Variant report

Variant	rs9860473
Chromosome Location	chr3:113273654-113273655
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr3:113206409..113208737-chr3:113273069..113276271,3	MCF-7	breast:
2	chr3:113233433..113235581-chr3:113273255..113276149,3	MCF-7	breast:
3	chr3:113267576..113271162-chr3:113272689..113275342,3	K562	blood:
4	chr3:113230896..113236069-chr3:113272608..113276294,6	MCF-7	breast:

Variant related genes	Relation type
ENSG00000163611	Chromatin interaction

Extended variants
information (count: 34 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:30)

rs_ID	r²[population]
rs13326562	0.86[EUR][1000 genomes]
rs13327031	0.95[EUR][1000 genomes]
rs13353449	0.95[EUR][1000 genomes]
rs2399487	0.95[EUR][1000 genomes]
rs28539944	0.93[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs28614095	0.86[EUR][1000 genomes]
rs4419353	0.95[EUR][1000 genomes]
rs6438154	0.95[EUR][1000 genomes]
rs6763234	0.95[EUR][1000 genomes]
rs6779241	0.95[EUR][1000 genomes]
rs6780720	0.95[EUR][1000 genomes]
rs6781507	0.95[EUR][1000 genomes]
rs6797630	0.87[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs6808103	0.95[EUR][1000 genomes]
rs72950893	0.87[AMR][1000 genomes]
rs72950895	0.86[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs7612448	0.87[EUR][1000 genomes]
rs7625829	0.91[EUR][1000 genomes]
rs7629636	0.95[EUR][1000 genomes]
rs7645188	0.95[EUR][1000 genomes]
rs9810059	0.95[EUR][1000 genomes]
rs9810754	0.93[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs9827490	0.87[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs9827772	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs9829540	0.87[AMR][1000 genomes]
rs9846529	0.86[EUR][1000 genomes]
rs9851183	0.86[EUR][1000 genomes]
rs9851407	0.91[EUR][1000 genomes]
rs9852068	0.95[EUR][1000 genomes]
rs9878186	0.95[EUR][1000 genomes]

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	nsv1013506	chr3:112890608-113680951	Weak transcription Bivalent/Poised TSS Enhancers Strong transcription ZNF genes & repeats Genic enhancers Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	51 gene(s)	inside rSNPs	diseases
2	nsv1004000	chr3:113116778-113513899	Weak transcription Strong transcription ZNF genes & repeats Active TSS Enhancers Flanking Active TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	34 gene(s)	inside rSNPs	diseases
3	nsv877349	chr3:113208224-113323787	Enhancers Flanking Active TSS Strong transcription Active TSS Weak transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	13 gene(s)	inside rSNPs	diseases
4	nsv877350	chr3:113208224-113332235	Strong transcription Weak transcription Enhancers Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	13 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:26 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:113255400-113278800	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
2	chr3:113255600-113274800	Weak transcription	Sigmoid Colon	Sigmoid Colon
3	chr3:113255600-113278400	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
4	chr3:113256000-113279000	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
5	chr3:113257200-113277400	Weak transcription	Primary T helper naive cells from peripheral blood	blood
6	chr3:113257200-113283400	Weak transcription	Primary B cells from cord blood	blood
7	chr3:113261200-113276200	Weak transcription	Rectal Mucosa Donor 29	rectum
8	chr3:113262600-113278800	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
9	chr3:113266800-113276400	Weak transcription	Primary T helper cells PMA-I stimulated	--
10	chr3:113267400-113276200	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
11	chr3:113267400-113278400	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
12	chr3:113268200-113279400	Weak transcription	Primary hematopoietic stem cells	blood
13	chr3:113269200-113276600	Weak transcription	Primary T killer memory cells from peripheral blood	blood
14	chr3:113269400-113276200	Weak transcription	Primary T helper cells fromperipheralblood	blood
15	chr3:113271000-113277600	Enhancers	HepG2	liver
16	chr3:113271400-113276400	Weak transcription	Stomach Mucosa	stomach
17	chr3:113271600-113274000	Weak transcription	Rectal Mucosa Donor 31	rectum
18	chr3:113272000-113276600	Weak transcription	Primary B cells from peripheral blood	blood
19	chr3:113272200-113276000	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
20	chr3:113273000-113274400	Strong transcription	Primary T cells from cord blood	blood
21	chr3:113273200-113275000	Weak transcription	A549	lung
22	chr3:113273200-113275800	Weak transcription	Primary T cells fromperipheralblood	blood
23	chr3:113273200-113276200	Weak transcription	GM12878-XiMat	blood
24	chr3:113273600-113273800	Active TSS	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
25	chr3:113273600-113274000	Enhancers	Foreskin Melanocyte Primary Cells skin01	Skin
26	chr3:113273600-113275000	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin

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