Variant report

Variant	rs4849086
Chromosome Location	chr2:113394119-113394120
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	chr2:113392494..113394338-chr2:113475169..113476676,2	MCF-7	breast:
2	chr2:113391817..113395681-chr2:113402206..113404439,3	MCF-7	breast:

Variant related genes	Relation type
ENSG00000144136	Chromatin interaction
ENSG00000237753	Chromatin interaction

Extended variants
information (count: 29 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:25)

rs_ID	r²[population]
rs10171024	0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10184339	0.91[EUR][1000 genomes]
rs1053652	0.89[CEU][hapmap];0.94[CHB][hapmap]
rs10758	0.89[CEU][hapmap];0.94[CHB][hapmap];0.89[CHD][hapmap];0.87[MEX][hapmap];0.82[TSI][hapmap];0.82[EUR][1000 genomes]
rs11680446	0.94[CHB][hapmap]
rs12479380	0.85[CHB][hapmap]
rs12612089	0.80[EUR][1000 genomes]
rs13023016	0.89[CHB][hapmap]
rs13387435	0.83[CEU][hapmap];0.80[CHB][hapmap];0.97[TSI][hapmap];0.83[EUR][1000 genomes]
rs17515708	0.91[EUR][1000 genomes]
rs17515715	0.83[EUR][1000 genomes]
rs2048873	0.84[CEU][hapmap];0.83[CHB][hapmap]
rs35048989	0.83[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs3827758	0.83[CHB][hapmap]
rs4368335	0.83[CHB][hapmap]
rs4849084	0.89[CHB][hapmap]
rs4849091	0.89[CHB][hapmap];0.83[CHD][hapmap]
rs57033895	0.81[ASN][1000 genomes]
rs58662040	0.91[EUR][1000 genomes]
rs60372418	0.80[EUR][1000 genomes]
rs6542074	0.94[CHB][hapmap]
rs6705487	0.94[CHB][hapmap]
rs6725228	0.93[EUR][1000 genomes]
rs7371700	0.82[CHB][hapmap]
rs908545	0.89[CHB][hapmap]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv458997	chr2:113313794-113431092	Flanking Active TSS Strong transcription Weak transcription Genic enhancers Enhancers Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	73 gene(s)	inside rSNPs	diseases
2	nsv582708	chr2:113313794-113431092	Strong transcription Weak transcription Enhancers Flanking Active TSS Genic enhancers Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	73 gene(s)	inside rSNPs	diseases
3	nsv470480	chr2:113373950-113429752	Flanking Active TSS Strong transcription Enhancers Weak transcription Genic enhancers Bivalent Enhancer Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	51 gene(s)	inside rSNPs	diseases
4	nsv428724	chr2:113376894-113555421	Genic enhancers Strong transcription Weak transcription Enhancers Transcr. at gene 5' and 3' Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	56 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs4849086	IL3	trans	cerebellum	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:113385000-113396000	Weak transcription	Colonic Mucosa	Colon
2	chr2:113385000-113402600	Weak transcription	Esophagus	oesophagus
3	chr2:113385800-113401800	Weak transcription	Brain Hippocampus Middle	brain
4	chr2:113388800-113394800	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
5	chr2:113388800-113398200	Weak transcription	Lung	lung
6	chr2:113389000-113395000	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
7	chr2:113389000-113395000	Enhancers	Primary T helper cells fromperipheralblood	blood
8	chr2:113389200-113394800	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
9	chr2:113389200-113394800	Enhancers	Fetal Thymus	thymus
10	chr2:113389400-113395000	Enhancers	Primary T cells fromperipheralblood	blood
11	chr2:113389400-113402000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
12	chr2:113389600-113394800	Enhancers	Primary T helper cells PMA-I stimulated	--
13	chr2:113389600-113395000	Enhancers	Primary T cells from cord blood	blood
14	chr2:113389600-113402200	Weak transcription	Primary B cells from cord blood	blood
15	chr2:113389800-113395200	Enhancers	Primary T helper naive cells from peripheral blood	blood
16	chr2:113389800-113398400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
17	chr2:113389800-113400400	Weak transcription	Fetal Intestine Small	intestine
18	chr2:113390000-113396800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
19	chr2:113390000-113397200	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
20	chr2:113390000-113398000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
21	chr2:113390600-113394600	Weak transcription	Muscle Satellite Cultured Cells	--
22	chr2:113390800-113397400	Weak transcription	K562	blood
23	chr2:113391400-113394800	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
24	chr2:113391400-113398000	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
25	chr2:113391800-113395000	Enhancers	Primary T killer memory cells from peripheral blood	blood
26	chr2:113392000-113397000	Weak transcription	HMEC	breast
27	chr2:113392200-113394400	Weak transcription	Duodenum Mucosa	Duodenum
28	chr2:113392200-113397600	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
29	chr2:113392600-113395000	Enhancers	Primary T killer naive cells fromperipheralblood	blood
30	chr2:113392600-113397800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
31	chr2:113392800-113394400	Enhancers	Primary T helper naive cells fromperipheralblood	blood
32	chr2:113392800-113402000	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
33	chr2:113393200-113396800	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
34	chr2:113393400-113394200	Enhancers	Monocytes-CD14+_RO01746	blood
35	chr2:113393400-113395000	Enhancers	Placenta	Placenta
36	chr2:113393600-113394400	Bivalent Enhancer	HepG2	liver
37	chr2:113393600-113394800	Enhancers	Primary hematopoietic stem cells short term culture	blood
38	chr2:113393600-113395600	Enhancers	Primary monocytes fromperipheralblood	blood
39	chr2:113393800-113394800	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
40	chr2:113393800-113394800	Enhancers	Rectal Mucosa Donor 29	rectum
41	chr2:113393800-113395000	Enhancers	Primary neutrophils fromperipheralblood	blood
42	chr2:113394000-113394200	Enhancers	Primary mononuclear cells fromperipheralblood	Blood
43	chr2:113394000-113394200	Enhancers	Spleen	Spleen
44	chr2:113394000-113394200	Flanking Active TSS	GM12878-XiMat	blood
45	chr2:113394000-113394400	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
46	chr2:113394000-113394600	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
47	chr2:113394000-113394800	Enhancers	Primary B cells from peripheral blood	blood
48	chr2:113394000-113395000	Enhancers	Sigmoid Colon	Sigmoid Colon
49	chr2:113394000-113396000	Weak transcription	Rectal Mucosa Donor 31	rectum
50	chr2:113394000-113398000	Weak transcription	Skeletal Muscle Female	skeletal muscle

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