Variant report

Variant	rs12622987
Chromosome Location	chr2:86106547-86106548
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	chr2:86093232..86096131-chr2:86104153..86108444,3	K562	blood:
2	chr2:86101610..86104056-chr2:86104461..86106996,3	MCF-7	breast:

Variant related genes	Relation type
ENSG00000115525	Chromatin interaction

Extended variants
information (count: 52 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:52)

rs_ID	r²[population]
rs10496320	1.00[CEU][hapmap];0.94[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.92[MEX][hapmap];0.96[TSI][hapmap];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs10865480	0.89[ASN][1000 genomes]
rs11127003	0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11127004	0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11127006	0.89[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11127007	0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11127008	0.96[ASN][1000 genomes]
rs11127009	0.96[ASN][1000 genomes]
rs11694145	0.83[AMR][1000 genomes]
rs12614498	0.82[CEU][hapmap];1.00[CHB][hapmap];0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12618873	0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12990400	0.82[AMR][1000 genomes]
rs13014421	0.89[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];0.90[AMR][1000 genomes];0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs13014890	0.94[CEU][hapmap];0.88[CHB][hapmap];1.00[GIH][hapmap];0.96[TSI][hapmap];0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs13016226	0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13033743	0.89[AMR][1000 genomes]
rs1543972	0.84[JPT][hapmap]
rs17026675	1.00[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1878898	0.84[JPT][hapmap]
rs1878904	0.84[JPT][hapmap]
rs1878905	0.96[ASN][1000 genomes]
rs2280312	0.90[AMR][1000 genomes];0.94[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2577768	0.84[JPT][hapmap]
rs2577769	0.84[JPT][hapmap]
rs2679710	0.84[JPT][hapmap]
rs2679711	0.84[JPT][hapmap]
rs2679712	0.84[JPT][hapmap]
rs2679713	0.84[JPT][hapmap]
rs3770097	0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs3810821	0.89[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.83[MEX][hapmap];0.96[TSI][hapmap];0.88[AMR][1000 genomes];0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4832016	0.89[CHB][hapmap];1.00[JPT][hapmap];0.96[ASN][1000 genomes]
rs4832210	0.89[CHB][hapmap];1.00[JPT][hapmap];0.93[ASN][1000 genomes]
rs4832217	0.84[JPT][hapmap]
rs56049132	0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs56083339	0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs62147537	0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs62147538	0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs62147540	0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6547636	0.89[CHB][hapmap];0.97[CHD][hapmap];1.00[JPT][hapmap];0.95[ASN][1000 genomes]
rs6547640	0.96[ASN][1000 genomes]
rs6720161	0.89[CHB][hapmap];0.92[CHD][hapmap];1.00[JPT][hapmap];0.96[ASN][1000 genomes]
rs6735629	0.84[JPT][hapmap]
rs6750686	0.95[ASN][1000 genomes]
rs6751743	0.96[ASN][1000 genomes]
rs72842060	0.88[AMR][1000 genomes];0.91[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs72842061	0.88[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs7558479	0.87[CEU][hapmap];0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7572209	0.89[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7587003	0.96[ASN][1000 genomes]
rs764471	0.84[JPT][hapmap]
rs954176	0.84[JPT][hapmap]
rs959313	0.84[JPT][hapmap]

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs12622987	IMMT	cis	cerebellum	SCAN
rs12622987	MRPL35	cis	parietal	SCAN
rs12622987	C2orf51	cis	cerebellum	SCAN

Chromatin state (count:89 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:86075400-86114000	Weak transcription	Aorta	Aorta
2	chr2:86081000-86112400	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
3	chr2:86086800-86113000	Weak transcription	Rectal Mucosa Donor 29	rectum
4	chr2:86088600-86111600	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
5	chr2:86090600-86109000	Weak transcription	Fetal Stomach	stomach
6	chr2:86090600-86110600	Weak transcription	Fetal Muscle Trunk	muscle
7	chr2:86093400-86106800	Weak transcription	Duodenum Smooth Muscle	Duodenum
8	chr2:86093400-86112400	Weak transcription	Colonic Mucosa	Colon
9	chr2:86093600-86111600	Weak transcription	Colon Smooth Muscle	Colon
10	chr2:86093800-86113000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
11	chr2:86096200-86108400	Genic enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
12	chr2:86096800-86107600	Enhancers	Brain Hippocampus Middle	brain
13	chr2:86097600-86108600	Weak transcription	Cortex derived primary cultured neurospheres	brain
14	chr2:86097600-86109200	Weak transcription	NHEK	skin
15	chr2:86100200-86111800	Weak transcription	K562	blood
16	chr2:86100400-86109000	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
17	chr2:86101200-86111600	Weak transcription	NHDF-Ad	bronchial
18	chr2:86101400-86108600	Enhancers	Primary T killer naive cells fromperipheralblood	blood
19	chr2:86102800-86107400	Enhancers	Primary T helper cells PMA-I stimulated	--
20	chr2:86102800-86115200	Weak transcription	Small Intestine	intestine
21	chr2:86103200-86107400	Enhancers	Primary T killer memory cells from peripheral blood	blood
22	chr2:86103200-86108200	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
23	chr2:86103400-86108600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
24	chr2:86103600-86108200	Weak transcription	Primary B cells from cord blood	blood
25	chr2:86103600-86111800	Weak transcription	Fetal Muscle Leg	muscle
26	chr2:86104200-86106600	Weak transcription	Adipose Nuclei	Adipose
27	chr2:86104200-86112400	Weak transcription	Monocytes-CD14+_RO01746	blood
28	chr2:86104400-86107400	Enhancers	Brain Cingulate Gyrus	brain
29	chr2:86104400-86108000	Weak transcription	Primary monocytes fromperipheralblood	blood
30	chr2:86104600-86107600	Enhancers	Primary T helper cells fromperipheralblood	blood
31	chr2:86104600-86107600	Enhancers	Brain Angular Gyrus	brain
32	chr2:86104600-86112000	Weak transcription	Stomach Mucosa	stomach
33	chr2:86104800-86106600	Enhancers	HUVEC	blood vessel
34	chr2:86104800-86106800	Enhancers	A549	lung
35	chr2:86104800-86107000	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
36	chr2:86104800-86113400	Weak transcription	Pancreatic Islets	Pancreatic Islet
37	chr2:86105000-86107200	Enhancers	Brain Dorsolateral Prefrontal Cortex	brain
38	chr2:86105000-86107600	Enhancers	Brain Substantia Nigra	brain
39	chr2:86105200-86107400	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
40	chr2:86105200-86107600	Enhancers	Primary T helper naive cells fromperipheralblood	blood
41	chr2:86105400-86106800	Genic enhancers	Thymus	Thymus
42	chr2:86105400-86107000	Enhancers	Osteobl	bone
43	chr2:86105400-86107200	Enhancers	Primary hematopoietic stem cells short term culture	blood
44	chr2:86105400-86107200	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
45	chr2:86105400-86107400	Enhancers	Primary hematopoietic stem cells	blood
46	chr2:86105400-86107400	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
47	chr2:86105400-86107400	Enhancers	Brain Inferior Temporal Lobe	brain
48	chr2:86105400-86107600	Enhancers	Brain Anterior Caudate	brain
49	chr2:86105400-86107800	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
50	chr2:86105400-86112400	Weak transcription	Ovary	ovary

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