Variant report

Variant	rs12434854
Chromosome Location	chr14:65896234-65896235
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr14:65878501..65880315-chr14:65894328..65896691,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000033170	Chromatin interaction

Extended variants
information (count: 51 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:47)

rs_ID	r²[population]
rs10083344	0.82[EUR][1000 genomes]
rs10138765	0.86[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs10146374	0.83[EUR][1000 genomes]
rs11844747	1.00[ASW][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];0.94[YRI][hapmap];0.90[AFR][1000 genomes];0.90[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11845794	0.89[CHB][hapmap]
rs11850160	0.90[CHB][hapmap];0.96[GIH][hapmap];0.80[MEX][hapmap]
rs11850847	0.81[CHB][hapmap];0.82[JPT][hapmap];0.81[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs11851013	0.90[CHB][hapmap];1.00[JPT][hapmap];0.85[AFR][1000 genomes]
rs11851772	0.81[CHB][hapmap];0.82[JPT][hapmap];0.80[YRI][hapmap];0.82[AFR][1000 genomes]
rs12431420	0.95[CHB][hapmap];1.00[CHD][hapmap];0.96[GIH][hapmap];1.00[JPT][hapmap];0.82[MEX][hapmap];1.00[TSI][hapmap];0.83[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs12433827	0.81[CHB][hapmap];0.86[CHD][hapmap];0.90[GIH][hapmap];0.82[JPT][hapmap];0.90[MEX][hapmap];0.90[MKK][hapmap];1.00[TSI][hapmap]
rs12434585	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];0.86[AMR][1000 genomes];0.89[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs12437427	0.85[AFR][1000 genomes];0.85[EUR][1000 genomes]
rs17246007	0.88[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs17246035	1.00[ASW][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];0.94[YRI][hapmap];0.87[AFR][1000 genomes];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs17246042	0.87[AFR][1000 genomes];0.90[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs17826580	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];0.86[AMR][1000 genomes];0.89[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs1953417	1.00[ASW][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.82[AFR][1000 genomes];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2152375	1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[AMR][1000 genomes];0.87[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2184602	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];0.86[AMR][1000 genomes];0.89[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs28668545	0.85[EUR][1000 genomes]
rs56156482	0.82[EUR][1000 genomes]
rs57298509	0.82[EUR][1000 genomes]
rs57640052	0.82[EUR][1000 genomes]
rs58115860	0.84[AFR][1000 genomes];0.81[EUR][1000 genomes]
rs59676254	0.96[AFR][1000 genomes];0.86[AMR][1000 genomes];0.89[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs59685862	0.81[EUR][1000 genomes]
rs59822422	0.90[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs59921977	0.83[AFR][1000 genomes]
rs60396689	0.83[AFR][1000 genomes];0.85[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs60927973	0.95[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7140261	0.83[EUR][1000 genomes]
rs7145574	0.95[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.86[AFR][1000 genomes];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7150362	0.86[AMR][1000 genomes];0.91[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7150564	0.82[AFR][1000 genomes];0.90[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7153679	0.89[CHB][hapmap];1.00[JPT][hapmap]
rs73282213	0.85[EUR][1000 genomes]
rs73282250	0.85[EUR][1000 genomes]
rs73282260	0.87[EUR][1000 genomes]
rs73284121	0.96[AFR][1000 genomes];0.86[AMR][1000 genomes];0.89[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs73284133	0.96[AFR][1000 genomes];0.86[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs73284143	0.90[AFR][1000 genomes];0.86[AMR][1000 genomes];0.85[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs73286169	0.81[EUR][1000 genomes]
rs8005309	0.95[CHB][hapmap];1.00[JPT][hapmap];0.80[YRI][hapmap];0.81[EUR][1000 genomes]
rs8018909	0.87[AFR][1000 genomes];0.86[AMR][1000 genomes];0.85[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs884247	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9635251	0.96[AFR][1000 genomes];0.86[AMR][1000 genomes];0.89[EUR][1000 genomes];0.90[ASN][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	nsv1036403	chr14:65724229-66208114	Weak transcription ZNF genes & repeats Enhancers Flanking Active TSS Genic enhancers Flanking Bivalent TSS/Enh Strong transcription Active TSS Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	35 gene(s)	inside rSNPs	diseases
2	nsv1043943	chr14:65782466-66698411	Strong transcription Enhancers Weak transcription Flanking Active TSS Active TSS ZNF genes & repeats Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	55 gene(s)	inside rSNPs	diseases
3	nsv542120	chr14:65782466-66698411	Enhancers Weak transcription Active TSS Strong transcription Flanking Active TSS ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA	55 gene(s)	inside rSNPs	diseases
4	nsv1039168	chr14:65811750-66308343	Enhancers Weak transcription Flanking Active TSS Strong transcription ZNF genes & repeats Genic enhancers Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA	35 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	chr14:65880600-65899400	Weak transcription	Sigmoid Colon	Sigmoid Colon
2	chr14:65880600-65899400	Weak transcription	Small Intestine	intestine
3	chr14:65880800-65896800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
4	chr14:65880800-65898000	Weak transcription	Gastric	stomach
5	chr14:65880800-65904800	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
6	chr14:65881000-65899400	Weak transcription	Primary T cells fromperipheralblood	blood
7	chr14:65881000-65902600	Weak transcription	Fetal Intestine Small	intestine
8	chr14:65881800-65901000	Weak transcription	Primary hematopoietic stem cells	blood
9	chr14:65881800-65902000	Weak transcription	Primary B cells from cord blood	blood
10	chr14:65881800-65902000	Weak transcription	Fetal Intestine Large	intestine
11	chr14:65882600-65900200	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
12	chr14:65886600-65905600	Weak transcription	Duodenum Mucosa	Duodenum
13	chr14:65886800-65898000	Weak transcription	Dnd41	blood
14	chr14:65887400-65898400	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
15	chr14:65888200-65898800	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
16	chr14:65888200-65898800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
17	chr14:65888400-65898800	Weak transcription	H9 Cell Line	embryonic stem cell
18	chr14:65888400-65905400	Weak transcription	Ovary	ovary
19	chr14:65888800-65898800	Weak transcription	Primary B cells from peripheral blood	blood
20	chr14:65889000-65898800	Weak transcription	iPS-15b Cell Line	embryonic stem cell
21	chr14:65889000-65901400	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
22	chr14:65889200-65898000	Weak transcription	Breast Myoepithelial Primary Cells	Breast
23	chr14:65889200-65899400	Weak transcription	Colon Smooth Muscle	Colon
24	chr14:65889200-65899400	Weak transcription	NHDF-Ad	bronchial
25	chr14:65891000-65898800	Weak transcription	Stomach Mucosa	stomach
26	chr14:65891000-65899200	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
27	chr14:65891200-65900400	Weak transcription	Pancreatic Islets	Pancreatic Islet
28	chr14:65891600-65904000	Weak transcription	Lung	lung
29	chr14:65891800-65898800	Weak transcription	Primary T helper cells fromperipheralblood	blood
30	chr14:65891800-65904400	Weak transcription	Primary T killer memory cells from peripheral blood	blood
31	chr14:65892800-65929600	Weak transcription	Duodenum Smooth Muscle	Duodenum
32	chr14:65893000-65917600	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
33	chr14:65893400-65898400	Weak transcription	Osteobl	bone
34	chr14:65893600-65902200	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
35	chr14:65893800-65898400	Weak transcription	Muscle Satellite Cultured Cells	--
36	chr14:65894400-65898600	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
37	chr14:65895000-65898600	Weak transcription	GM12878-XiMat	blood
38	chr14:65895200-65899200	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
39	chr14:65895400-65898400	Weak transcription	Brain Cingulate Gyrus	brain
40	chr14:65895400-65898800	Weak transcription	Primary T helper cells PMA-I stimulated	--
41	chr14:65895600-65898800	Weak transcription	Brain Substantia Nigra	brain
42	chr14:65895600-65899600	Weak transcription	Brain Angular Gyrus	brain
43	chr14:65895800-65898200	Weak transcription	Brain Anterior Caudate	brain
44	chr14:65895800-65898400	Weak transcription	K562	blood
45	chr14:65895800-65898600	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
46	chr14:65895800-65899200	Weak transcription	Brain Inferior Temporal Lobe	brain
47	chr14:65895800-65899400	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
48	chr14:65895800-65899400	Weak transcription	Brain Hippocampus Middle	brain
49	chr14:65896000-65899800	Weak transcription	Primary T cells from cord blood	blood
50	chr14:65896200-65897200	Enhancers	Placenta	Placenta

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