Variant report

Variant	rs72942856
Chromosome Location	chr2:98497854-98497855
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	chr2:98497589..98500393-chr2:98543704..98546124,2	MCF-7	breast:

Extended variants
information (count: 68 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:58)

rs_ID	r²[population]
rs11892146	1.00[AMR][1000 genomes]
rs11895466	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs11898394	0.80[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs11900781	1.00[AMR][1000 genomes]
rs11900903	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs11903844	0.86[AFR][1000 genomes]
rs1503201	1.00[AMR][1000 genomes]
rs1503203	1.00[AMR][1000 genomes]
rs17022209	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs17022289	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs17022557	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs17022726	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs17022736	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs17025339	1.00[AMR][1000 genomes]
rs2309318	0.86[AFR][1000 genomes]
rs35774346	0.82[AFR][1000 genomes]
rs56065241	1.00[AMR][1000 genomes]
rs57434542	1.00[AMR][1000 genomes]
rs58187838	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs60828800	1.00[AMR][1000 genomes]
rs60885334	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs61712471	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs6543226	1.00[AMR][1000 genomes]
rs6726775	1.00[AMR][1000 genomes]
rs6734701	1.00[AMR][1000 genomes]
rs6736475	1.00[AMR][1000 genomes]
rs6737992	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs6742955	0.86[AFR][1000 genomes]
rs6746457	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs72942824	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs72942830	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs72942834	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs72942836	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs72942862	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs72942871	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs72942872	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs72942876	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs72942882	0.90[AFR][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	0.84[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs72944812	0.84[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs72944813	0.84[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs72944825	1.00[AMR][1000 genomes]
rs72944834	1.00[AMR][1000 genomes]
rs72944842	1.00[AMR][1000 genomes]
rs72946409	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs72946410	0.86[AFR][1000 genomes]
rs72946417	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs72946421	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs72946425	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs72946431	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs72946447	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs72946448	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs72946453	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs7579764	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:10 , 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

No data

Chromatin state (count:94 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:98447800-98502800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
2	chr2:98478600-98502200	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
3	chr2:98478600-98502800	Weak transcription	Colonic Mucosa	Colon
4	chr2:98478600-98502800	Weak transcription	Pancreas	Pancrea
5	chr2:98487200-98502800	Weak transcription	Aorta	Aorta
6	chr2:98487400-98502400	Weak transcription	Rectal Mucosa Donor 31	rectum
7	chr2:98487400-98502600	Weak transcription	Rectal Mucosa Donor 29	rectum
8	chr2:98487600-98501000	Weak transcription	Brain Hippocampus Middle	brain
9	chr2:98487800-98501000	Weak transcription	Primary B cells from cord blood	blood
10	chr2:98488200-98502200	Weak transcription	Primary T cells fromperipheralblood	blood
11	chr2:98488200-98502200	Weak transcription	Stomach Smooth Muscle	stomach
12	chr2:98488200-98502600	Weak transcription	Duodenum Mucosa	Duodenum
13	chr2:98488400-98498600	Weak transcription	Brain Anterior Caudate	brain
14	chr2:98488400-98501000	Weak transcription	HSMM	muscle
15	chr2:98488400-98502000	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
16	chr2:98488400-98502000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
17	chr2:98488400-98502000	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
18	chr2:98488400-98502200	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
19	chr2:98488400-98502800	Weak transcription	Sigmoid Colon	Sigmoid Colon
20	chr2:98488400-98502800	Weak transcription	NHDF-Ad	bronchial
21	chr2:98488400-98502800	Weak transcription	NHLF	lung
22	chr2:98488600-98502000	Weak transcription	Muscle Satellite Cultured Cells	--
23	chr2:98488600-98502200	Weak transcription	Duodenum Smooth Muscle	Duodenum
24	chr2:98488600-98502400	Weak transcription	A549	lung
25	chr2:98488800-98501200	Weak transcription	NH-A	brain
26	chr2:98488800-98502000	Weak transcription	Osteobl	bone
27	chr2:98489000-98501600	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
28	chr2:98489000-98502000	Weak transcription	HSMMtube	muscle
29	chr2:98489000-98502200	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
30	chr2:98489000-98502600	Weak transcription	Brain Inferior Temporal Lobe	brain
31	chr2:98489000-98502800	Weak transcription	Ovary	ovary
32	chr2:98489200-98502200	Weak transcription	Primary T killer memory cells from peripheral blood	blood
33	chr2:98489200-98502600	Weak transcription	HMEC	breast
34	chr2:98489200-98502800	Weak transcription	Colon Smooth Muscle	Colon
35	chr2:98489200-98502800	Weak transcription	Psoas Muscle	Psoas
36	chr2:98489600-98501200	Weak transcription	Fetal Intestine Large	intestine
37	chr2:98489600-98502800	Weak transcription	Spleen	Spleen
38	chr2:98490000-98502000	Weak transcription	Primary T helper cells PMA-I stimulated	--
39	chr2:98490000-98502000	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
40	chr2:98490000-98502200	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
41	chr2:98490000-98502800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
42	chr2:98490000-98502800	Weak transcription	Lung	lung
43	chr2:98490200-98502000	Weak transcription	Primary T helper cells fromperipheralblood	blood
44	chr2:98490200-98502800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
45	chr2:98490200-98502800	Weak transcription	Fetal Stomach	stomach
46	chr2:98490400-98501400	Weak transcription	Skeletal Muscle Female	skeletal muscle
47	chr2:98490400-98502000	Weak transcription	Skeletal Muscle Male	skeletal muscle
48	chr2:98491600-98501600	Weak transcription	Primary hematopoietic stem cells	blood
49	chr2:98492000-98499200	Weak transcription	HepG2	liver
50	chr2:98492600-98500800	Weak transcription	Fetal Muscle Leg	muscle

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