Variant report

Variant	rs399582
Chromosome Location	chr3:42549343-42549344
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr3:42542738..42545212-chr3:42547259..42551511,4	MCF-7	breast:
2	chr3:42530093..42535343-chr3:42545492..42550064,6	MCF-7	breast:
3	chr3:42546908..42549650-chr3:42559175..42561054,2	MCF-7	breast:
4	chr3:42542139..42544178-chr3:42546531..42549362,2	K562	blood:

Variant related genes	Relation type
ENSG00000114812	Chromatin interaction

Extended variants
information (count: 12 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:7)

rs_ID	r²[population]
rs1078008	0.94[CEU][hapmap];0.92[EUR][1000 genomes]
rs182921	0.88[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs342542	0.90[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs406683	0.94[CEU][hapmap];0.83[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs421558	1.00[CEU][hapmap];0.99[AFR][1000 genomes];0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62248806	0.80[AMR][1000 genomes]
rs673560	0.83[AMR][1000 genomes];0.98[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv529987	chr3:41921995-42591771	Bivalent Enhancer Weak transcription Flanking Active TSS Strong transcription Enhancers Flanking Bivalent TSS/Enh Active TSS Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	32 gene(s)	inside rSNPs	diseases
2	nsv1005533	chr3:41953873-42596375	Enhancers Flanking Bivalent TSS/Enh Genic enhancers Weak transcription Flanking Active TSS Strong transcription Bivalent/Poised TSS Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	31 gene(s)	inside rSNPs	diseases
3	esv1804804	chr3:42515186-42582403	Flanking Active TSS Enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Weak transcription Transcr. at gene 5' and 3' Strong transcription Genic enhancers Bivalent/Poised TSS Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
4	nsv527430	chr3:42534042-42557199	Weak transcription Enhancers Genic enhancers Active TSS Bivalent Enhancer Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Strong transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
5	esv1814102	chr3:42539966-42582403	Flanking Active TSS Weak transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Enhancers Active TSS Genic enhancers Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:67 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:42544600-42551600	Weak transcription	Pancreas	Pancrea
2	chr3:42544800-42550600	Weak transcription	Right Atrium	heart
3	chr3:42545000-42549800	Weak transcription	Small Intestine	intestine
4	chr3:42545400-42551400	Enhancers	Primary T helper cells fromperipheralblood	blood
5	chr3:42545400-42553800	Enhancers	Primary T helper cells PMA-I stimulated	--
6	chr3:42545600-42550200	Enhancers	Primary T cells fromperipheralblood	blood
7	chr3:42546000-42549400	Weak transcription	Brain Anterior Caudate	brain
8	chr3:42546600-42553800	Enhancers	Primary T helper naive cells fromperipheralblood	blood
9	chr3:42547200-42561800	Genic enhancers	Fetal Intestine Small	intestine
10	chr3:42547600-42549600	Weak transcription	Brain Inferior Temporal Lobe	brain
11	chr3:42547600-42579000	Weak transcription	Rectal Smooth Muscle	rectum
12	chr3:42547800-42550000	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
13	chr3:42547800-42551000	Enhancers	Primary T helper naive cells from peripheral blood	blood
14	chr3:42548000-42550200	Enhancers	Fetal Intestine Large	intestine
15	chr3:42548200-42549400	Enhancers	HUES6 Cell Line	embryonic stem cell
16	chr3:42548400-42549600	Enhancers	Primary T regulatory cells fromperipheralblood	blood
17	chr3:42548400-42550000	Enhancers	Primary T killer memory cells from peripheral blood	blood
18	chr3:42548400-42551000	Enhancers	Primary T killer naive cells fromperipheralblood	blood
19	chr3:42548400-42552400	Enhancers	Colonic Mucosa	Colon
20	chr3:42548600-42549400	Enhancers	ES-I3 Cell Line	embryonic stem cell
21	chr3:42548600-42549400	Enhancers	HUES48 Cell Line	embryonic stem cell
22	chr3:42548600-42549400	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
23	chr3:42548600-42549400	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
24	chr3:42548600-42549400	Flanking Active TSS	Rectal Mucosa Donor 29	rectum
25	chr3:42548600-42549400	Enhancers	Monocytes-CD14+_RO01746	blood
26	chr3:42548600-42549600	Enhancers	HUES64 Cell Line	embryonic stem cell
27	chr3:42548600-42549600	Enhancers	iPS-18 Cell Line	embryonic stem cell
28	chr3:42548600-42549800	Enhancers	H1 Cell Line	embryonic stem cell
29	chr3:42548600-42549800	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
30	chr3:42548600-42549800	Enhancers	Breast Myoepithelial Primary Cells	Breast
31	chr3:42548600-42549800	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
32	chr3:42548600-42549800	Enhancers	Primary mononuclear cells fromperipheralblood	Blood
33	chr3:42548600-42549800	Enhancers	Fetal Heart	heart
34	chr3:42548600-42549800	Enhancers	Placenta	Placenta
35	chr3:42548600-42549800	Enhancers	Spleen	Spleen
36	chr3:42548600-42550400	Enhancers	Primary monocytes fromperipheralblood	blood
37	chr3:42548600-42550400	Enhancers	Fetal Thymus	thymus
38	chr3:42548600-42550800	Enhancers	Primary hematopoietic stem cells short term culture	blood
39	chr3:42548600-42550800	Enhancers	Primary T cells effector/memory enriched fromperipheralblood	blood
40	chr3:42548600-42553000	Enhancers	Stomach Mucosa	stomach
41	chr3:42548800-42549400	Enhancers	H9 Cell Line	embryonic stem cell
42	chr3:42548800-42549400	Enhancers	iPS-20b Cell Line	embryonic stem cell
43	chr3:42548800-42549600	Weak transcription	Liver	Liver
44	chr3:42548800-42549600	Enhancers	Thymus	Thymus
45	chr3:42548800-42549800	Enhancers	Primary hematopoietic stem cells	blood
46	chr3:42548800-42549800	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
47	chr3:42548800-42549800	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
48	chr3:42548800-42549800	Enhancers	Adipose Nuclei	Adipose
49	chr3:42548800-42551600	Enhancers	Lung	lung
50	chr3:42548800-42553200	Enhancers	Sigmoid Colon	Sigmoid Colon

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