Variant report

Variant	rs10183655
Chromosome Location	chr2:54210781-54210782
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr2:54196698..54199249-chr2:54209378..54211786,2	MCF-7	breast:
2	chr2:54196641..54201530-chr2:54208327..54212751,6	K562	blood:
3	chr2:54209836..54212670-chr2:54227485..54229972,3	MCF-7	breast:

Variant related genes	Relation type
ENSG00000170634	Chromatin interaction
ENSG00000068878	Chromatin interaction

Extended variants
information (count: 73 )
Associated
traits (count: 6 )

rSNPs within LD-proxies of this variant (count:72)

rs_ID	r²[population]
rs10084374	0.84[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs10167891	0.83[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs10168293	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs10181999	0.81[AFR][1000 genomes];0.86[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs10186566	0.88[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs11674724	0.89[ASN][1000 genomes]
rs11683741	0.91[ASN][1000 genomes]
rs11689025	0.94[ASN][1000 genomes]
rs11694711	0.89[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11890838	0.86[CHB][hapmap];0.81[CHD][hapmap]
rs11893270	0.86[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs13394278	0.84[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs1477258	0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs17039547	0.81[CHD][hapmap]
rs17045452	0.95[CHB][hapmap];0.98[CHD][hapmap];0.93[GIH][hapmap];0.91[MEX][hapmap];0.95[ASN][1000 genomes]
rs17045474	0.82[CHB][hapmap]
rs17045488	0.82[CHB][hapmap]
rs1877908	0.81[CHD][hapmap]
rs2112122	0.87[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2253760	0.81[CEU][hapmap];0.87[CHB][hapmap];0.80[JPT][hapmap]
rs2542571	0.85[CEU][hapmap];0.87[CHB][hapmap];0.80[JPT][hapmap];0.81[TSI][hapmap]
rs2542575	0.81[CEU][hapmap];0.87[CHB][hapmap];0.85[JPT][hapmap]
rs2692514	0.81[CHB][hapmap];0.80[JPT][hapmap]
rs2692516	0.83[CHB][hapmap]
rs2692534	0.83[CHB][hapmap]
rs28653587	0.87[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs28851028	0.83[ASN][1000 genomes]
rs2909459	0.95[CHB][hapmap];0.92[ASN][1000 genomes]
rs2949815	0.91[ASN][1000 genomes]
rs34498089	0.83[CHD][hapmap]
rs3731967	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];0.93[GIH][hapmap];0.90[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.93[MKK][hapmap];1.00[TSI][hapmap];0.96[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4671742	0.98[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4671746	0.88[ASN][1000 genomes]
rs4671747	0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs55692047	0.88[ASN][1000 genomes]
rs56302494	0.87[ASN][1000 genomes]
rs62139336	0.95[ASN][1000 genomes]
rs6545377	0.88[ASN][1000 genomes]
rs6545380	0.90[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs66773232	0.98[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6711105	0.86[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs6711217	0.83[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs6713088	0.84[JPT][hapmap]
rs6715488	0.80[AFR][1000 genomes];0.91[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs6742042	0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs6743455	0.81[AFR][1000 genomes];0.86[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs6746965	1.00[CEU][hapmap];0.95[CHB][hapmap];0.94[JPT][hapmap];0.87[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6748976	0.87[ASN][1000 genomes]
rs6748997	0.85[ASN][1000 genomes]
rs6751105	0.89[JPT][hapmap]
rs698855	0.87[CHB][hapmap];0.81[MEX][hapmap]
rs72799298	0.87[ASN][1000 genomes]
rs72904908	0.94[AMR][1000 genomes];0.91[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7559947	0.95[ASN][1000 genomes]
rs7564912	0.87[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7591431	0.89[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs805309	0.80[CEU][hapmap]
rs805310	0.95[CHB][hapmap];0.92[ASN][1000 genomes]
rs805321	0.87[CHB][hapmap]
rs805328	0.90[CHB][hapmap]
rs805344	0.92[ASN][1000 genomes]
rs805351	0.87[CHB][hapmap]
rs805352	0.87[CHB][hapmap];0.83[CHD][hapmap];0.80[GIH][hapmap];0.81[MEX][hapmap]
rs805365	0.87[CHB][hapmap];0.83[CHD][hapmap];0.80[GIH][hapmap];0.81[MEX][hapmap]
rs805386	0.87[CHB][hapmap]
rs805399	0.87[CHB][hapmap];0.81[MEX][hapmap]
rs805401	0.87[CHB][hapmap]
rs805404	0.87[CHB][hapmap];0.81[MEX][hapmap]
rs805408	0.87[CHB][hapmap]
rs805416	0.85[AMR][1000 genomes]
rs805426	0.87[CHB][hapmap];0.80[GIH][hapmap];0.81[MEX][hapmap]
rs9631059	0.90[EUR][1000 genomes];0.88[ASN][1000 genomes]

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	nsv1001246	chr2:54195654-54434832	Enhancers ZNF genes & repeats Weak transcription Active TSS Flanking Active TSS Strong transcription Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	42 gene(s)	inside rSNPs	diseases

mRNA abundance (count:6)

SNP	Gene	Cis/trans	Tissue	Source
rs10183655	MTIF2	cis	cerebellum	SCAN
rs10183655	PSME4	cis	lymphoblastoid	seeQTL
rs10183655	RAE1	trans	cerebellum	SCAN
rs10183655	ACYP2	cis	multi-tissue	Pritchard
rs10183655	TSPYL6	cis	cerebellum	SCAN
rs10183655	ASB3	cis	cerebellum	SCAN

Chromatin state (count:99 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:54198600-54212000	Weak transcription	Spleen	Spleen
2	chr2:54199000-54214200	Weak transcription	Stomach Mucosa	stomach
3	chr2:54199000-54214400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
4	chr2:54199000-54215600	Weak transcription	Sigmoid Colon	Sigmoid Colon
5	chr2:54199000-54221600	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
6	chr2:54199000-54228800	Weak transcription	Aorta	Aorta
7	chr2:54199200-54213800	Weak transcription	Psoas Muscle	Psoas
8	chr2:54199200-54213800	Weak transcription	Small Intestine	intestine
9	chr2:54199200-54214200	Weak transcription	Colonic Mucosa	Colon
10	chr2:54199200-54214200	Weak transcription	Fetal Heart	heart
11	chr2:54199200-54214200	Weak transcription	Fetal Kidney	kidney
12	chr2:54199200-54214200	Weak transcription	Pancreatic Islets	Pancreatic Islet
13	chr2:54199200-54214200	Weak transcription	Rectal Smooth Muscle	rectum
14	chr2:54199200-54214200	Weak transcription	NH-A	brain
15	chr2:54199200-54214400	Weak transcription	A549	lung
16	chr2:54199200-54214600	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
17	chr2:54200000-54214200	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
18	chr2:54200200-54211400	Strong transcription	Fetal Muscle Leg	muscle
19	chr2:54200200-54212800	Weak transcription	HUES6 Cell Line	embryonic stem cell
20	chr2:54200200-54216600	Weak transcription	Right Ventricle	heart
21	chr2:54200400-54218400	Weak transcription	Primary T killer memory cells from peripheral blood	blood
22	chr2:54201400-54211400	Strong transcription	Breast Myoepithelial Primary Cells	Breast
23	chr2:54201400-54211400	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
24	chr2:54201800-54211600	Strong transcription	Primary T cells from cord blood	blood
25	chr2:54202200-54212600	Weak transcription	HepG2	liver
26	chr2:54202600-54211800	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
27	chr2:54202600-54214200	Weak transcription	Muscle Satellite Cultured Cells	--
28	chr2:54202600-54214400	Weak transcription	NHDF-Ad	bronchial
29	chr2:54202800-54214800	Weak transcription	NHLF	lung
30	chr2:54202800-54215800	Weak transcription	NHEK	skin
31	chr2:54203200-54214200	Weak transcription	Colon Smooth Muscle	Colon
32	chr2:54203600-54214800	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
33	chr2:54203800-54211600	Weak transcription	Placenta Amnion	Placenta Amnion
34	chr2:54203800-54214200	Weak transcription	Brain Anterior Caudate	brain
35	chr2:54204400-54226400	Weak transcription	Pancreas	Pancrea
36	chr2:54204600-54214000	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
37	chr2:54204600-54214200	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
38	chr2:54205000-54213800	Weak transcription	Primary T helper cells PMA-I stimulated	--
39	chr2:54205200-54222600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
40	chr2:54205800-54211400	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
41	chr2:54205800-54212400	Weak transcription	Skeletal Muscle Female	skeletal muscle
42	chr2:54206000-54212800	Weak transcription	Left Ventricle	heart
43	chr2:54206000-54214200	Weak transcription	Primary T helper naive cells from peripheral blood	blood
44	chr2:54206000-54214200	Weak transcription	GM12878-XiMat	blood
45	chr2:54206000-54216600	Weak transcription	Esophagus	oesophagus
46	chr2:54206000-54221600	Weak transcription	Thymus	Thymus
47	chr2:54206000-54226400	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
48	chr2:54206200-54214200	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
49	chr2:54206200-54214200	Weak transcription	Adipose Nuclei	Adipose
50	chr2:54206200-54214200	Weak transcription	Brain Hippocampus Middle	brain

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