Variant report

Variant	rs2554026
Chromosome Location	chr15:57940144-57940145
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 42 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:37)

rs_ID	r²[population]
rs10162772	0.85[CEU][hapmap];0.90[EUR][1000 genomes]
rs11071337	0.84[CHB][hapmap];0.90[JPT][hapmap]
rs11071338	0.90[JPT][hapmap]
rs11071339	0.85[CEU][hapmap];0.89[EUR][1000 genomes]
rs11629719	0.93[CEU][hapmap];0.82[CHB][hapmap];1.00[JPT][hapmap];0.88[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs1346124	0.92[EUR][1000 genomes]
rs1425948	0.85[CEU][hapmap];0.90[EUR][1000 genomes]
rs1425949	0.92[CEU][hapmap];0.93[EUR][1000 genomes]
rs17240055	0.92[CEU][hapmap];0.90[JPT][hapmap];0.85[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs1834488	0.93[CEU][hapmap];0.93[EUR][1000 genomes]
rs2042698	0.86[YRI][hapmap]
rs2251762	0.89[CEU][hapmap];0.91[EUR][1000 genomes]
rs2433196	0.92[CEU][hapmap];0.82[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.91[AFR][1000 genomes];0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2433197	1.00[JPT][hapmap];1.00[YRI][hapmap];0.86[AFR][1000 genomes];0.80[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs2433198	0.92[CHB][hapmap];1.00[JPT][hapmap];0.97[ASN][1000 genomes]
rs2470356	0.90[JPT][hapmap]
rs2554040	0.92[CHB][hapmap];0.88[JPT][hapmap]
rs2733597	0.86[YRI][hapmap]
rs2733598	0.84[CHB][hapmap];0.90[JPT][hapmap]
rs2733601	0.82[CEU][hapmap];0.90[JPT][hapmap];0.87[EUR][1000 genomes]
rs2733602	0.82[CEU][hapmap];0.90[JPT][hapmap];0.87[EUR][1000 genomes]
rs2733603	0.81[JPT][hapmap]
rs2733604	0.89[CEU][hapmap];0.92[EUR][1000 genomes]
rs34270510	0.93[AFR][1000 genomes];0.94[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs36082771	0.93[AFR][1000 genomes];0.89[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs4578589	0.92[EUR][1000 genomes]
rs4774277	0.84[CHB][hapmap];0.90[JPT][hapmap]
rs4774979	0.96[CEU][hapmap];0.81[JPT][hapmap];0.81[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs6493939	1.00[JPT][hapmap]
rs7169211	0.92[CEU][hapmap];0.90[JPT][hapmap];0.85[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs7172191	0.86[YRI][hapmap]
rs7176042	0.84[CEU][hapmap];0.81[JPT][hapmap];0.93[YRI][hapmap];0.95[AFR][1000 genomes];0.95[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs7181013	0.85[CEU][hapmap];0.83[EUR][1000 genomes]
rs8034146	0.93[CEU][hapmap];0.91[EUR][1000 genomes]
rs9302201	0.92[CEU][hapmap];0.93[EUR][1000 genomes]
rs9806740	0.85[CEU][hapmap];0.90[EUR][1000 genomes]
rs986868	0.81[CEU][hapmap];0.88[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1045611	chr15:57350965-58070807	Weak transcription Enhancers Strong transcription Genic enhancers Flanking Active TSS Active TSS ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	49 gene(s)	inside rSNPs	diseases
2	nsv1054547	chr15:57600488-57977659	Active TSS Weak transcription Enhancers Strong transcription Flanking Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	19 gene(s)	inside rSNPs	diseases
3	nsv530682	chr15:57912502-58108285	Weak transcription Flanking Active TSS Strong transcription Active TSS Enhancers Genic enhancers Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS 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	nsv1038667	chr15:57933076-58481870	Flanking Active TSS Enhancers Genic enhancers Active TSS Weak transcription Flanking Bivalent TSS/Enh Strong transcription Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	22 gene(s)	inside rSNPs	diseases
5	nsv542400	chr15:57933076-58481870	Weak transcription Enhancers Flanking Active TSS ZNF genes & repeats Active TSS Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS Strong transcription Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	22 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:46 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:57900600-57941600	Weak transcription	Colonic Mucosa	Colon
2	chr15:57905000-57940800	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
3	chr15:57919400-57946800	Weak transcription	Fetal Lung	lung
4	chr15:57919400-57959400	Weak transcription	Duodenum Smooth Muscle	Duodenum
5	chr15:57932200-57942200	Weak transcription	Breast Myoepithelial Primary Cells	Breast
6	chr15:57932200-57967400	Weak transcription	Aorta	Aorta
7	chr15:57933400-57982600	Weak transcription	Esophagus	oesophagus
8	chr15:57934400-57940800	Weak transcription	Brain Angular Gyrus	brain
9	chr15:57936600-57954000	Weak transcription	Rectal Mucosa Donor 31	rectum
10	chr15:57937000-57944200	Weak transcription	Fetal Stomach	stomach
11	chr15:57937000-57946800	Weak transcription	Rectal Mucosa Donor 29	rectum
12	chr15:57937200-57946600	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
13	chr15:57937600-57942000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
14	chr15:57937800-57940200	Strong transcription	Duodenum Mucosa	Duodenum
15	chr15:57938200-57940200	Genic enhancers	Adipose Nuclei	Adipose
16	chr15:57938200-57940800	Enhancers	Primary B cells from peripheral blood	blood
17	chr15:57938200-57940800	Strong transcription	Stomach Smooth Muscle	stomach
18	chr15:57938600-57944000	Genic enhancers	Fetal Heart	heart
19	chr15:57938800-57941600	Enhancers	Skeletal Muscle Male	skeletal muscle
20	chr15:57939200-57940200	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
21	chr15:57939200-57940200	Enhancers	Fetal Kidney	kidney
22	chr15:57939200-57940200	Enhancers	Fetal Muscle Trunk	muscle
23	chr15:57939200-57940200	Enhancers	Gastric	stomach
24	chr15:57939200-57940200	Enhancers	Pancreas	Pancrea
25	chr15:57939200-57940200	Enhancers	Right Atrium	heart
26	chr15:57939200-57940200	Enhancers	Spleen	Spleen
27	chr15:57939200-57940400	Enhancers	Placenta	Placenta
28	chr15:57939200-57940400	Enhancers	Skeletal Muscle Female	skeletal muscle
29	chr15:57939200-57940400	Enhancers	HUVEC	blood vessel
30	chr15:57939200-57940800	Enhancers	Fetal Intestine Large	intestine
31	chr15:57939400-57940400	Enhancers	Stomach Mucosa	stomach
32	chr15:57939600-57940800	Enhancers	Fetal Adrenal Gland	Adrenal Gland
33	chr15:57939800-57940200	Enhancers	Fetal Muscle Leg	muscle
34	chr15:57939800-57940200	Transcr. at gene 5' and 3'	Left Ventricle	heart
35	chr15:57939800-57940200	Enhancers	Lung	lung
36	chr15:57939800-57940200	Enhancers	Right Ventricle	heart
37	chr15:57939800-57940600	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
38	chr15:57939800-57940800	Enhancers	Psoas Muscle	Psoas
39	chr15:57939800-57940800	Enhancers	GM12878-XiMat	blood
40	chr15:57940000-57940200	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
41	chr15:57940000-57940200	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
42	chr15:57940000-57940200	Bivalent Enhancer	Primary mononuclear cells fromperipheralblood	Blood
43	chr15:57940000-57940800	Enhancers	Fetal Intestine Small	intestine
44	chr15:57940000-57941400	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
45	chr15:57940000-57942200	Enhancers	HMEC	breast
46	chr15:57940000-57943800	Weak transcription	Brain Cingulate Gyrus	brain

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