1.00[TSI][hapmap];0.87[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2679713	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2679714	0.85[ASN][1000 genomes]
rs2679715	0.85[ASN][1000 genomes]
rs2679716	0.86[ASN][1000 genomes]
rs2679717	0.87[ASN][1000 genomes]
rs2679718	0.87[ASN][1000 genomes]
rs2679719	0.86[ASN][1000 genomes]
rs2679720	0.89[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2679721	0.89[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2679722	0.96[CEU][hapmap];0.98[GIH][hapmap];0.83[EUR][1000 genomes]
rs2679725	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28364794	0.84[EUR][1000 genomes]
rs2918014	0.93[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2918015	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2918016	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2945823	0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2945824	0.83[EUR][1000 genomes]
rs2945825	0.93[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2945826	0.90[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs35153287	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs3810821	0.84[JPT][hapmap]
rs4832016	0.89[CEU][hapmap];0.88[CHB][hapmap];0.84[JPT][hapmap]
rs4832210	0.89[CEU][hapmap];0.88[CHB][hapmap];0.84[JPT][hapmap]
rs4832216	0.85[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs4832217	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];0.87[MEX][hapmap];0.98[TSI][hapmap];0.85[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs4832218	0.86[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs62150576	0.82[ASN][1000 genomes]
rs6547636	0.89[CEU][hapmap];0.88[CHB][hapmap];0.86[GIH][hapmap];0.84[JPT][hapmap];0.83[MEX][hapmap]
rs6720161	0.89[CEU][hapmap];0.88[CHB][hapmap];0.86[GIH][hapmap];0.84[JPT][hapmap]
rs6734115	0.86[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs6735629	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs6747179	0.86[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs6747294	0.86[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs6750686	0.87[CEU][hapmap]
rs7572209	0.84[JPT][hapmap]
rs7593080	0.87[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs764471	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs954176	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs959313	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[EUR][1000 genomes];0.87[ASN][1000 genomes]

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs2577786	IMMT	cis	cerebellum	SCAN
rs2577786	C2orf51	cis	cerebellum	SCAN
rs2577786	ST3GAL5	cis	cerebellum	SCAN
rs2577786	PTCD3	cis	cerebellum	SCAN

Chromatin state (count:43 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:86133200-86149200	Weak transcription	Stomach Smooth Muscle	stomach
2	chr2:86133200-86152000	Weak transcription	Skeletal Muscle Female	skeletal muscle
3	chr2:86134400-86148000	Weak transcription	Thymus	Thymus
4	chr2:86135400-86143800	Weak transcription	Spleen	Spleen
5	chr2:86135400-86148000	Weak transcription	Pancreas	Pancrea
6	chr2:86135400-86151600	Weak transcription	Fetal Muscle Trunk	muscle
7	chr2:86135400-86151600	Weak transcription	Lung	lung
8	chr2:86135400-86152600	Weak transcription	Psoas Muscle	Psoas
9	chr2:86137400-86143600	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
10	chr2:86138000-86143200	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
11	chr2:86138200-86151600	Weak transcription	Fetal Muscle Leg	muscle
12	chr2:86138600-86147400	Weak transcription	Fetal Thymus	thymus
13	chr2:86139600-86143200	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
14	chr2:86140000-86148000	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
15	chr2:86140400-86144800	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
16	chr2:86141400-86145000	Weak transcription	NHEK	skin
17	chr2:86141600-86145000	Weak transcription	HMEC	breast
18	chr2:86142000-86143400	Enhancers	Ovary	ovary
19	chr2:86142000-86143600	Enhancers	Brain Dorsolateral Prefrontal Cortex	brain
20	chr2:86142000-86147200	Weak transcription	Adipose Nuclei	Adipose
21	chr2:86142200-86143200	Enhancers	Breast Myoepithelial Primary Cells	Breast
22	chr2:86142200-86143200	Enhancers	Brain Angular Gyrus	brain
23	chr2:86142200-86143400	Genic enhancers	Brain Anterior Caudate	brain
24	chr2:86142200-86145000	Weak transcription	A549	lung
25	chr2:86142200-86155800	Weak transcription	Primary T cells from cord blood	blood
26	chr2:86142400-86143600	Enhancers	Brain Hippocampus Middle	brain
27	chr2:86142400-86143600	Enhancers	Brain Substantia Nigra	brain
28	chr2:86142400-86145000	Weak transcription	Hela-S3	cervix
29	chr2:86142400-86148000	Weak transcription	K562	blood
30	chr2:86142400-86151800	Weak transcription	Primary B cells from peripheral blood	blood
31	chr2:86142400-86157800	Weak transcription	Aorta	Aorta
32	chr2:86142600-86143400	Enhancers	Foreskin Melanocyte Primary Cells skin01	Skin
33	chr2:86142600-86143400	Enhancers	Brain Cingulate Gyrus	brain
34	chr2:86142600-86143400	Weak transcription	Right Atrium	heart
35	chr2:86142600-86147400	Weak transcription	Liver	Liver
36	chr2:86142600-86151000	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
37	chr2:86142600-86151600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
38	chr2:86142800-86143200	Enhancers	Cortex derived primary cultured neurospheres	brain
39	chr2:86142800-86143400	Enhancers	Brain Inferior Temporal Lobe	brain
40	chr2:86142800-86143400	Enhancers	Colon Smooth Muscle	Colon
41	chr2:86142800-86143600	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
42	chr2:86142800-86143600	Enhancers	NHDF-Ad	bronchial
43	chr2:86143000-86143200	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin

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