Variant report

Variant	rs28758860
Chromosome Location	chr3:52434546-52434547
allele	A/C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr3:52424863..52429708-chr3:52432804..52436017,4	MCF-7	breast:
2	chr3:52420073..52422449-chr3:52434521..52436360,2	K562	blood:
3	chr3:52433533..52435348-chr3:52441662..52443180,2	MCF-7	breast:
4	chr3:52433460..52436241-chr3:52446322..52448131,2	K562	blood:

Variant related genes	Relation type
ENSG00000010318	Chromatin interaction
ENSG00000114841	Chromatin interaction
ENSG00000163930	Chromatin interaction

Extended variants
information (count: 13 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:8)

rs_ID	r²[population]
rs17052020	1.00[MEX][hapmap]
rs17052095	1.00[YRI][hapmap];0.95[AFR][1000 genomes]
rs17052269	1.00[MEX][hapmap]
rs57465701	1.00[AMR][1000 genomes]
rs61738524	0.95[AFR][1000 genomes]
rs7614535	1.00[MEX][hapmap]
rs7615736	0.87[ASW][hapmap];0.87[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[YRI][hapmap];0.90[AFR][1000 genomes]
rs7630920	1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[YRI][hapmap];1.00[AMR][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	nsv876789	chr3:52247110-52575831	Flanking Active TSS Bivalent Enhancer Strong transcription Weak transcription Enhancers Genic enhancers Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	117 gene(s)	inside rSNPs	diseases
2	nsv984542	chr3:52285682-52516115	Weak transcription Enhancers Strong transcription Bivalent Enhancer Flanking Active TSS Genic enhancers Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA	94 gene(s)	inside rSNPs	diseases
3	nsv834696	chr3:52317478-52479537	Flanking Active TSS Active TSS Strong transcription Weak transcription Bivalent Enhancer Enhancers Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA	45 gene(s)	inside rSNPs	diseases
4	nsv834697	chr3:52400578-52579417	Weak transcription Active TSS Genic enhancers Strong transcription Flanking Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Enhancers ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	49 gene(s)	inside rSNPs	diseases
5	nsv876792	chr3:52430526-52575831	Flanking Active TSS Weak transcription Enhancers Strong transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Genic enhancers Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	45 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:124 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:52385400-52434600	Weak transcription	Small Intestine	intestine
2	chr3:52393200-52434800	Weak transcription	Colon Smooth Muscle	Colon
3	chr3:52395000-52443200	Weak transcription	Right Atrium	heart
4	chr3:52408000-52436600	Weak transcription	Fetal Kidney	kidney
5	chr3:52410600-52435400	Weak transcription	Primary hematopoietic stem cells	blood
6	chr3:52414000-52435400	Weak transcription	Fetal Lung	lung
7	chr3:52414800-52434800	Weak transcription	Primary T killer memory cells from peripheral blood	blood
8	chr3:52418600-52442200	Strong transcription	Fetal Intestine Small	intestine
9	chr3:52418800-52441800	Strong transcription	Brain Anterior Caudate	brain
10	chr3:52419000-52441800	Strong transcription	Liver	Liver
11	chr3:52419000-52442000	Strong transcription	Brain Hippocampus Middle	brain
12	chr3:52419000-52442600	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
13	chr3:52419200-52435400	Weak transcription	iPS-15b Cell Line	embryonic stem cell
14	chr3:52419200-52441600	Strong transcription	Fetal Stomach	stomach
15	chr3:52419200-52441800	Strong transcription	Brain Angular Gyrus	brain
16	chr3:52419200-52442000	Strong transcription	Brain Inferior Temporal Lobe	brain
17	chr3:52419600-52435600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
18	chr3:52420000-52442000	Strong transcription	Primary neutrophils fromperipheralblood	blood
19	chr3:52420200-52442400	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
20	chr3:52420200-52442400	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
21	chr3:52420200-52442600	Strong transcription	Fetal Intestine Large	intestine
22	chr3:52422600-52441800	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
23	chr3:52425600-52442000	Strong transcription	Spleen	Spleen
24	chr3:52426200-52436000	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
25	chr3:52426600-52442200	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
26	chr3:52427400-52434600	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
27	chr3:52427800-52436000	Weak transcription	Primary T helper naive cells from peripheral blood	blood
28	chr3:52428800-52434600	Weak transcription	Duodenum Smooth Muscle	Duodenum
29	chr3:52428800-52434600	Weak transcription	Ovary	ovary
30	chr3:52428800-52435200	Weak transcription	Pancreas	Pancrea
31	chr3:52429000-52434800	Weak transcription	Colonic Mucosa	Colon
32	chr3:52430000-52442400	Strong transcription	Brain Substantia Nigra	brain
33	chr3:52430200-52442000	Strong transcription	Primary T cells from cord blood	blood
34	chr3:52430600-52434800	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
35	chr3:52430800-52434600	Weak transcription	HUES48 Cell Line	embryonic stem cell
36	chr3:52430800-52442600	Strong transcription	Primary monocytes fromperipheralblood	blood
37	chr3:52430800-52442600	Strong transcription	Brain Cingulate Gyrus	brain
38	chr3:52431000-52441600	Strong transcription	Primary T helper naive cells fromperipheralblood	blood
39	chr3:52431200-52435000	Strong transcription	Primary T cells fromperipheralblood	blood
40	chr3:52431200-52437200	Strong transcription	Fetal Muscle Trunk	muscle
41	chr3:52431800-52434800	Weak transcription	GM12878-XiMat	blood
42	chr3:52431800-52435600	Weak transcription	H9 Cell Line	embryonic stem cell
43	chr3:52431800-52437800	Strong transcription	Adipose Nuclei	Adipose
44	chr3:52431800-52440800	Strong transcription	Brain Dorsolateral Prefrontal Cortex	brain
45	chr3:52432000-52435000	Weak transcription	iPS-18 Cell Line	embryonic stem cell
46	chr3:52432000-52442400	Strong transcription	Primary hematopoietic stem cells short term culture	blood
47	chr3:52432200-52434800	Weak transcription	HMEC	breast
48	chr3:52432200-52440400	Strong transcription	Primary B cells from cord blood	blood
49	chr3:52432200-52442400	Strong transcription	Lung	lung
50	chr3:52432400-52434800	Weak transcription	H1 Cell Line	embryonic stem cell

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