Variant report

Variant	rs12079123
Chromosome Location	chr1:227812941-227812942
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	chr1:227803218..227804951-chr1:227810975..227813465,2	MCF-7	breast:
2	chr1:227797075..227799559-chr1:227811537..227814521,3	MCF-7	breast:

Extended variants
information (count: 95 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:89)

rs_ID	r²[population]
rs1021553	0.92[EUR][1000 genomes]
rs1021554	0.92[EUR][1000 genomes]
rs10495276	0.91[EUR][1000 genomes]
rs10799423	0.91[EUR][1000 genomes]
rs10799431	0.90[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10799432	0.90[AMR][1000 genomes];0.98[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs10799433	0.95[AFR][1000 genomes];0.91[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10799434	0.88[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10799435	0.90[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10916158	0.90[EUR][1000 genomes]
rs10916159	0.86[EUR][1000 genomes]
rs10916165	0.94[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs10916169	0.95[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs10916175	0.84[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs10916176	0.90[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10916179	0.90[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10916182	0.90[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10916183	0.90[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10916184	0.90[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10916185	0.90[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10916187	0.90[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11484723	0.94[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs11580570	0.88[EUR][1000 genomes]
rs12023298	0.91[EUR][1000 genomes]
rs12025815	0.95[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs12040302	0.86[EUR][1000 genomes]
rs12070002	0.95[AFR][1000 genomes];0.91[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12070036	0.93[AFR][1000 genomes];0.91[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12080321	0.92[AFR][1000 genomes];0.90[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12132444	0.89[EUR][1000 genomes]
rs12740317	0.84[EUR][1000 genomes]
rs1407718	0.81[AMR][1000 genomes];0.95[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs1495842	0.88[EUR][1000 genomes]
rs1495845	0.91[EUR][1000 genomes]
rs1495847	0.91[EUR][1000 genomes]
rs1845758	0.87[EUR][1000 genomes]
rs2018401	0.87[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2088210	0.95[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2088211	0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2088212	0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2088214	0.90[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2093609	0.90[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2093610	0.90[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2132367	0.95[AFR][1000 genomes];0.91[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2201571	0.90[EUR][1000 genomes]
rs2644140	0.87[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs28407112	0.91[EUR][1000 genomes]
rs2935145	0.85[AMR][1000 genomes];0.95[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2935146	0.85[AMR][1000 genomes];0.95[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2935147	0.84[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2935152	0.85[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2935155	0.81[AMR][1000 genomes];0.95[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2999741	0.84[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2999743	0.82[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2999744	0.85[AMR][1000 genomes];0.94[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2999745	0.85[AMR][1000 genomes];0.95[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2999746	0.85[AMR][1000 genomes];0.94[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs3010183	0.91[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs3010186	0.83[AMR][1000 genomes];0.95[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs3010190	0.85[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs3010191	0.85[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs3010192	0.85[AMR][1000 genomes];0.96[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs3010193	0.85[AMR][1000 genomes];0.95[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs3010194	0.84[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs3010195	0.85[AMR][1000 genomes];0.95[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs3010196	0.85[AMR][1000 genomes];0.95[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs4359006	0.90[EUR][1000 genomes]
rs4653512	0.90[EUR][1000 genomes]
rs4653514	0.95[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs4653515	0.95[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs4653848	0.91[EUR][1000 genomes]
rs4653849	0.91[EUR][1000 genomes]
rs4653850	0.90[EUR][1000 genomes]
rs4653853	0.91[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs6664682	0.90[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6671825	0.86[AMR][1000 genomes];0.97[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs6697867	0.93[EUR][1000 genomes]
rs7512348	0.91[EUR][1000 genomes]
rs7523915	0.91[EUR][1000 genomes]
rs7528094	0.91[EUR][1000 genomes]
rs7539914	0.90[EUR][1000 genomes]
rs7542685	0.82[EUR][1000 genomes]
rs7551459	0.92[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs903683	0.88[EUR][1000 genomes]
rs903684	0.87[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs903690	0.91[EUR][1000 genomes]
rs903697	0.91[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs951083	0.88[EUR][1000 genomes]
rs976959	0.90[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv534002	chr1:227315186-228047108	Bivalent/Poised TSS Weak transcription Enhancers ZNF genes & repeats Strong transcription Bivalent Enhancer Flanking Active TSS Flanking Bivalent TSS/Enh Active TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	54 gene(s)	inside rSNPs	diseases
2	nsv873246	chr1:227694948-227884465	Active TSS Weak transcription ZNF genes & repeats Flanking Active TSS Flanking Bivalent TSS/Enh Enhancers Bivalent Enhancer Strong transcription Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
3	nsv1007479	chr1:227695868-227984466	Genic enhancers Flanking Active TSS Active TSS Weak transcription Strong transcription Enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	33 gene(s)	inside rSNPs	diseases
4	esv3327012	chr1:227741102-227890968	Weak transcription ZNF genes & repeats Enhancers Flanking Active TSS Strong transcription Bivalent/Poised TSS Active TSS Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
5	nsv1010605	chr1:227770415-228332690	Flanking Active TSS ZNF genes & repeats Weak transcription Strong transcription Genic enhancers Enhancers Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	73 gene(s)	inside rSNPs	diseases
6	nsv945673	chr1:227799341-227819395	ZNF genes & repeats Weak transcription Strong transcription Enhancers Active TSS	Chromatin interactive region	1 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:29 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:227770000-227853800	ZNF genes & repeats	Primary hematopoietic stem cells G-CSF-mobilized Male	--
2	chr1:227790400-227834800	Weak transcription	Placenta Amnion	Placenta Amnion
3	chr1:227800200-227820600	Weak transcription	Skeletal Muscle Male	skeletal muscle
4	chr1:227800400-227814200	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
5	chr1:227801200-227821800	Weak transcription	Stomach Smooth Muscle	stomach
6	chr1:227805800-227823600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
7	chr1:227809200-227814200	Weak transcription	Left Ventricle	heart
8	chr1:227809200-227815000	Weak transcription	Ovary	ovary
9	chr1:227809800-227814600	ZNF genes & repeats	Primary hematopoietic stem cells G-CSF-mobilized Female	--
10	chr1:227810400-227813400	ZNF genes & repeats	Duodenum Smooth Muscle	Duodenum
11	chr1:227810600-227813000	ZNF genes & repeats	Ganglion Eminence derived primary cultured neurospheres	brain
12	chr1:227810800-227813000	Weak transcription	Small Intestine	intestine
13	chr1:227811600-227813000	ZNF genes & repeats	Fetal Adrenal Gland	Adrenal Gland
14	chr1:227811800-227814400	ZNF genes & repeats	Monocytes-CD14+_RO01746	blood
15	chr1:227811800-227814800	Weak transcription	Brain Hippocampus Middle	brain
16	chr1:227811800-227814800	ZNF genes & repeats	Fetal Brain Female	brain
17	chr1:227811800-227830600	ZNF genes & repeats	Liver	Liver
18	chr1:227812000-227813000	ZNF genes & repeats	Cortex derived primary cultured neurospheres	brain
19	chr1:227812000-227813000	ZNF genes & repeats	Aorta	Aorta
20	chr1:227812000-227813000	ZNF genes & repeats	Sigmoid Colon	Sigmoid Colon
21	chr1:227812000-227814600	ZNF genes & repeats	Duodenum Mucosa	Duodenum
22	chr1:227812200-227813000	ZNF genes & repeats	H1 Derived Mesenchymal Stem Cells	ES cell derived
23	chr1:227812200-227813000	ZNF genes & repeats	IMR90 fetal lung fibroblasts Cell Line	lung
24	chr1:227812200-227813000	ZNF genes & repeats	Primary mononuclear cells fromperipheralblood	Blood
25	chr1:227812200-227813200	ZNF genes & repeats	Fetal Intestine Small	intestine
26	chr1:227812200-227813400	ZNF genes & repeats	Spleen	Spleen
27	chr1:227812200-227814600	ZNF genes & repeats	Fetal Stomach	stomach
28	chr1:227812200-227814600	ZNF genes & repeats	Lung	lung
29	chr1:227812400-227816400	Weak transcription	Psoas Muscle	Psoas

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