Variant report

Variant	rs72944834
Chromosome Location	chr2:98590454-98590455
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	chr2:98586492..98590623-chr2:98609849..98613256,4	MCF-7	breast:

Variant related genes	Relation type
ENSG00000075568	Chromatin interaction

Extended variants
information (count: 70 )
Associated
traits (count: 0)

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

rs_ID	r²[population]
rs11892146	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs11895466	1.00[AMR][1000 genomes]
rs11898394	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs11900781	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs11900903	1.00[AMR][1000 genomes]
rs11903844	0.81[AFR][1000 genomes]
rs1503201	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs1503203	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs17022209	0.80[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs17022289	0.84[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs17022557	0.80[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs17022726	1.00[AMR][1000 genomes]
rs17022736	1.00[AMR][1000 genomes]
rs17025339	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs2309318	0.81[AFR][1000 genomes]
rs35774346	0.85[AFR][1000 genomes]
rs56065241	1.00[AMR][1000 genomes]
rs57434542	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs58187838	1.00[AMR][1000 genomes]
rs60828800	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs60885334	1.00[AMR][1000 genomes]
rs61712471	1.00[AMR][1000 genomes]
rs6543226	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs6726775	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs6734701	0.80[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs6736475	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs6737992	0.84[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs6742955	0.81[AFR][1000 genomes]
rs6746457	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs72942824	1.00[AMR][1000 genomes]
rs72942830	1.00[AMR][1000 genomes]
rs72942834	1.00[AMR][1000 genomes]
rs72942836	1.00[AMR][1000 genomes]
rs72942856	1.00[AMR][1000 genomes]
rs72942862	1.00[AMR][1000 genomes]
rs72942871	0.80[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs72942872	0.80[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs72942876	0.80[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs72942885	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs72942894	0.82[AFR][1000 genomes]
rs72942896	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs72942898	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs72944808	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs72944812	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs72944813	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs72944818	0.94[AFR][1000 genomes]
rs72944825	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs72944842	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs72946409	0.83[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs72946410	0.81[AFR][1000 genomes]
rs72946417	0.80[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs72946421	0.80[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs72946425	0.80[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs72946431	0.84[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs72946447	1.00[AMR][1000 genomes]
rs72946448	1.00[AMR][1000 genomes]
rs72946453	1.00[AMR][1000 genomes]
rs7579764	1.00[AMR][1000 genomes]
rs9308889	1.00[AMR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:11 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv526360	chr2:98403683-98814054	Weak transcription Strong transcription Active TSS Enhancers Bivalent Enhancer Flanking Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
2	nsv521568	chr2:98403683-98826203	Weak transcription Enhancers Strong transcription Flanking Active TSS ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Active TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
3	nsv1004220	chr2:98423421-98816010	Weak transcription Enhancers Bivalent Enhancer Strong transcription Flanking Active TSS Bivalent/Poised TSS ZNF genes & repeats Active TSS 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
4	nsv1007259	chr2:98429744-98818080	Enhancers Weak transcription Active TSS Bivalent Enhancer Strong transcription Flanking Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
5	nsv535832	chr2:98429744-98818080	Weak transcription Flanking Active TSS Enhancers ZNF genes & repeats Strong transcription Bivalent/Poised TSS Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
6	nsv1009218	chr2:98442640-98816010	Strong transcription Weak transcription Enhancers Flanking Active TSS ZNF genes & repeats Active TSS Flanking Bivalent TSS/Enh Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
7	nsv1003925	chr2:98442640-98821102	Enhancers Strong transcription Weak transcription Flanking Active TSS Bivalent Enhancer Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
8	nsv999442	chr2:98448732-98816010	Weak transcription Enhancers Flanking Bivalent TSS/Enh Active TSS Genic enhancers Flanking Active TSS ZNF genes & repeats Strong transcription Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
9	nsv1013902	chr2:98454309-98818080	ZNF genes & repeats Weak transcription Bivalent/Poised TSS Active TSS Enhancers Strong transcription Genic enhancers Flanking Active TSS Bivalent Enhancer 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
10	nsv1013416	chr2:98472701-98688729	Enhancers Flanking Active TSS Weak transcription Active TSS Strong transcription ZNF genes & repeats Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
11	nsv518056	chr2:98586842-99156296	Weak transcription Enhancers Flanking Active TSS Genic enhancers ZNF genes & repeats Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:31 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:98568200-98599200	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
2	chr2:98568400-98592000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
3	chr2:98575200-98592600	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
4	chr2:98575400-98595000	Weak transcription	HSMM	muscle
5	chr2:98583600-98595800	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
6	chr2:98584600-98597000	Weak transcription	Thymus	Thymus
7	chr2:98585000-98608400	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
8	chr2:98585400-98591200	Weak transcription	Primary T helper naive cells from peripheral blood	blood
9	chr2:98585600-98594800	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
10	chr2:98586800-98590600	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
11	chr2:98587000-98594800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
12	chr2:98587000-98595600	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
13	chr2:98587200-98591200	Weak transcription	Monocytes-CD14+_RO01746	blood
14	chr2:98587400-98592400	Weak transcription	Ovary	ovary
15	chr2:98587400-98599600	Weak transcription	Spleen	Spleen
16	chr2:98587800-98595400	Weak transcription	Primary T helper cells fromperipheralblood	blood
17	chr2:98587800-98600000	Weak transcription	Gastric	stomach
18	chr2:98588200-98592600	ZNF genes & repeats	Cortex derived primary cultured neurospheres	brain
19	chr2:98588200-98596000	Weak transcription	Stomach Mucosa	stomach
20	chr2:98588600-98598200	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
21	chr2:98589000-98590600	ZNF genes & repeats	Pancreatic Islets	Pancreatic Islet
22	chr2:98589200-98591600	ZNF genes & repeats	Primary B cells from peripheral blood	blood
23	chr2:98589200-98597400	ZNF genes & repeats	Primary hematopoietic stem cells G-CSF-mobilized Male	--
24	chr2:98589400-98592000	ZNF genes & repeats	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
25	chr2:98589600-98591000	ZNF genes & repeats	Primary hematopoietic stem cells	blood
26	chr2:98589800-98593400	ZNF genes & repeats	Primary B cells from cord blood	blood
27	chr2:98590000-98590800	ZNF genes & repeats	Primary T cells from cord blood	blood
28	chr2:98590000-98595400	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
29	chr2:98590200-98591200	Weak transcription	Liver	Liver
30	chr2:98590200-98592600	Weak transcription	Skeletal Muscle Male	skeletal muscle
31	chr2:98590200-98595000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast

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