Variant report

Variant	rs7569954
Chromosome Location	chr2:54216979-54216980
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr2:54196870..54199646-chr2:54215437..54217712,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000068878	Chromatin interaction
ENSG00000170634	Chromatin interaction

Extended variants
information (count: 5 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:4)

rs_ID	r²[population]
rs10198376	0.81[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs11888025	0.90[ASN][1000 genomes]
rs6545375	0.93[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];0.83[JPT][hapmap];1.00[MEX][hapmap];0.83[MKK][hapmap];0.98[TSI][hapmap];1.00[AMR][1000 genomes];0.91[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7561987	0.85[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:2)

SNP	Gene	Cis/trans	Tissue	Source
rs7569954	PSME4	Cis_1M	lymphoblastoid	RTeQTL
rs7569954	MTIF2	cis	cerebellum	SCAN

Chromatin state (count:63 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:54199000-54221600	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
2	chr2:54199000-54228800	Weak transcription	Aorta	Aorta
3	chr2:54200400-54218400	Weak transcription	Primary T killer memory cells from peripheral blood	blood
4	chr2:54204400-54226400	Weak transcription	Pancreas	Pancrea
5	chr2:54205200-54222600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
6	chr2:54206000-54221600	Weak transcription	Thymus	Thymus
7	chr2:54206000-54226400	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
8	chr2:54206400-54220000	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
9	chr2:54208200-54221400	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
10	chr2:54208400-54248200	Weak transcription	Lung	lung
11	chr2:54208600-54219000	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
12	chr2:54208600-54220200	Weak transcription	Primary hematopoietic stem cells short term culture	blood
13	chr2:54209000-54221400	Weak transcription	Fetal Thymus	thymus
14	chr2:54209000-54221600	Weak transcription	Dnd41	blood
15	chr2:54211200-54219000	Weak transcription	Primary T cells fromperipheralblood	blood
16	chr2:54211200-54220600	Weak transcription	Primary hematopoietic stem cells	blood
17	chr2:54211400-54217800	Weak transcription	Fetal Muscle Trunk	muscle
18	chr2:54211400-54220200	Weak transcription	Primary B cells from cord blood	blood
19	chr2:54211400-54243000	Weak transcription	Fetal Muscle Leg	muscle
20	chr2:54213600-54249800	Weak transcription	Left Ventricle	heart
21	chr2:54213800-54217200	Enhancers	Skeletal Muscle Male	skeletal muscle
22	chr2:54214200-54217000	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
23	chr2:54214800-54217200	Weak transcription	Fetal Stomach	stomach
24	chr2:54214800-54219000	Weak transcription	Primary T helper naive cells from peripheral blood	blood
25	chr2:54215000-54219000	Weak transcription	Primary T helper cells PMA-I stimulated	--
26	chr2:54215000-54219200	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
27	chr2:54215000-54220600	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
28	chr2:54215000-54226000	Weak transcription	Duodenum Smooth Muscle	Duodenum
29	chr2:54215000-54226000	Weak transcription	HSMMtube	muscle
30	chr2:54215000-54242800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
31	chr2:54215200-54219200	Weak transcription	Primary T helper cells fromperipheralblood	blood
32	chr2:54215200-54219400	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
33	chr2:54215200-54220000	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
34	chr2:54215200-54220000	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
35	chr2:54215200-54220400	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
36	chr2:54215200-54220400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
37	chr2:54215200-54225200	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
38	chr2:54215400-54220200	Weak transcription	Primary B cells from peripheral blood	blood
39	chr2:54215400-54220200	Weak transcription	Muscle Satellite Cultured Cells	--
40	chr2:54215600-54217000	Enhancers	Sigmoid Colon	Sigmoid Colon
41	chr2:54215800-54217200	Enhancers	HepG2	liver
42	chr2:54216000-54217000	Enhancers	Psoas Muscle	Psoas
43	chr2:54216200-54217000	Enhancers	Right Atrium	heart
44	chr2:54216200-54217000	Enhancers	Skeletal Muscle Female	skeletal muscle
45	chr2:54216400-54217000	Enhancers	Osteobl	bone
46	chr2:54216400-54242000	Weak transcription	Fetal Intestine Small	intestine
47	chr2:54216600-54217000	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
48	chr2:54216600-54217000	Enhancers	Primary T cells from cord blood	blood
49	chr2:54216600-54217000	Enhancers	Adipose Nuclei	Adipose
50	chr2:54216600-54217000	Enhancers	Liver	Liver

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