Variant report

Variant	rs2899113
Chromosome Location	chr15:44644875-44644876
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	chr15:44643947..44646779-chr15:44717762..44720215,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000137770	Chromatin interaction
ENSG00000259595	Chromatin interaction

Extended variants
information (count: 99 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:86)

rs_ID	r²[population]
rs10152710	1.00[EUR][1000 genomes]
rs1021800	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10467977	0.94[EUR][1000 genomes]
rs11070426	1.00[ASN][1000 genomes]
rs12591178	0.94[EUR][1000 genomes]
rs12591581	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12591811	0.88[EUR][1000 genomes]
rs12592995	0.94[EUR][1000 genomes]
rs12593125	0.94[EUR][1000 genomes]
rs12593325	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12593686	0.88[EUR][1000 genomes]
rs12593943	0.88[EUR][1000 genomes]
rs12594110	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12594139	0.88[EUR][1000 genomes]
rs12594167	0.94[EUR][1000 genomes]
rs12594621	0.88[EUR][1000 genomes]
rs12594645	0.88[EUR][1000 genomes]
rs12594746	0.94[EUR][1000 genomes]
rs12595484	0.88[EUR][1000 genomes]
rs17551416	1.00[EUR][1000 genomes]
rs2055061	0.94[EUR][1000 genomes]
rs2288341	1.00[EUR][1000 genomes]
rs2288342	0.94[EUR][1000 genomes]
rs2303577	1.00[EUR][1000 genomes]
rs2303578	0.93[EUR][1000 genomes]
rs2412883	0.94[EUR][1000 genomes]
rs2412909	0.94[EUR][1000 genomes]
rs2433350	0.94[EUR][1000 genomes]
rs2555353	0.94[EUR][1000 genomes]
rs2556566	0.94[EUR][1000 genomes]
rs2556567	0.88[EUR][1000 genomes]
rs28508235	0.88[EUR][1000 genomes]
rs28561508	0.94[EUR][1000 genomes]
rs35555389	0.94[EUR][1000 genomes]
rs3784565	0.94[EUR][1000 genomes]
rs3784567	0.94[EUR][1000 genomes]
rs3809471	0.94[EUR][1000 genomes]
rs3816928	0.94[EUR][1000 genomes]
rs3986142	0.94[EUR][1000 genomes]
rs3986143	0.94[EUR][1000 genomes]
rs4415978	0.94[EUR][1000 genomes]
rs4477677	0.94[EUR][1000 genomes]
rs4577056	0.94[EUR][1000 genomes]
rs57270586	0.94[EUR][1000 genomes]
rs58956090	0.94[EUR][1000 genomes]
rs59230801	0.94[EUR][1000 genomes]
rs59997416	0.88[EUR][1000 genomes]
rs60003667	0.94[EUR][1000 genomes]
rs60399672	0.94[EUR][1000 genomes]
rs61185650	0.94[EUR][1000 genomes]
rs61234123	0.94[EUR][1000 genomes]
rs61258861	0.94[EUR][1000 genomes]
rs61278540	0.88[EUR][1000 genomes]
rs61329003	0.94[EUR][1000 genomes]
rs61501839	0.94[EUR][1000 genomes]
rs6493103	0.88[EUR][1000 genomes]
rs7162671	0.88[EUR][1000 genomes]
rs7162802	0.88[EUR][1000 genomes]
rs7163529	0.88[EUR][1000 genomes]
rs7164709	0.88[EUR][1000 genomes]
rs7166278	0.94[EUR][1000 genomes]
rs7166945	0.94[EUR][1000 genomes]
rs7167752	0.88[EUR][1000 genomes]
rs7169333	0.94[EUR][1000 genomes]
rs7170248	0.94[EUR][1000 genomes]
rs7172106	0.94[EUR][1000 genomes]
rs7175200	0.88[EUR][1000 genomes]
rs7178318	0.94[EUR][1000 genomes]
rs7179894	0.88[EUR][1000 genomes]
rs7181772	0.94[EUR][1000 genomes]
rs7183109	0.83[EUR][1000 genomes]
rs8023453	0.94[EUR][1000 genomes]
rs8024623	0.88[EUR][1000 genomes]
rs8024805	0.88[EUR][1000 genomes]
rs8025727	0.88[EUR][1000 genomes]
rs8025876	0.94[EUR][1000 genomes]
rs8025955	0.88[EUR][1000 genomes]
rs8026945	0.94[EUR][1000 genomes]
rs8027036	0.94[EUR][1000 genomes]
rs8028509	0.94[EUR][1000 genomes]
rs8028907	0.88[EUR][1000 genomes]
rs8032079	0.88[EUR][1000 genomes]
rs8037395	0.88[EUR][1000 genomes]
rs883943	0.94[EUR][1000 genomes]
rs9672237	0.94[EUR][1000 genomes]
rs9673085	0.94[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:13 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv431387	chr15:43929378-44862930	Weak transcription Strong transcription Active TSS ZNF genes & repeats Enhancers Flanking Active TSS Bivalent/Poised TSS Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	158 gene(s)	inside rSNPs	diseases
2	nsv931051	chr15:43988761-44833518	Strong transcription Enhancers Weak transcription Active TSS Flanking Active TSS ZNF genes & repeats 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 miRNA target site	154 gene(s)	inside rSNPs	diseases
3	nsv1052511	chr15:44266441-44719023	Flanking Active TSS Enhancers Weak transcription Strong transcription Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	29 gene(s)	inside rSNPs	diseases
4	nsv542371	chr15:44266441-44719023	Flanking Active TSS Enhancers Weak transcription Active TSS Strong transcription ZNF genes & repeats 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	29 gene(s)	inside rSNPs	diseases
5	esv3410956	chr15:44425145-44823647	Strong transcription Weak transcription Enhancers Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Flanking Active TSS Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	37 gene(s)	inside rSNPs	diseases
6	nsv1044686	chr15:44489534-44697482	Strong transcription Weak transcription Active TSS Enhancers Transcr. at gene 5' and 3' Flanking Active TSS Genic enhancers Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	19 gene(s)	inside rSNPs	diseases
7	nsv1043822	chr15:44491220-44686957	Weak transcription ZNF genes & repeats Strong transcription Transcr. at gene 5' and 3' Active TSS Enhancers Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	19 gene(s)	inside rSNPs	diseases
8	nsv1035386	chr15:44498905-44677174	Enhancers Weak transcription Strong transcription Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases
9	nsv904177	chr15:44582886-44821843	Weak transcription Strong transcription Active TSS Flanking Active TSS Enhancers ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	31 gene(s)	inside rSNPs	diseases
10	nsv569299	chr15:44598642-44776075	Weak transcription Flanking Active TSS Enhancers Strong transcription Active TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	29 gene(s)	inside rSNPs	diseases
11	nsv904178	chr15:44609796-44724287	Active TSS Weak transcription Strong transcription ZNF genes & repeats Enhancers Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	25 gene(s)	inside rSNPs	diseases
12	nsv569300	chr15:44609796-44763598	Weak transcription Enhancers Strong transcription Active TSS ZNF genes & repeats Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	26 gene(s)	inside rSNPs	diseases
13	nsv904179	chr15:44614684-44821843	Strong transcription Weak transcription ZNF genes & repeats Enhancers Flanking Active TSS Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	27 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:78 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:44582800-44672200	Weak transcription	HSMM	muscle
2	chr15:44598600-44646800	Weak transcription	Right Ventricle	heart
3	chr15:44628000-44646800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
4	chr15:44633200-44647000	Weak transcription	NHEK	skin
5	chr15:44633200-44647200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
6	chr15:44633200-44653200	Weak transcription	NH-A	brain
7	chr15:44634600-44648200	Weak transcription	Small Intestine	intestine
8	chr15:44637600-44647200	Weak transcription	H9 Cell Line	embryonic stem cell
9	chr15:44640400-44646400	Weak transcription	Pancreas	Pancrea
10	chr15:44640600-44646800	Weak transcription	NHLF	lung
11	chr15:44640800-44646400	Weak transcription	Primary T helper cells fromperipheralblood	blood
12	chr15:44640800-44646800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
13	chr15:44640800-44646800	Weak transcription	HSMMtube	muscle
14	chr15:44640800-44672000	Weak transcription	Duodenum Smooth Muscle	Duodenum
15	chr15:44641000-44645400	Weak transcription	Fetal Kidney	kidney
16	chr15:44641000-44646800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
17	chr15:44641000-44646800	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
18	chr15:44641000-44646800	Weak transcription	Esophagus	oesophagus
19	chr15:44641000-44646800	Weak transcription	Skeletal Muscle Female	skeletal muscle
20	chr15:44641000-44646800	Weak transcription	Thymus	Thymus
21	chr15:44641000-44646800	Weak transcription	Dnd41	blood
22	chr15:44641000-44646800	Weak transcription	Osteobl	bone
23	chr15:44641000-44647000	Weak transcription	Pancreatic Islets	Pancreatic Islet
24	chr15:44641000-44647200	Weak transcription	Gastric	stomach
25	chr15:44641000-44647200	Weak transcription	Hela-S3	cervix
26	chr15:44641000-44648600	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
27	chr15:44641000-44648600	Weak transcription	A549	lung
28	chr15:44641000-44649400	Weak transcription	Brain Cingulate Gyrus	brain
29	chr15:44641000-44651000	Weak transcription	Brain Angular Gyrus	brain
30	chr15:44641000-44666600	Weak transcription	Stomach Smooth Muscle	stomach
31	chr15:44641000-44668800	Weak transcription	Brain Substantia Nigra	brain
32	chr15:44641000-44677000	Weak transcription	Brain Anterior Caudate	brain
33	chr15:44641000-44681600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
34	chr15:44641000-44696000	Weak transcription	Rectal Smooth Muscle	rectum
35	chr15:44641200-44645800	Weak transcription	Breast Myoepithelial Primary Cells	Breast
36	chr15:44641200-44645800	Weak transcription	Primary T cells from cord blood	blood
37	chr15:44641200-44646800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
38	chr15:44641200-44646800	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
39	chr15:44641200-44646800	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
40	chr15:44641200-44646800	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
41	chr15:44641200-44646800	Weak transcription	Aorta	Aorta
42	chr15:44641200-44646800	Weak transcription	Sigmoid Colon	Sigmoid Colon
43	chr15:44641200-44646800	Weak transcription	Skeletal Muscle Male	skeletal muscle
44	chr15:44641200-44646800	Weak transcription	Spleen	Spleen
45	chr15:44641200-44647000	Weak transcription	Brain Inferior Temporal Lobe	brain
46	chr15:44641200-44647000	Weak transcription	Duodenum Mucosa	Duodenum
47	chr15:44641200-44647000	Weak transcription	Left Ventricle	heart
48	chr15:44641200-44647400	Weak transcription	Ovary	ovary
49	chr15:44641200-44648600	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
50	chr15:44641200-44650800	Weak transcription	Primary B cells from peripheral blood	blood

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