Variant report

Variant	rs6728889
Chromosome Location	chr2:54389961-54389962
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr2:54341229..54346589-chr2:54385136..54390434,5	MCF-7	breast:

Variant related genes	Relation type
ENSG00000170634	Chromatin interaction

Extended variants
information (count: 49 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:33)

rs_ID	r²[population]
rs1001296	1.00[EUR][1000 genomes]
rs1001297	1.00[EUR][1000 genomes]
rs10181309	1.00[EUR][1000 genomes]
rs10195704	1.00[EUR][1000 genomes]
rs11886475	1.00[EUR][1000 genomes]
rs11889533	0.84[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs11890605	0.84[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs11897209	1.00[EUR][1000 genomes]
rs11899522	0.86[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs13395449	1.00[EUR][1000 genomes]
rs13399915	1.00[EUR][1000 genomes]
rs13401548	0.84[AMR][1000 genomes]
rs17045575	0.84[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs1872327	1.00[EUR][1000 genomes]
rs1872328	0.84[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2090182	0.84[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs2357955	1.00[EUR][1000 genomes]
rs4553857	0.96[EUR][1000 genomes]
rs57113434	0.93[EUR][1000 genomes]
rs58842028	0.84[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs59531016	1.00[EUR][1000 genomes]
rs6757204	0.86[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs72908723	0.84[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs72908725	0.84[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs72908727	0.84[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs72908736	0.96[EUR][1000 genomes]
rs73935097	0.96[EUR][1000 genomes]
rs7564849	0.96[EUR][1000 genomes]
rs7567556	1.00[EUR][1000 genomes]
rs7567614	0.93[EUR][1000 genomes]
rs7567816	0.81[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7594400	0.81[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7604464	1.00[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:16 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1001246	chr2:54195654-54434832	Enhancers ZNF genes & repeats Weak transcription Active TSS Flanking Active TSS Strong transcription Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	42 gene(s)	inside rSNPs	diseases
2	nsv1003205	chr2:54220049-54700843	Weak transcription Active TSS Enhancers Transcr. at gene 5' and 3' Flanking Active TSS ZNF genes & repeats Strong transcription Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	21 gene(s)	inside rSNPs	diseases
3	esv2762639	chr2:54220049-54700855	Flanking Bivalent TSS/Enh Weak transcription Transcr. at gene 5' and 3' Enhancers Flanking Active TSS Active TSS Strong transcription ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	21 gene(s)	inside rSNPs	diseases
4	nsv1011790	chr2:54220049-54714553	Flanking Active TSS ZNF genes & repeats Weak transcription Enhancers Active TSS Flanking Bivalent TSS/Enh Strong transcription Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	21 gene(s)	inside rSNPs	diseases
5	nsv1002891	chr2:54227005-54682169	Enhancers ZNF genes & repeats Weak transcription Flanking Active TSS Bivalent Enhancer Active TSS Strong transcription Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	21 gene(s)	inside rSNPs	diseases
6	nsv535722	chr2:54227005-54682169	Strong transcription Weak transcription Enhancers Flanking Bivalent TSS/Enh Flanking Active TSS Active TSS ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	21 gene(s)	inside rSNPs	diseases
7	nsv1011690	chr2:54255361-54700843	Flanking Active TSS Weak transcription Enhancers Active TSS Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	21 gene(s)	inside rSNPs	diseases
8	nsv431069	chr2:54260132-54434049	Enhancers Weak transcription Flanking Active TSS Strong transcription ZNF genes & repeats Active TSS Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	19 gene(s)	inside rSNPs	diseases
9	nsv1007731	chr2:54331179-54452329	Active TSS Strong transcription Weak transcription Enhancers Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region	14 gene(s)	inside rSNPs	diseases
10	nsv535723	chr2:54331179-54452329	Flanking Active TSS ZNF genes & repeats Weak transcription Active TSS Strong transcription Enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region	14 gene(s)	inside rSNPs	diseases
11	nsv874148	chr2:54344325-54432222	Weak transcription Enhancers Flanking Active TSS ZNF genes & repeats Strong transcription Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region	5 gene(s)	inside rSNPs	diseases
12	nsv1000652	chr2:54345892-54469703	Enhancers Weak transcription Strong transcription Flanking Active TSS Genic enhancers ZNF genes & repeats Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region	3 gene(s)	inside rSNPs	diseases
13	nsv1003889	chr2:54347750-54424601	Weak transcription Enhancers Strong transcription Flanking Active TSS ZNF genes & repeats Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Genic enhancers	TF binding region CpG island Chromatin interactive region	3 gene(s)	inside rSNPs	diseases
14	nsv1011433	chr2:54351145-54424601	ZNF genes & repeats Enhancers Weak transcription Strong transcription Active TSS Genic enhancers Flanking Active TSS Bivalent/Poised TSS	TF binding region Chromatin interactive region	2 gene(s)	inside rSNPs	diseases
15	nsv1012230	chr2:54351988-54422959	Weak transcription ZNF genes & repeats Enhancers Strong transcription Active TSS Flanking Active TSS Bivalent/Poised TSS Genic enhancers	TF binding region Chromatin interactive region	2 gene(s)	inside rSNPs	diseases
16	nsv874149	chr2:54358517-54432222	Weak transcription ZNF genes & repeats Enhancers Strong transcription Active TSS Flanking Active TSS Genic enhancers Bivalent/Poised TSS	TF binding region Chromatin interactive region	2 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:41 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:54352200-54411400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
2	chr2:54362000-54416400	Weak transcription	Primary T cells fromperipheralblood	blood
3	chr2:54362200-54391400	Weak transcription	Sigmoid Colon	Sigmoid Colon
4	chr2:54362200-54411200	Weak transcription	Stomach Smooth Muscle	stomach
5	chr2:54366400-54391200	Weak transcription	Spleen	Spleen
6	chr2:54366400-54397200	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
7	chr2:54366600-54409600	Weak transcription	Psoas Muscle	Psoas
8	chr2:54367400-54416600	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
9	chr2:54369600-54416600	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
10	chr2:54377400-54391200	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
11	chr2:54380600-54429200	Weak transcription	Primary B cells from peripheral blood	blood
12	chr2:54380600-54434400	Weak transcription	Ovary	ovary
13	chr2:54382800-54394800	Weak transcription	Fetal Brain Male	brain
14	chr2:54382800-54414600	Weak transcription	Fetal Intestine Small	intestine
15	chr2:54383000-54393200	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
16	chr2:54383200-54390400	Weak transcription	Primary hematopoietic stem cells	blood
17	chr2:54383800-54393000	Weak transcription	Primary B cells from cord blood	blood
18	chr2:54385200-54390600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
19	chr2:54385800-54415800	Weak transcription	Left Ventricle	heart
20	chr2:54386600-54390800	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
21	chr2:54387200-54393200	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
22	chr2:54387800-54390800	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
23	chr2:54387800-54393200	Weak transcription	Liver	Liver
24	chr2:54387800-54393800	Weak transcription	Skeletal Muscle Male	skeletal muscle
25	chr2:54387800-54414200	Weak transcription	Skeletal Muscle Female	skeletal muscle
26	chr2:54387800-54457400	Weak transcription	Aorta	Aorta
27	chr2:54388000-54406000	Weak transcription	Brain Cingulate Gyrus	brain
28	chr2:54388400-54391400	Weak transcription	Small Intestine	intestine
29	chr2:54388400-54403800	Weak transcription	Brain Anterior Caudate	brain
30	chr2:54388400-54424600	Weak transcription	Brain Substantia Nigra	brain
31	chr2:54388400-54435000	Weak transcription	Brain Angular Gyrus	brain
32	chr2:54388600-54414400	Weak transcription	HSMMtube	muscle
33	chr2:54388600-54416600	Weak transcription	Primary T helper cells fromperipheralblood	blood
34	chr2:54389200-54390000	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
35	chr2:54389200-54390000	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
36	chr2:54389600-54390000	Enhancers	Fetal Muscle Leg	muscle
37	chr2:54389800-54390200	Strong transcription	Primary T cells from cord blood	blood
38	chr2:54389800-54390200	Enhancers	Fetal Muscle Trunk	muscle
39	chr2:54389800-54391000	Strong transcription	Breast Myoepithelial Primary Cells	Breast
40	chr2:54389800-54391400	Weak transcription	Colon Smooth Muscle	Colon
41	chr2:54389800-54420000	Weak transcription	Fetal Stomach	stomach

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