Variant report

Variant	rs6445537
Chromosome Location	chr3:52874099-52874100
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	chr3:52803715..52805902-chr3:52874029..52875964,2	MCF-7	breast:
2	chr3:52864085..52867017-chr3:52872869..52875445,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000114904	Chromatin interaction
ENSG00000055955	Chromatin interaction

Extended variants
information (count: 128 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:124)

rs_ID	r²[population]
rs10049313	1.00[EUR][1000 genomes]
rs1052728	0.83[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs13066997	1.00[EUR][1000 genomes]
rs17052421	1.00[EUR][1000 genomes]
rs1986738	1.00[EUR][1000 genomes]
rs1986739	1.00[EUR][1000 genomes]
rs2001733	1.00[EUR][1000 genomes]
rs2001734	1.00[TSI][hapmap];1.00[EUR][1000 genomes]
rs2245536	1.00[EUR][1000 genomes]
rs2246888	1.00[EUR][1000 genomes]
rs2246889	1.00[EUR][1000 genomes]
rs2256728	1.00[EUR][1000 genomes]
rs2256734	1.00[TSI][hapmap];1.00[EUR][1000 genomes]
rs2276814	1.00[EUR][1000 genomes]
rs2276819	1.00[EUR][1000 genomes]
rs2276821	1.00[EUR][1000 genomes]
rs2276822	1.00[TSI][hapmap]
rs2336155	1.00[TSI][hapmap];1.00[EUR][1000 genomes]
rs2336156	1.00[TSI][hapmap]
rs2336157	1.00[AFR][1000 genomes];0.83[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2336158	1.00[EUR][1000 genomes]
rs2336159	1.00[EUR][1000 genomes]
rs2336161	1.00[TSI][hapmap];1.00[EUR][1000 genomes]
rs2336556	1.00[EUR][1000 genomes]
rs2336557	1.00[EUR][1000 genomes]
rs2336559	1.00[EUR][1000 genomes]
rs2535615	1.00[EUR][1000 genomes]
rs2535616	1.00[EUR][1000 genomes]
rs2535618	1.00[EUR][1000 genomes]
rs2535619	1.00[TSI][hapmap];1.00[EUR][1000 genomes]
rs2535620	1.00[EUR][1000 genomes]
rs2535621	0.83[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2535622	1.00[EUR][1000 genomes]
rs2535623	1.00[EUR][1000 genomes]
rs2535624	1.00[EUR][1000 genomes]
rs2535626	1.00[EUR][1000 genomes]
rs2535628	1.00[EUR][1000 genomes]
rs2535631	1.00[EUR][1000 genomes]
rs2535632	1.00[TSI][hapmap];1.00[EUR][1000 genomes]
rs2535636	1.00[EUR][1000 genomes]
rs2535637	1.00[TSI][hapmap];1.00[EUR][1000 genomes]
rs2535638	0.83[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2535639	1.00[EUR][1000 genomes]
rs2535641	1.00[EUR][1000 genomes]
rs2535642	1.00[EUR][1000 genomes]
rs2535645	1.00[EUR][1000 genomes]
rs2535646	1.00[EUR][1000 genomes]
rs2564946	1.00[EUR][1000 genomes]
rs2577828	1.00[EUR][1000 genomes]
rs2577829	1.00[EUR][1000 genomes]
rs2577830	1.00[EUR][1000 genomes]
rs2581814	1.00[EUR][1000 genomes]
rs2590840	1.00[EUR][1000 genomes]
rs2590841	1.00[EUR][1000 genomes]
rs2710315	1.00[TSI][hapmap];1.00[EUR][1000 genomes]
rs2710316	1.00[EUR][1000 genomes]
rs2710318	1.00[EUR][1000 genomes]
rs2710319	1.00[EUR][1000 genomes]
rs2710320	1.00[EUR][1000 genomes]
rs2710321	1.00[EUR][1000 genomes]
rs2710324	1.00[TSI][hapmap];1.00[EUR][1000 genomes]
rs2710325	0.85[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2710327	1.00[EUR][1000 genomes]
rs2710328	1.00[EUR][1000 genomes]
rs2710329	1.00[TSI][hapmap];1.00[EUR][1000 genomes]
rs2710336	1.00[TSI][hapmap];1.00[EUR][1000 genomes]
rs2710340	1.00[EUR][1000 genomes]
rs2710343	1.00[ASW][hapmap];1.00[LWK][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];0.83[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2710344	1.00[EUR][1000 genomes]
rs2878633	1.00[TSI][hapmap];1.00[EUR][1000 genomes]
rs2878634	1.00[EUR][1000 genomes]
rs2878635	1.00[ASW][hapmap];1.00[LWK][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.83[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2878636	1.00[EUR][1000 genomes]
rs3774361	1.00[EUR][1000 genomes]
rs4234635	1.00[EUR][1000 genomes]
rs4234636	1.00[EUR][1000 genomes]
rs4234637	1.00[EUR][1000 genomes]
rs4687555	1.00[EUR][1000 genomes]
rs4687557	0.84[AFR][1000 genomes];0.83[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs4687659	1.00[EUR][1000 genomes]
rs4687661	1.00[EUR][1000 genomes]
rs4687665	1.00[TSI][hapmap];1.00[EUR][1000 genomes]
rs4687666	1.00[EUR][1000 genomes]
rs4687667	1.00[EUR][1000 genomes]
rs4687668	0.83[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs4687669	0.85[AFR][1000 genomes];0.83[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs4687670	1.00[EUR][1000 genomes]
rs4687671	1.00[EUR][1000 genomes]
rs4687674	1.00[EUR][1000 genomes]
rs4687675	1.00[EUR][1000 genomes]
rs4687685	1.00[TSI][hapmap];1.00[EUR][1000 genomes]
rs4687690	1.00[EUR][1000 genomes]
rs57430179	1.00[EUR][1000 genomes]
rs59094265	1.00[EUR][1000 genomes]
rs61274383	1.00[EUR][1000 genomes]
rs61641433	1.00[EUR][1000 genomes]
rs6445540	0.83[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs6445542	1.00[TSI][hapmap];0.83[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs6445548	1.00[EUR][1000 genomes]
rs6774869	1.00[TSI][hapmap];1.00[EUR][1000 genomes]
rs6776862	1.00[EUR][1000 genomes]
rs6776990	1.00[EUR][1000 genomes]
rs6787916	1.00[EUR][1000 genomes]
rs6791937	1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.83[AMR][1000 genomes]
rs6794706	1.00[EUR][1000 genomes]
rs6795138	1.00[EUR][1000 genomes]
rs6797070	1.00[TSI][hapmap];1.00[EUR][1000 genomes]
rs72961745	1.00[EUR][1000 genomes]
rs72961755	1.00[EUR][1000 genomes]
rs7623667	1.00[EUR][1000 genomes]
rs7629350	1.00[EUR][1000 genomes]
rs7629528	0.83[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7637212	1.00[EUR][1000 genomes]
rs7647534	1.00[EUR][1000 genomes]
rs7649515	1.00[EUR][1000 genomes]
rs7650966	0.83[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7652175	1.00[EUR][1000 genomes]
rs7652476	1.00[EUR][1000 genomes]
rs9681089	1.00[TSI][hapmap];1.00[EUR][1000 genomes]
rs9682449	0.83[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs9682819	1.00[EUR][1000 genomes]
rs9815408	1.00[EUR][1000 genomes]
rs9846827	1.00[EUR][1000 genomes]
rs9877711	1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.83[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	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
2	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
3	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
4	nsv967253	chr3:52871714-52877079	Genic enhancers Strong transcription Weak transcription Enhancers Flanking Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:118 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:52854200-52874200	Weak transcription	H9 Cell Line	embryonic stem cell
2	chr3:52854800-52888400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
3	chr3:52856000-52875000	Weak transcription	Fetal Intestine Large	intestine
4	chr3:52862000-52882600	Weak transcription	Placenta Amnion	Placenta Amnion
5	chr3:52864400-52875800	Strong transcription	Primary neutrophils fromperipheralblood	blood
6	chr3:52865600-52874200	Weak transcription	Sigmoid Colon	Sigmoid Colon
7	chr3:52865600-52875200	Weak transcription	Dnd41	blood
8	chr3:52865800-52878600	Weak transcription	Small Intestine	intestine
9	chr3:52866000-52884800	Weak transcription	HMEC	breast
10	chr3:52866200-52885200	Weak transcription	NHEK	skin
11	chr3:52866600-52879200	Weak transcription	Osteobl	bone
12	chr3:52866800-52876400	Strong transcription	Monocytes-CD14+_RO01746	blood
13	chr3:52866800-52878200	Strong transcription	Fetal Brain Female	brain
14	chr3:52866800-52879600	Genic enhancers	Fetal Thymus	thymus
15	chr3:52867000-52876400	Strong transcription	Primary monocytes fromperipheralblood	blood
16	chr3:52867000-52881600	Weak transcription	iPS-15b Cell Line	embryonic stem cell
17	chr3:52867000-52881800	Weak transcription	HUES64 Cell Line	embryonic stem cell
18	chr3:52867200-52875200	Weak transcription	HUES48 Cell Line	embryonic stem cell
19	chr3:52868000-52878800	Strong transcription	Primary hematopoietic stem cells short term culture	blood
20	chr3:52868000-52883200	Weak transcription	Rectal Mucosa Donor 31	rectum
21	chr3:52868400-52877800	Strong transcription	Brain Germinal Matrix	brain
22	chr3:52868600-52875200	Weak transcription	Primary hematopoietic stem cells	blood
23	chr3:52868800-52876800	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
24	chr3:52869000-52878800	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
25	chr3:52869000-52879400	Strong transcription	Fetal Intestine Small	intestine
26	chr3:52869000-52881800	Weak transcription	Fetal Kidney	kidney
27	chr3:52869400-52874200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
28	chr3:52869400-52875200	Weak transcription	Muscle Satellite Cultured Cells	--
29	chr3:52869400-52875600	Weak transcription	Colonic Mucosa	Colon
30	chr3:52869600-52875000	Strong transcription	Brain Angular Gyrus	brain
31	chr3:52869600-52875200	Strong transcription	Brain Inferior Temporal Lobe	brain
32	chr3:52869600-52878600	Weak transcription	NHDF-Ad	bronchial
33	chr3:52869600-52879600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
34	chr3:52869600-52881800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
35	chr3:52869800-52874200	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
36	chr3:52869800-52875600	Weak transcription	iPS-20b Cell Line	embryonic stem cell
37	chr3:52869800-52876600	Weak transcription	iPS-18 Cell Line	embryonic stem cell
38	chr3:52869800-52882000	Weak transcription	H1 Cell Line	embryonic stem cell
39	chr3:52869800-52884000	Strong transcription	Foreskin Melanocyte Primary Cells skin01	Skin
40	chr3:52870000-52874400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
41	chr3:52870000-52875000	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
42	chr3:52870000-52878800	Genic enhancers	Fetal Muscle Leg	muscle
43	chr3:52870000-52901000	Weak transcription	Fetal Brain Male	brain
44	chr3:52870200-52874200	Weak transcription	Placenta	Placenta
45	chr3:52870200-52875600	Strong transcription	Stomach Smooth Muscle	stomach
46	chr3:52870200-52876600	Strong transcription	Fetal Stomach	stomach
47	chr3:52870400-52875800	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
48	chr3:52870400-52876400	Strong transcription	Duodenum Smooth Muscle	Duodenum
49	chr3:52870400-52877400	Strong transcription	Lung	lung
50	chr3:52870600-52875000	Weak transcription	Primary B cells from peripheral blood	blood

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