Variant report

Variant	rs2535644
Chromosome Location	chr3:52856230-52856231
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr3:52804845..52806455-chr3:52854968..52857676,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000114904	Chromatin interaction

Extended variants
information (count: 98 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:91)

rs_ID	r²[population]
rs10049313	1.00[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs1052728	0.86[AFR][1000 genomes];0.91[AMR][1000 genomes]
rs12637566	0.82[ASN][1000 genomes]
rs13066997	1.00[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs1986738	1.00[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs1986739	1.00[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs2001733	1.00[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs2001734	1.00[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs2245536	1.00[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs2246888	1.00[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs2246889	1.00[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs2256728	1.00[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs2256734	1.00[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs2276814	1.00[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs2276819	1.00[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs2276820	0.82[ASN][1000 genomes]
rs2276821	1.00[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs2336155	1.00[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs2336157	0.91[AMR][1000 genomes]
rs2336158	1.00[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs2336159	1.00[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs2336546	1.00[AMR][1000 genomes]
rs2336556	1.00[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs2336557	1.00[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs2336559	1.00[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs2535615	1.00[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs2535616	1.00[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs2535617	0.82[ASN][1000 genomes]
rs2535618	1.00[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs2535619	1.00[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs2535620	1.00[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs2535621	0.91[AMR][1000 genomes]
rs2535622	1.00[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs2535623	1.00[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs2535626	1.00[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs2535628	1.00[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs2535631	1.00[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs2535632	1.00[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs2535636	1.00[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs2535637	1.00[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs2535638	0.91[AMR][1000 genomes]
rs2535639	1.00[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs2535641	1.00[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs2535642	1.00[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs2535643	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs2535645	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs2535646	0.82[ASN][1000 genomes]
rs2710318	1.00[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs2710319	1.00[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs2710320	1.00[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs2710321	1.00[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs2710324	1.00[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs2710328	1.00[AMR][1000 genomes]
rs2710341	0.82[ASN][1000 genomes]
rs2710343	0.91[AMR][1000 genomes]
rs2710344	1.00[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs2878633	1.00[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs2878634	1.00[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs2878635	0.91[AMR][1000 genomes]
rs2878636	1.00[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs3774361	1.00[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs4234637	1.00[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs4687555	1.00[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs4687557	0.91[AMR][1000 genomes]
rs4687659	1.00[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs4687661	1.00[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs4687665	1.00[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs4687666	1.00[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs4687667	1.00[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs4687668	0.91[AMR][1000 genomes]
rs4687669	0.91[AMR][1000 genomes]
rs4687670	1.00[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs4687671	1.00[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs4687674	1.00[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs4687675	1.00[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs6445540	0.91[AMR][1000 genomes]
rs6445542	0.91[AMR][1000 genomes]
rs6774869	1.00[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs6776990	1.00[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs6791937	0.91[AMR][1000 genomes]
rs7623667	1.00[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs7629528	0.91[AMR][1000 genomes]
rs7637212	1.00[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs7647534	1.00[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs7649515	1.00[AMR][1000 genomes]
rs7650966	0.91[AMR][1000 genomes]
rs7652476	1.00[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs9681089	1.00[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs9682449	0.91[AMR][1000 genomes]
rs9682819	1.00[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs9877711	0.91[AMR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:7 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv984563	chr3:52516115-52867075	Weak transcription Strong transcription Enhancers Active TSS Flanking Active TSS Genic enhancers ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	63 gene(s)	inside rSNPs	diseases
2	nsv834698	chr3:52749983-52928219	Weak transcription Enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Strong transcription ZNF genes & repeats Active TSS Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	27 gene(s)	inside rSNPs	diseases
3	esv2762328	chr3:52774884-53002150	Strong transcription Enhancers Active TSS Flanking Active TSS Weak transcription Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	27 gene(s)	inside rSNPs	diseases
4	esv3446915	chr3:52786850-53049217	Strong transcription Active TSS Transcr. at gene 5' and 3' Flanking Active TSS Bivalent Enhancer Weak transcription Enhancers Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	27 gene(s)	inside rSNPs	diseases
5	esv1810629	chr3:52817031-52869635	Weak transcription Active TSS Strong transcription Bivalent Enhancer Enhancers Flanking Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	diseases
6	nsv876797	chr3:52817675-52873984	Weak transcription Enhancers Strong transcription Genic enhancers Bivalent Enhancer Active TSS Transcr. at gene 5' and 3' Flanking Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	diseases
7	nsv590308	chr3:52854335-52860806	Strong transcription Weak transcription Enhancers Genic enhancers Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:59 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:52844200-52856600	Weak transcription	Primary T cells from cord blood	blood
2	chr3:52844400-52857200	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
3	chr3:52844600-52856800	Weak transcription	Fetal Intestine Small	intestine
4	chr3:52844600-52857600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
5	chr3:52846400-52860800	Weak transcription	Esophagus	oesophagus
6	chr3:52846800-52857000	Weak transcription	Aorta	Aorta
7	chr3:52847000-52857400	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
8	chr3:52847200-52861200	Genic enhancers	Liver	Liver
9	chr3:52847400-52857000	Weak transcription	Brain Hippocampus Middle	brain
10	chr3:52847600-52865000	Weak transcription	Psoas Muscle	Psoas
11	chr3:52848400-52865800	Weak transcription	Ovary	ovary
12	chr3:52850200-52868400	Weak transcription	Colonic Mucosa	Colon
13	chr3:52850600-52857800	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
14	chr3:52850600-52864200	Strong transcription	Stomach Smooth Muscle	stomach
15	chr3:52850800-52865400	Strong transcription	Fetal Stomach	stomach
16	chr3:52851000-52856800	Weak transcription	Fetal Brain Female	brain
17	chr3:52851600-52863400	Strong transcription	Breast Myoepithelial Primary Cells	Breast
18	chr3:52851800-52856800	Weak transcription	Lung	lung
19	chr3:52851800-52858000	Weak transcription	Placenta	Placenta
20	chr3:52852200-52869200	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
21	chr3:52852800-52869200	Weak transcription	Primary B cells from cord blood	blood
22	chr3:52853000-52857000	Weak transcription	Gastric	stomach
23	chr3:52853000-52857000	Enhancers	HepG2	liver
24	chr3:52853000-52857000	Weak transcription	Monocytes-CD14+_RO01746	blood
25	chr3:52853000-52858400	Strong transcription	Brain Angular Gyrus	brain
26	chr3:52853000-52868000	Weak transcription	Primary hematopoietic stem cells short term culture	blood
27	chr3:52853200-52859400	Strong transcription	Thymus	Thymus
28	chr3:52853400-52856600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
29	chr3:52853400-52857600	Strong transcription	Spleen	Spleen
30	chr3:52853400-52861200	Strong transcription	Fetal Muscle Leg	muscle
31	chr3:52854000-52856600	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
32	chr3:52854000-52858800	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
33	chr3:52854000-52859000	Strong transcription	Primary neutrophils fromperipheralblood	blood
34	chr3:52854000-52861200	Strong transcription	Pancreas	Pancrea
35	chr3:52854200-52859000	Strong transcription	Brain Cingulate Gyrus	brain
36	chr3:52854200-52874200	Weak transcription	H9 Cell Line	embryonic stem cell
37	chr3:52854400-52856800	Weak transcription	Brain Germinal Matrix	brain
38	chr3:52854400-52861600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
39	chr3:52854600-52857400	Weak transcription	Primary T cells fromperipheralblood	blood
40	chr3:52854800-52869200	Weak transcription	Primary T helper cells fromperipheralblood	blood
41	chr3:52854800-52888400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
42	chr3:52855000-52861600	Strong transcription	Skeletal Muscle Female	skeletal muscle
43	chr3:52855200-52856600	Weak transcription	Brain Anterior Caudate	brain
44	chr3:52855200-52860800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
45	chr3:52855200-52865400	Weak transcription	Brain Substantia Nigra	brain
46	chr3:52855400-52857000	Weak transcription	Primary monocytes fromperipheralblood	blood
47	chr3:52855600-52856600	Weak transcription	Fetal Muscle Trunk	muscle
48	chr3:52855600-52857200	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
49	chr3:52855600-52857200	Weak transcription	Duodenum Smooth Muscle	Duodenum
50	chr3:52855600-52862000	Strong transcription	Skeletal Muscle Male	skeletal muscle

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