Variant report

Variant	rs9853946
Chromosome Location	chr3:42590532-42590533
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr3:42587762..42590603-chr3:42632314..42633856,2	K562	blood:
2	chr3:42589409..42591800-chr3:42596445..42599442,2	K562	blood:
3	chr3:42588925..42591573-chr3:42621859..42623455,2	K562	blood:
4	chr3:42588703..42591647-chr3:42620630..42623474,3	K562	blood:
5	chr3:42590321..42592623-chr3:42611370..42613403,2	MCF-7	breast:
6	chr3:42576192..42579713-chr3:42587519..42590896,6	K562	blood:
7	chr3:42584276..42586986-chr3:42587983..42591334,3	K562	blood:

Variant related genes	Relation type
ENSG00000093183	Chromatin interaction
ENSG00000008324	Chromatin interaction

Extended variants
information (count: 28 )
Associated
traits (count: 0)

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

rs_ID	r²[population]
rs10154957	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs13320598	1.00[AMR][1000 genomes]
rs13320629	1.00[YRI][hapmap]
rs13325536	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs28508060	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs28549046	1.00[AMR][1000 genomes]
rs28830825	0.81[AFR][1000 genomes]
rs580447	1.00[AMR][1000 genomes]
rs58273990	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs9311325	1.00[YRI][hapmap]
rs9812538	1.00[AMR][1000 genomes]
rs9812673	1.00[AMR][1000 genomes]
rs9816776	0.81[AFR][1000 genomes]
rs9822273	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs9832720	1.00[AMR][1000 genomes]
rs9841926	1.00[AMR][1000 genomes]
rs9844154	1.00[YRI][hapmap];0.81[AFR][1000 genomes]
rs9847303	1.00[YRI][hapmap];0.84[AFR][1000 genomes]
rs9849556	1.00[YRI][hapmap]
rs9855071	1.00[AMR][1000 genomes]
rs9869491	0.84[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs9876937	1.00[ASW][hapmap];1.00[LWK][hapmap];1.00[MKK][hapmap];1.00[YRI][hapmap];1.00[AMR][1000 genomes]
rs9884030	1.00[ASW][hapmap];1.00[AMR][1000 genomes]
rs9985232	1.00[ASW][hapmap];1.00[AMR][1000 genomes]
rs9985361	0.81[AFR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 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	nsv1002944	chr3:42559762-42728909	Strong transcription Flanking Active TSS Weak transcription Enhancers Genic enhancers Transcr. at gene 5' and 3' Active TSS ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	41 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:123 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:42575200-42594400	Weak transcription	Placenta Amnion	Placenta Amnion
2	chr3:42577400-42590800	Weak transcription	H9 Cell Line	embryonic stem cell
3	chr3:42577400-42592800	Weak transcription	HUES64 Cell Line	embryonic stem cell
4	chr3:42577600-42592000	Weak transcription	HUES48 Cell Line	embryonic stem cell
5	chr3:42577800-42597600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
6	chr3:42578400-42593200	Weak transcription	Primary T helper naive cells from peripheral blood	blood
7	chr3:42578400-42593400	Weak transcription	iPS-18 Cell Line	embryonic stem cell
8	chr3:42581800-42591200	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
9	chr3:42581800-42594400	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
10	chr3:42582000-42593600	Weak transcription	Primary T helper cells fromperipheralblood	blood
11	chr3:42582000-42593600	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
12	chr3:42582000-42594400	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
13	chr3:42582200-42594400	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
14	chr3:42582800-42591600	Weak transcription	Primary T helper cells PMA-I stimulated	--
15	chr3:42582800-42592000	Weak transcription	Ovary	ovary
16	chr3:42583000-42590600	Weak transcription	Fetal Heart	heart
17	chr3:42585000-42590800	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
18	chr3:42586000-42591000	Weak transcription	Primary hematopoietic stem cells	blood
19	chr3:42586000-42591200	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
20	chr3:42586000-42593400	Weak transcription	NH-A	brain
21	chr3:42586200-42595000	Weak transcription	Fetal Brain Male	brain
22	chr3:42586400-42591800	Weak transcription	Duodenum Smooth Muscle	Duodenum
23	chr3:42586400-42593200	Weak transcription	Muscle Satellite Cultured Cells	--
24	chr3:42586400-42593800	Weak transcription	Brain Angular Gyrus	brain
25	chr3:42586400-42594400	Weak transcription	NHEK	skin
26	chr3:42586600-42590600	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
27	chr3:42586600-42593400	Weak transcription	A549	lung
28	chr3:42586600-42593800	Weak transcription	Right Ventricle	heart
29	chr3:42586800-42590600	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
30	chr3:42587000-42591000	Weak transcription	Fetal Intestine Large	intestine
31	chr3:42587000-42591200	Weak transcription	Brain Cingulate Gyrus	brain
32	chr3:42587000-42594200	Weak transcription	Rectal Mucosa Donor 29	rectum
33	chr3:42587000-42594200	Weak transcription	HSMMtube	muscle
34	chr3:42587000-42594400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
35	chr3:42587000-42602400	Weak transcription	Colonic Mucosa	Colon
36	chr3:42587200-42591600	Strong transcription	Foreskin Melanocyte Primary Cells skin01	Skin
37	chr3:42587400-42591000	Weak transcription	Skeletal Muscle Male	skeletal muscle
38	chr3:42587400-42591800	Weak transcription	iPS-20b Cell Line	embryonic stem cell
39	chr3:42587400-42591800	Weak transcription	Fetal Lung	lung
40	chr3:42587400-42597000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
41	chr3:42587400-42597200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
42	chr3:42587400-42606800	Weak transcription	Small Intestine	intestine
43	chr3:42587600-42591400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
44	chr3:42587600-42594400	Weak transcription	HepG2	liver
45	chr3:42587800-42597000	Strong transcription	Fetal Thymus	thymus
46	chr3:42587800-42597000	Strong transcription	Thymus	Thymus
47	chr3:42587800-42611800	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
48	chr3:42588000-42613000	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
49	chr3:42588200-42591600	Weak transcription	Primary B cells from cord blood	blood
50	chr3:42588400-42590600	Strong transcription	NHLF	lung

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