Variant report

Variant	rs4340700
Chromosome Location	chr3:50665068-50665069
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr3:50654234..50656006-chr3:50663612..50665188,2	K562	blood:
2	chr3:50645081..50647837-chr3:50662367..50665362,2	MCF-7	breast:
3	chr3:50664439..50666105-chr3:50681790..50684639,2	MCF-7	breast:
4	chr3:50664856..50665760-chr3:51426226..51426978,2	MCF-7	breast:
5	chr3:50653773..50657088-chr3:50661909..50665179,4	MCF-7	breast:

Variant related genes	Relation type
ENSG00000114738	Chromatin interaction

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

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

rs_ID	r²[population]
rs1038415	1.00[YRI][hapmap];0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs107457	0.80[YRI][hapmap];0.83[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs11130258	0.83[AMR][1000 genomes]
rs11923336	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs13092850	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs13325937	1.00[AMR][1000 genomes]
rs1552255	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs1552256	0.83[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs17051012	1.00[EUR][1000 genomes]
rs17051016	1.00[EUR][1000 genomes]
rs17051017	1.00[EUR][1000 genomes]
rs17051404	1.00[EUR][1000 genomes]
rs1843073	1.00[YRI][hapmap];0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2129069	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs2232251	1.00[EUR][1000 genomes]
rs2262848	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2355337	1.00[YRI][hapmap];0.85[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2355701	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2459450	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2608994	0.81[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs2608996	0.81[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs2609004	1.00[YRI][hapmap];0.81[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs2609014	1.00[AMR][1000 genomes]
rs2609015	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2609027	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2609030	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2675775	1.00[YRI][hapmap];1.00[AMR][1000 genomes]
rs2675779	0.83[YRI][hapmap]
rs2675781	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2675785	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2675797	1.00[AMR][1000 genomes]
rs2675798	1.00[AMR][1000 genomes]
rs2675815	0.83[YRI][hapmap];1.00[AMR][1000 genomes]
rs2675823	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2675824	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2675826	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2675833	1.00[YRI][hapmap];0.83[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs407164	1.00[YRI][hapmap];0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs421689	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs4234694	1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs4234695	1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs4267639	1.00[YRI][hapmap];0.91[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs4401355	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs4423762	1.00[AMR][1000 genomes]
rs4440121	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs4688675	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs4688704	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs4688717	0.83[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs55852678	1.00[EUR][1000 genomes]
rs56112107	1.00[EUR][1000 genomes]
rs56198179	1.00[EUR][1000 genomes]
rs56341000	1.00[EUR][1000 genomes]
rs56413944	1.00[EUR][1000 genomes]
rs57756789	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs57987466	1.00[EUR][1000 genomes]
rs58854038	1.00[EUR][1000 genomes]
rs58911362	1.00[EUR][1000 genomes]
rs59065723	1.00[EUR][1000 genomes]
rs59337835	1.00[EUR][1000 genomes]
rs59340349	1.00[EUR][1000 genomes]
rs59944295	1.00[EUR][1000 genomes]
rs60132317	0.93[AFR][1000 genomes];0.83[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs60455882	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs609678	1.00[EUR][1000 genomes]
rs61032466	1.00[EUR][1000 genomes]
rs61455710	1.00[EUR][1000 genomes]
rs621975	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs628865	1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs6446223	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs650473	1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs665943	1.00[EUR][1000 genomes]
rs6768539	1.00[EUR][1000 genomes]
rs6789552	1.00[EUR][1000 genomes]
rs6807662	1.00[AMR][1000 genomes]
rs73833231	1.00[EUR][1000 genomes]
rs73833232	1.00[EUR][1000 genomes]
rs73833239	1.00[EUR][1000 genomes]
rs73833247	1.00[EUR][1000 genomes]
rs73833251	1.00[AMR][1000 genomes]
rs73833935	1.00[EUR][1000 genomes]
rs73835518	1.00[EUR][1000 genomes]
rs73835533	1.00[EUR][1000 genomes]
rs73835535	1.00[EUR][1000 genomes]
rs73835537	1.00[EUR][1000 genomes]
rs73835538	1.00[EUR][1000 genomes]
rs936714	1.00[YRI][hapmap];0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs9825283	1.00[YRI][hapmap];0.90[AFR][1000 genomes]
rs9840476	1.00[YRI][hapmap];0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs9851304	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs9854588	1.00[AMR][1000 genomes]
rs9857033	1.00[YRI][hapmap];0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][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	nsv1013225	chr3:50440826-50700448	Flanking Active TSS Enhancers Genic enhancers Weak transcription Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS Strong transcription Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	35 gene(s)	inside rSNPs	diseases
2	nsv536566	chr3:50440826-50700448	Genic enhancers Weak transcription Flanking Active TSS Enhancers Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Strong transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	35 gene(s)	inside rSNPs	diseases
3	nsv984540	chr3:50473691-50669310	Enhancers Weak transcription Genic enhancers Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent Enhancer Active TSS Bivalent/Poised TSS Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	28 gene(s)	inside rSNPs	diseases
4	nsv1012501	chr3:50483037-50679591	Bivalent Enhancer Flanking Active TSS Enhancers Weak transcription Genic enhancers Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Strong transcription Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	27 gene(s)	inside rSNPs	diseases
5	nsv536567	chr3:50483037-50679591	Bivalent Enhancer Strong transcription Flanking Active TSS Weak transcription Enhancers Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	27 gene(s)	inside rSNPs	diseases
6	nsv460533	chr3:50574213-50678151	Bivalent/Poised TSS Weak transcription Enhancers Flanking Active TSS Genic enhancers Flanking Bivalent TSS/Enh Active TSS Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	25 gene(s)	inside rSNPs	diseases
7	nsv590273	chr3:50574213-50678151	Weak transcription Active TSS Enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Active TSS Genic enhancers Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	25 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	chr3:50655400-50677800	Weak transcription	Aorta	Aorta
2	chr3:50655600-50681200	Weak transcription	Fetal Brain Female	brain
3	chr3:50655800-50666000	Enhancers	Fetal Heart	heart
4	chr3:50656000-50675600	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
5	chr3:50656000-50677800	Weak transcription	Rectal Smooth Muscle	rectum
6	chr3:50657600-50678200	Weak transcription	Duodenum Smooth Muscle	Duodenum
7	chr3:50658400-50669000	Strong transcription	Fetal Stomach	stomach
8	chr3:50658600-50665400	Weak transcription	Brain Anterior Caudate	brain
9	chr3:50659400-50665800	Enhancers	Right Atrium	heart
10	chr3:50660200-50666200	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
11	chr3:50660200-50666200	Enhancers	Lung	lung
12	chr3:50660200-50671600	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
13	chr3:50660200-50677000	Weak transcription	Liver	Liver
14	chr3:50661000-50665400	Enhancers	Sigmoid Colon	Sigmoid Colon
15	chr3:50661000-50665800	Enhancers	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
16	chr3:50661200-50668800	Strong transcription	Fetal Intestine Small	intestine
17	chr3:50661400-50671600	Enhancers	Left Ventricle	heart
18	chr3:50661600-50667200	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
19	chr3:50661600-50670600	Enhancers	Primary T killer naive cells fromperipheralblood	blood
20	chr3:50661600-50674400	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
21	chr3:50661600-50675800	Enhancers	Primary T helper cells fromperipheralblood	blood
22	chr3:50661600-50688200	Weak transcription	Small Intestine	intestine
23	chr3:50661800-50665200	Weak transcription	Brain Inferior Temporal Lobe	brain
24	chr3:50661800-50666600	Enhancers	Placenta	Placenta
25	chr3:50661800-50669000	Strong transcription	Fetal Intestine Large	intestine
26	chr3:50662000-50665400	Enhancers	Primary T killer memory cells from peripheral blood	blood
27	chr3:50662000-50668600	Genic enhancers	Spleen	Spleen
28	chr3:50662200-50666400	Enhancers	Primary T cells from cord blood	blood
29	chr3:50662200-50667600	Weak transcription	K562	blood
30	chr3:50662200-50669000	Genic enhancers	Primary T cells fromperipheralblood	blood
31	chr3:50662400-50665200	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
32	chr3:50662400-50665200	Weak transcription	Colon Smooth Muscle	Colon
33	chr3:50662400-50665600	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
34	chr3:50662400-50670000	Weak transcription	Fetal Lung	lung
35	chr3:50662400-50671000	Enhancers	Primary T helper naive cells from peripheral blood	blood
36	chr3:50662400-50672000	Enhancers	Primary hematopoietic stem cells	blood
37	chr3:50662400-50678200	Weak transcription	H9 Cell Line	embryonic stem cell
38	chr3:50662600-50667400	Weak transcription	HepG2	liver
39	chr3:50662600-50667600	Enhancers	Primary T helper cells PMA-I stimulated	--
40	chr3:50662600-50675800	Enhancers	Primary T helper naive cells fromperipheralblood	blood
41	chr3:50662800-50665600	Enhancers	Primary monocytes fromperipheralblood	blood
42	chr3:50662800-50666400	Enhancers	Primary T regulatory cells fromperipheralblood	blood
43	chr3:50663200-50667200	Weak transcription	Rectal Mucosa Donor 29	rectum
44	chr3:50663200-50667600	Weak transcription	Rectal Mucosa Donor 31	rectum
45	chr3:50663200-50667800	Enhancers	Primary neutrophils fromperipheralblood	blood
46	chr3:50663200-50669200	Genic enhancers	Fetal Thymus	thymus
47	chr3:50663200-50677600	Weak transcription	HUES48 Cell Line	embryonic stem cell
48	chr3:50663400-50665800	Genic enhancers	Primary Natural Killer cells fromperipheralblood	blood
49	chr3:50663400-50668600	Weak transcription	Primary B cells from peripheral blood	blood
50	chr3:50663400-50690000	Weak transcription	ES-WA7 Cell Line	embryonic stem cell

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