Variant report

Variant	rs3176824
Chromosome Location	chr3:46248385-46248386
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr3:46202705..46205195-chr3:46247195..46250047,2	MCF-7	breast:
2	chr3:46234025..46236211-chr3:46246101..46248526,2	MCF-7	breast:
3	chr3:46247078..46249229-chr3:46254602..46257153,3	MCF-7	breast:

Variant related genes	Relation type
ENSG00000183625	Chromatin interaction

Extended variants
information (count: 140 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:138)

rs_ID	r²[population]
rs10510748	0.86[EUR][1000 genomes]
rs10510749	0.88[EUR][1000 genomes]
rs11919943	1.00[ASN][1000 genomes]
rs11926063	1.00[ASN][1000 genomes]
rs11929489	0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13059906	0.88[EUR][1000 genomes]
rs13060713	0.86[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs13060802	0.86[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs13061548	0.88[EUR][1000 genomes]
rs13062450	0.88[EUR][1000 genomes]
rs13062523	0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13067058	1.00[ASN][1000 genomes]
rs13069467	0.86[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs13069750	1.00[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs13069845	1.00[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs13070099	1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13075270	0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13075836	0.93[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs13080979	1.00[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs13082995	0.88[EUR][1000 genomes]
rs13083881	0.93[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs13083914	0.88[EUR][1000 genomes]
rs13084057	0.87[EUR][1000 genomes]
rs13084175	0.87[EUR][1000 genomes]
rs13088766	0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13089907	0.88[EUR][1000 genomes]
rs13090848	0.86[EUR][1000 genomes]
rs13092160	0.93[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13095940	1.00[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13095946	1.00[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13096307	1.00[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13096325	0.93[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs13096371	1.00[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13096873	0.93[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs13097340	0.93[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs13097666	1.00[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs13098911	1.00[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs1542755	0.86[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs17216717	0.93[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs17282797	1.00[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs17282922	1.00[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs2131092	0.86[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs2373156	1.00[ASN][1000 genomes]
rs3091314	0.93[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs3136672	0.88[EUR][1000 genomes]
rs3136673	0.88[EUR][1000 genomes]
rs3176825	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3176826	1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3181076	1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3181078	1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3181080	1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs33998492	1.00[ASN][1000 genomes]
rs34005848	0.86[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs34013035	0.88[EUR][1000 genomes]
rs34047458	1.00[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34059564	0.88[EUR][1000 genomes]
rs34101673	0.86[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs34134191	0.86[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs34194160	0.86[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs34198655	0.88[EUR][1000 genomes]
rs34280313	1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34289272	0.86[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs34340501	1.00[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs34376347	0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34378541	1.00[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs34401473	0.87[EUR][1000 genomes]
rs34409248	0.86[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs34414382	0.86[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs34423195	1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34498313	0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34523728	0.86[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs34531115	1.00[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34558763	0.93[AMR][1000 genomes]
rs34567015	0.86[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs34570200	0.86[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs34611049	0.88[EUR][1000 genomes]
rs34625088	1.00[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34677490	0.86[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs34692251	1.00[ASN][1000 genomes]
rs34693386	0.86[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs34745455	0.86[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs34759782	0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34865316	1.00[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34870159	0.87[EUR][1000 genomes]
rs34897745	0.86[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs34919616	1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34920132	0.87[EUR][1000 genomes]
rs34985947	0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34996127	0.86[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs35111399	0.92[EUR][1000 genomes]
rs35178150	0.93[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs35195804	0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35288652	0.86[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs35335084	1.00[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35354367	1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35429781	1.00[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35431271	1.00[ASN][1000 genomes]
rs35434266	0.86[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs35481399	1.00[ASN][1000 genomes]
rs35560301	0.86[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs35566550	0.86[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs35587265	1.00[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35613615	0.86[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs35614049	1.00[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35617677	1.00[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35678191	1.00[ASN][1000 genomes]
rs35685805	0.86[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs35754688	0.87[EUR][1000 genomes]
rs35775079	1.00[AMR][1000 genomes];0.92[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs35853141	0.86[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs35919278	0.86[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs35942803	0.86[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs35960950	0.86[EUR][1000 genomes]
rs35984988	0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs36000011	1.00[ASN][1000 genomes]
rs36010446	1.00[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs36189995	0.87[EUR][1000 genomes]
rs3774630	0.89[EUR][1000 genomes]
rs41432345	0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs41537946	0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs57115330	0.86[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6765904	0.88[EUR][1000 genomes]
rs6775046	1.00[ASN][1000 genomes]
rs71327035	0.86[EUR][1000 genomes]
rs71327036	0.86[EUR][1000 genomes]
rs71327038	1.00[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs71327039	1.00[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs71327040	0.86[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs71327041	0.86[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs71327042	0.86[AMR][1000 genomes]
rs71327043	1.00[ASN][1000 genomes]
rs71327044	1.00[ASN][1000 genomes]
rs71615441	0.86[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs7620586	1.00[ASN][1000 genomes]
rs7624155	1.00[ASN][1000 genomes]
rs7628489	1.00[ASN][1000 genomes]
rs7631551	0.86[EUR][1000 genomes]
rs7651539	1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv876734	chr3:45725031-46468467	Weak transcription Enhancers Active TSS Flanking Active TSS Genic enhancers Bivalent/Poised TSS Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	42 gene(s)	inside rSNPs	diseases
2	nsv498008	chr3:45733423-46319401	Strong transcription Active TSS Genic enhancers Enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Weak transcription Flanking Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	29 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:51 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:46235400-46249600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
2	chr3:46239800-46249400	Weak transcription	Primary T cells from cord blood	blood
3	chr3:46243000-46249000	Weak transcription	Primary hematopoietic stem cells short term culture	blood
4	chr3:46243800-46249400	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
5	chr3:46245200-46248800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
6	chr3:46245600-46251800	Weak transcription	Spleen	Spleen
7	chr3:46246600-46249000	Flanking Active TSS	Primary monocytes fromperipheralblood	blood
8	chr3:46246800-46249600	Active TSS	Brain Hippocampus Middle	brain
9	chr3:46247000-46248600	Weak transcription	Primary T helper naive cells from peripheral blood	blood
10	chr3:46247000-46249800	Active TSS	Fetal Muscle Leg	muscle
11	chr3:46247000-46251800	Enhancers	Primary B cells from peripheral blood	blood
12	chr3:46247200-46249600	Weak transcription	Thymus	Thymus
13	chr3:46247200-46250000	Flanking Active TSS	Primary Natural Killer cells fromperipheralblood	blood
14	chr3:46247200-46250200	Enhancers	Primary T killer memory cells from peripheral blood	blood
15	chr3:46247200-46250600	Flanking Active TSS	Primary neutrophils fromperipheralblood	blood
16	chr3:46247400-46249000	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
17	chr3:46247400-46249600	Active TSS	Brain Substantia Nigra	brain
18	chr3:46247600-46249800	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
19	chr3:46247600-46249800	Active TSS	Placenta	Placenta
20	chr3:46247600-46250000	Active TSS	Duodenum Smooth Muscle	Duodenum
21	chr3:46247800-46248400	Enhancers	iPS DF 6.9 Cell Line	embryonic stem cell
22	chr3:46247800-46248600	Flanking Active TSS	Adipose Nuclei	Adipose
23	chr3:46247800-46249000	Flanking Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
24	chr3:46248000-46248400	Enhancers	iPS-20b Cell Line	embryonic stem cell
25	chr3:46248000-46248400	Active TSS	Brain Angular Gyrus	brain
26	chr3:46248000-46248400	Flanking Active TSS	Duodenum Mucosa	Duodenum
27	chr3:46248000-46248600	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
28	chr3:46248000-46248600	Active TSS	Colonic Mucosa	Colon
29	chr3:46248000-46248800	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
30	chr3:46248000-46249000	Active TSS	Rectal Smooth Muscle	rectum
31	chr3:46248000-46249600	Active TSS	Brain Anterior Caudate	brain
32	chr3:46248000-46249600	Active TSS	Rectal Mucosa Donor 29	rectum
33	chr3:46248000-46249800	Active TSS	Liver	Liver
34	chr3:46248000-46250000	Flanking Active TSS	Primary T cells fromperipheralblood	blood
35	chr3:46248200-46248400	Enhancers	H1 Cell Line	embryonic stem cell
36	chr3:46248200-46248400	Enhancers	Primary B cells from cord blood	blood
37	chr3:46248200-46248400	Flanking Active TSS	Primary mononuclear cells fromperipheralblood	Blood
38	chr3:46248200-46248400	Enhancers	GM12878-XiMat	blood
39	chr3:46248200-46248600	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
40	chr3:46248200-46248800	Active TSS	Left Ventricle	heart
41	chr3:46248200-46249000	Flanking Active TSS	Fetal Thymus	thymus
42	chr3:46248200-46249400	Weak transcription	Cortex derived primary cultured neurospheres	brain
43	chr3:46248200-46249400	Weak transcription	Brain Cingulate Gyrus	brain
44	chr3:46248200-46249400	Active TSS	Fetal Lung	lung
45	chr3:46248200-46249400	Active TSS	Skeletal Muscle Female	skeletal muscle
46	chr3:46248200-46249800	Weak transcription	HUES48 Cell Line	embryonic stem cell
47	chr3:46248200-46249800	Active TSS	Stomach Smooth Muscle	stomach
48	chr3:46248200-46250000	Weak transcription	Lung	lung
49	chr3:46248200-46250200	Enhancers	Primary T helper cells fromperipheralblood	blood
50	chr3:46248200-46250400	Enhancers	Primary T helper memory cells from peripheral blood 2	blood

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