Variant report

Variant	rs4419353
Chromosome Location	chr3:113254937-113254938
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr3:113254497..113255223-chr3:113296850..113297376,2	MCF-7	breast:
2	chr3:113215914..113218639-chr3:113252642..113255587,3	MCF-7	breast:
3	chr3:113254930..113255834-chr3:113270582..113271304,2	MCF-7	breast:
4	chr3:113254346..113256305-chr3:113270288..113271550,7	MCF-7	breast:
5	chr3:113229615..113239929-chr3:113247196..113257849,45	MCF-7	breast:
6	chr3:113254658..113255498-chr3:113275897..113276863,4	MCF-7	breast:

Variant related genes	Relation type
ENSG00000163611	Chromatin interaction

Extended variants
information (count: 35 )
Associated
traits (count: 2 )

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

rs_ID	r²[population]
rs13326562	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs13327031	1.00[EUR][1000 genomes]
rs13353449	1.00[EUR][1000 genomes]
rs2399487	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs28539944	0.81[EUR][1000 genomes]
rs28614095	0.81[EUR][1000 genomes]
rs6438154	0.84[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs6763234	1.00[CEU][hapmap];0.89[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs6779241	1.00[CEU][hapmap];1.00[EUR][1000 genomes]
rs6780720	1.00[CEU][hapmap];0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs6781507	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs6797630	0.81[EUR][1000 genomes]
rs6808103	1.00[CEU][hapmap];0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs72950895	0.81[EUR][1000 genomes]
rs7612448	1.00[CEU][hapmap];1.00[MEX][hapmap];0.91[EUR][1000 genomes]
rs7618195	0.86[EUR][1000 genomes]
rs7625829	1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[TSI][hapmap];0.95[EUR][1000 genomes]
rs7629636	1.00[CEU][hapmap];0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7645188	1.00[CEU][hapmap];0.89[YRI][hapmap];0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs9810059	1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[TSI][hapmap];0.89[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs9810754	1.00[GIH][hapmap];1.00[TSI][hapmap];0.81[EUR][1000 genomes]
rs9811168	0.90[EUR][1000 genomes]
rs9827490	0.81[EUR][1000 genomes]
rs9827772	1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[TSI][hapmap];0.86[EUR][1000 genomes]
rs9836199	0.90[EUR][1000 genomes]
rs9846529	0.81[EUR][1000 genomes]
rs9851183	1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[TSI][hapmap];0.89[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs9851407	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs9852068	1.00[CEU][hapmap];1.00[EUR][1000 genomes]
rs9860473	0.95[EUR][1000 genomes]
rs9878186	1.00[CEU][hapmap];0.88[YRI][hapmap];0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[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

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs4419353	KLF4	trans	brain	seeQTL
rs4419353	CCL3	trans	brain	seeQTL

Chromatin state (count:34 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:113252400-113255000	Weak transcription	Gastric	stomach
2	chr3:113252600-113256400	Weak transcription	Esophagus	oesophagus
3	chr3:113252800-113255000	Weak transcription	Primary hematopoietic stem cells short term culture	blood
4	chr3:113253400-113256000	Enhancers	Primary T cells effector/memory enriched fromperipheralblood	blood
5	chr3:113253600-113255000	Weak transcription	Primary hematopoietic stem cells	blood
6	chr3:113253600-113255400	Weak transcription	Small Intestine	intestine
7	chr3:113253800-113255000	Active TSS	Rectal Mucosa Donor 29	rectum
8	chr3:113253800-113255000	Weak transcription	Stomach Mucosa	stomach
9	chr3:113253800-113255600	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
10	chr3:113253800-113257200	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
11	chr3:113253800-113257200	Enhancers	Primary T killer naive cells fromperipheralblood	blood
12	chr3:113253800-113257200	Enhancers	Primary T killer memory cells from peripheral blood	blood
13	chr3:113253800-113257400	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
14	chr3:113253800-113260800	Weak transcription	Thymus	Thymus
15	chr3:113254000-113256200	Enhancers	Primary T helper naive cells from peripheral blood	blood
16	chr3:113254000-113256200	Enhancers	Primary T helper cells fromperipheralblood	blood
17	chr3:113254000-113257200	Enhancers	Rectal Mucosa Donor 31	rectum
18	chr3:113254000-113257800	Weak transcription	Spleen	Spleen
19	chr3:113254000-113258400	Enhancers	Primary T helper naive cells fromperipheralblood	blood
20	chr3:113254200-113260000	Weak transcription	Fetal Thymus	thymus
21	chr3:113254400-113255200	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
22	chr3:113254400-113256600	Genic enhancers	Primary T cells from cord blood	blood
23	chr3:113254400-113256800	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
24	chr3:113254400-113258400	Genic enhancers	Primary T helper cells PMA-I stimulated	--
25	chr3:113254600-113255600	Enhancers	Sigmoid Colon	Sigmoid Colon
26	chr3:113254600-113255600	Enhancers	Dnd41	blood
27	chr3:113254600-113255800	Genic enhancers	Primary T cells fromperipheralblood	blood
28	chr3:113254600-113256200	Transcr. at gene 5' and 3'	GM12878-XiMat	blood
29	chr3:113254600-113256400	Genic enhancers	Primary B cells from peripheral blood	blood
30	chr3:113254600-113257200	Genic enhancers	Primary T regulatory cells fromperipheralblood	blood
31	chr3:113254800-113255000	Enhancers	A549	lung
32	chr3:113254800-113255400	Enhancers	Primary mononuclear cells fromperipheralblood	Blood
33	chr3:113254800-113257000	Genic enhancers	Primary Natural Killer cells fromperipheralblood	blood
34	chr3:113254800-113257200	Strong transcription	Primary B cells from cord blood	blood

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