Variant report

Variant	rs12596857
Chromosome Location	chr16:75653146-75653147
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr16:75496396..75498894-chr16:75652662..75656672,3	MCF-7	breast:
2	chr16:75575437..75578213-chr16:75652785..75655591,2	K562	blood:
3	chr16:75638796..75640828-chr16:75652296..75655145,2	MCF-7	breast:
4	chr16:75587027..75591762-chr16:75651045..75658145,7	K562	blood:
5	chr16:75648280..75653154-chr16:75655873..75659174,5	K562	blood:

Variant related genes	Relation type
ENSG00000166822	Chromatin interaction
ENSG00000065457	Chromatin interaction
ENSG00000261717	Chromatin interaction
ENSG00000205084	Chromatin interaction

Extended variants
information (count: 66 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:59)

rs_ID	r²[population]
rs11149842	0.88[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs12446652	0.80[AMR][1000 genomes]
rs12596033	0.86[AMR][1000 genomes]
rs12596724	0.81[ASN][1000 genomes]
rs12598094	0.80[AMR][1000 genomes]
rs12598741	0.82[ASN][1000 genomes]
rs12599322	0.80[AMR][1000 genomes]
rs12600066	0.80[AMR][1000 genomes]
rs12600271	0.80[AMR][1000 genomes]
rs16940253	0.85[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs16940467	0.86[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs16941533	0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs17697211	0.85[AMR][1000 genomes]
rs17764821	0.82[AMR][1000 genomes]
rs1836547	0.81[AMR][1000 genomes]
rs1865493	0.86[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs1979717	0.84[AMR][1000 genomes];0.81[ASN][1000 genomes]
rs2082751	0.89[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs2164245	0.85[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs2278469	0.85[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs2289063	0.86[AMR][1000 genomes]
rs2738794	0.81[EUR][1000 genomes]
rs2903106	0.89[AMR][1000 genomes];0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs3743599	0.84[AMR][1000 genomes]
rs3743603	0.80[AMR][1000 genomes]
rs3743605	0.84[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs3784929	0.89[AMR][1000 genomes];0.95[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs41505349	0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4887833	0.81[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs4888436	0.80[AMR][1000 genomes];0.81[ASN][1000 genomes]
rs4888437	0.80[AMR][1000 genomes];0.81[ASN][1000 genomes]
rs4888440	0.86[AMR][1000 genomes]
rs4888442	0.85[AMR][1000 genomes]
rs5010692	0.90[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs57252551	0.85[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs57396453	0.91[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs58273293	0.84[ASN][1000 genomes]
rs58508930	0.84[AMR][1000 genomes]
rs58719566	0.80[AMR][1000 genomes]
rs59907199	0.85[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs60393074	0.80[AMR][1000 genomes]
rs60952428	0.80[AMR][1000 genomes]
rs61036571	0.85[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs61078946	0.86[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs6564268	0.80[AMR][1000 genomes]
rs7186966	0.88[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7187672	0.85[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs7193066	0.80[AMR][1000 genomes]
rs7195338	0.84[AMR][1000 genomes]
rs719574	0.83[AMR][1000 genomes]
rs73615030	0.96[ASN][1000 genomes]
rs74027438	0.84[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs8051241	0.97[ASN][1000 genomes]
rs8051713	0.85[AMR][1000 genomes];0.81[ASN][1000 genomes]
rs8060972	0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs8061505	0.89[AMR][1000 genomes];0.91[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs963820	0.86[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs9788802	0.84[AMR][1000 genomes]
rs9934159	0.87[AMR][1000 genomes];0.98[EUR][1000 genomes];0.90[ASN][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	nsv916502	chr16:74845880-75732365	Enhancers Weak transcription Flanking Active TSS Active TSS Transcr. at gene 5' and 3' Strong transcription ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	131 gene(s)	inside rSNPs	diseases
2	nsv931939	chr16:75261354-75765025	Weak transcription Bivalent/Poised TSS Strong transcription Enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Active TSS Genic enhancers Flanking Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	104 gene(s)	inside rSNPs	diseases
3	nsv532562	chr16:75614947-76371158	Weak transcription Active TSS Flanking Active TSS Enhancers ZNF genes & repeats Strong transcription Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	50 gene(s)	inside rSNPs	diseases
4	nsv1062010	chr16:75628562-75825725	Flanking Active TSS Strong transcription ZNF genes & repeats Genic enhancers Weak transcription Enhancers Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	37 gene(s)	inside rSNPs	diseases
5	nsv1064880	chr16:75628562-75895699	Enhancers Genic enhancers Weak transcription Strong transcription Active TSS Flanking Active TSS Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	43 gene(s)	inside rSNPs	diseases
6	nsv542960	chr16:75628562-75895699	ZNF genes & repeats Weak transcription Enhancers Flanking Active TSS Genic enhancers Strong transcription Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	43 gene(s)	inside rSNPs	diseases
7	nsv1065543	chr16:75631306-75800170	Weak transcription Strong transcription Enhancers Bivalent/Poised TSS Flanking Active TSS Genic enhancers Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	37 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:126 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr16:75629600-75654800	Strong transcription	Fetal Stomach	stomach
2	chr16:75630600-75654600	Strong transcription	Fetal Intestine Large	intestine
3	chr16:75631400-75654600	Strong transcription	Brain Hippocampus Middle	brain
4	chr16:75631400-75654600	Strong transcription	Fetal Muscle Leg	muscle
5	chr16:75631400-75655200	Strong transcription	Fetal Muscle Trunk	muscle
6	chr16:75632600-75654800	Strong transcription	HUES6 Cell Line	embryonic stem cell
7	chr16:75633000-75654400	Strong transcription	Primary monocytes fromperipheralblood	blood
8	chr16:75633000-75654400	Strong transcription	Fetal Thymus	thymus
9	chr16:75633200-75654800	Strong transcription	Liver	Liver
10	chr16:75633400-75653200	Strong transcription	Rectal Mucosa Donor 29	rectum
11	chr16:75634400-75654600	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
12	chr16:75634400-75654800	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
13	chr16:75636400-75653800	Strong transcription	Placenta	Placenta
14	chr16:75636600-75653800	Strong transcription	Primary neutrophils fromperipheralblood	blood
15	chr16:75636600-75654200	Strong transcription	Duodenum Mucosa	Duodenum
16	chr16:75636600-75654400	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
17	chr16:75636600-75654400	Strong transcription	Monocytes-CD14+_RO01746	blood
18	chr16:75636600-75654800	Strong transcription	HUES48 Cell Line	embryonic stem cell
19	chr16:75636800-75654200	Strong transcription	Fetal Brain Female	brain
20	chr16:75637000-75654400	Strong transcription	Primary B cells from peripheral blood	blood
21	chr16:75637000-75654400	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
22	chr16:75637000-75654600	Strong transcription	Primary T cells from cord blood	blood
23	chr16:75637000-75654600	Strong transcription	Fetal Intestine Small	intestine
24	chr16:75637200-75653400	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
25	chr16:75637200-75654400	Strong transcription	Primary hematopoietic stem cells short term culture	blood
26	chr16:75637400-75654600	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
27	chr16:75637400-75654600	Strong transcription	iPS-20b Cell Line	embryonic stem cell
28	chr16:75637400-75654800	Strong transcription	HUES64 Cell Line	embryonic stem cell
29	chr16:75637400-75655200	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
30	chr16:75637800-75654800	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
31	chr16:75637800-75655200	Weak transcription	Stomach Mucosa	stomach
32	chr16:75638000-75654000	Strong transcription	Dnd41	blood
33	chr16:75638000-75655000	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
34	chr16:75638800-75654600	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
35	chr16:75639200-75654400	Strong transcription	Duodenum Smooth Muscle	Duodenum
36	chr16:75639400-75654600	Strong transcription	Thymus	Thymus
37	chr16:75639400-75654800	Strong transcription	Cortex derived primary cultured neurospheres	brain
38	chr16:75639800-75653600	Strong transcription	Primary hematopoietic stem cells	blood
39	chr16:75639800-75654600	Strong transcription	Brain Anterior Caudate	brain
40	chr16:75639800-75654800	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
41	chr16:75640000-75654200	Strong transcription	Brain Inferior Temporal Lobe	brain
42	chr16:75640000-75654400	Strong transcription	Adipose Nuclei	Adipose
43	chr16:75640000-75654600	Strong transcription	Breast Myoepithelial Primary Cells	Breast
44	chr16:75640200-75653600	Strong transcription	Brain Germinal Matrix	brain
45	chr16:75640200-75654600	Strong transcription	H1 Cell Line	embryonic stem cell
46	chr16:75640200-75654600	Strong transcription	H9 Cell Line	embryonic stem cell
47	chr16:75640200-75654600	Strong transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
48	chr16:75640200-75654600	Strong transcription	Brain Substantia Nigra	brain
49	chr16:75640200-75654600	Strong transcription	A549	lung
50	chr16:75640200-75655200	Strong transcription	Stomach Smooth Muscle	stomach

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