Variant report

Variant	rs3752953
Chromosome Location	chr1:114242250-114242251
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	chr1:114240356..114244592-chr1:114247076..114250656,5	K562	blood:
2	chr1:114240657..114244104-chr1:114245278..114249575,4	MCF-7	breast:

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-RSBN1-5	chr1:114241506-114242253	NONHSAT005327

Variant related genes	Relation type
ENSG00000116793	Chromatin interaction

Extended variants
information (count: 33 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:31)

rs_ID	r²[population]
rs10489936	0.95[CEU][hapmap];1.00[JPT][hapmap]
rs1080307	0.95[CEU][hapmap];1.00[JPT][hapmap];0.80[TSI][hapmap];0.83[EUR][1000 genomes]
rs1217384	0.91[CEU][hapmap]
rs12734625	0.82[EUR][1000 genomes]
rs12746609	0.83[EUR][1000 genomes]
rs12752932	0.82[EUR][1000 genomes]
rs12758546	0.84[EUR][1000 genomes]
rs12760457	0.95[CEU][hapmap];1.00[JPT][hapmap]
rs13374352	0.81[EUR][1000 genomes]
rs17274550	0.84[EUR][1000 genomes]
rs17274620	0.84[EUR][1000 genomes]
rs17274634	0.95[CEU][hapmap];1.00[JPT][hapmap];0.83[TSI][hapmap];0.84[EUR][1000 genomes]
rs17359302	0.84[EUR][1000 genomes]
rs1885454	0.95[CEU][hapmap];1.00[JPT][hapmap];0.83[TSI][hapmap];0.84[EUR][1000 genomes]
rs2040040	0.95[CEU][hapmap];1.00[JPT][hapmap]
rs2359173	0.95[CEU][hapmap];1.00[JPT][hapmap];0.83[TSI][hapmap];0.84[EUR][1000 genomes]
rs2359174	0.95[CEU][hapmap];0.86[JPT][hapmap];0.83[TSI][hapmap];0.84[EUR][1000 genomes]
rs34258372	0.87[CEU][hapmap];1.00[JPT][hapmap];0.82[TSI][hapmap]
rs3747998	0.95[CEU][hapmap];1.00[JPT][hapmap];0.83[MEX][hapmap];0.84[EUR][1000 genomes]
rs3748003	0.95[CEU][hapmap];1.00[JPT][hapmap];0.83[TSI][hapmap];0.84[EUR][1000 genomes]
rs3761931	0.95[CEU][hapmap];1.00[JPT][hapmap];0.83[TSI][hapmap]
rs3789595	0.84[EUR][1000 genomes]
rs3789607	0.95[CEU][hapmap];1.00[JPT][hapmap]
rs3789609	0.95[CEU][hapmap];0.86[JPT][hapmap]
rs61817579	0.85[EUR][1000 genomes]
rs61817586	0.82[EUR][1000 genomes]
rs61820162	0.83[EUR][1000 genomes]
rs6668829	1.00[CEU][hapmap];1.00[JPT][hapmap]
rs6674848	0.95[CEU][hapmap];1.00[JPT][hapmap];0.83[TSI][hapmap];0.82[EUR][1000 genomes]
rs6703387	0.95[CEU][hapmap];1.00[JPT][hapmap]
rs9803891	0.95[CEU][hapmap];1.00[JPT][hapmap]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv872161	chr1:114162194-114280135	Enhancers Weak transcription Strong transcription ZNF genes & repeats Flanking Active TSS Genic enhancers Active TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	14 gene(s)	inside rSNPs	diseases
2	esv2752424	chr1:114189958-114712958	Strong transcription Flanking Active TSS Bivalent Enhancer Genic enhancers Weak transcription Enhancers Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	96 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs3752953	CD58	cis	cerebellum	SCAN

Chromatin state (count:112 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:114203200-114298600	Weak transcription	Fetal Brain Male	brain
2	chr1:114216000-114247000	Weak transcription	HMEC	breast
3	chr1:114216200-114279800	Weak transcription	Stomach Smooth Muscle	stomach
4	chr1:114216400-114250400	Weak transcription	Placenta	Placenta
5	chr1:114220400-114263800	Weak transcription	Fetal Kidney	kidney
6	chr1:114225200-114243800	Weak transcription	iPS-15b Cell Line	embryonic stem cell
7	chr1:114227000-114268200	Weak transcription	NHLF	lung
8	chr1:114227400-114252000	Weak transcription	Rectal Mucosa Donor 29	rectum
9	chr1:114228000-114287800	Weak transcription	Rectal Mucosa Donor 31	rectum
10	chr1:114228400-114249800	Weak transcription	Hela-S3	cervix
11	chr1:114231000-114251200	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
12	chr1:114233200-114245000	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
13	chr1:114236400-114300000	Weak transcription	Small Intestine	intestine
14	chr1:114237400-114256600	Weak transcription	Colonic Mucosa	Colon
15	chr1:114238000-114251400	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
16	chr1:114238000-114252800	Weak transcription	Duodenum Mucosa	Duodenum
17	chr1:114238000-114258200	Weak transcription	Fetal Heart	heart
18	chr1:114238200-114250200	Weak transcription	Brain Cingulate Gyrus	brain
19	chr1:114238200-114252200	Weak transcription	Fetal Brain Female	brain
20	chr1:114238200-114256000	Weak transcription	Muscle Satellite Cultured Cells	--
21	chr1:114238200-114264400	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
22	chr1:114238400-114242400	Strong transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
23	chr1:114238400-114243400	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
24	chr1:114238400-114243800	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
25	chr1:114238400-114244400	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
26	chr1:114238400-114266800	Weak transcription	NHEK	skin
27	chr1:114238600-114242800	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
28	chr1:114238600-114243400	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
29	chr1:114238800-114251000	Weak transcription	Breast Myoepithelial Primary Cells	Breast
30	chr1:114238800-114252400	Weak transcription	Primary T cells fromperipheralblood	blood
31	chr1:114238800-114252800	Weak transcription	Fetal Intestine Large	intestine
32	chr1:114238800-114252800	Weak transcription	K562	blood
33	chr1:114239000-114243600	Strong transcription	Monocytes-CD14+_RO01746	blood
34	chr1:114239000-114244200	Strong transcription	Cortex derived primary cultured neurospheres	brain
35	chr1:114239000-114260400	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
36	chr1:114239200-114279800	Weak transcription	Colon Smooth Muscle	Colon
37	chr1:114239400-114242400	Strong transcription	Brain Germinal Matrix	brain
38	chr1:114239400-114242400	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
39	chr1:114239400-114242600	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
40	chr1:114239400-114258600	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
41	chr1:114239600-114242600	Strong transcription	HUES6 Cell Line	embryonic stem cell
42	chr1:114239600-114244200	Strong transcription	Primary hematopoietic stem cells short term culture	blood
43	chr1:114239600-114244400	Strong transcription	GM12878-XiMat	blood
44	chr1:114239600-114245400	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
45	chr1:114239600-114249800	Weak transcription	Pancreatic Islets	Pancreatic Islet
46	chr1:114239800-114244200	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
47	chr1:114239800-114244200	Weak transcription	Primary B cells from peripheral blood	blood
48	chr1:114239800-114250800	Weak transcription	HepG2	liver
49	chr1:114240000-114242800	Strong transcription	Primary neutrophils fromperipheralblood	blood
50	chr1:114240200-114244000	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--

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