Variant report

Variant	rs12900038
Chromosome Location	chr15:57409449-57409450
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 38 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:35)

rs_ID	r²[population]
rs10518894	0.94[AFR][1000 genomes];0.84[AMR][1000 genomes];0.98[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs10518895	1.00[AFR][1000 genomes];0.84[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11071305	0.82[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs11635645	0.92[ASN][1000 genomes]
rs11636100	0.84[AFR][1000 genomes];0.85[AMR][1000 genomes];0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs11852340	0.82[AMR][1000 genomes];0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs11853331	0.83[AFR][1000 genomes];0.85[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs11855648	0.89[AFR][1000 genomes];0.99[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12899904	0.88[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12900589	0.84[ASN][1000 genomes]
rs12903578	0.80[AFR][1000 genomes];0.85[ASN][1000 genomes]
rs12909402	0.82[AMR][1000 genomes];0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12910094	0.83[AFR][1000 genomes];0.85[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12910170	0.80[AMR][1000 genomes];0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12912007	0.84[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12914182	0.83[AFR][1000 genomes];0.87[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12914410	0.83[AFR][1000 genomes];0.86[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12915473	0.85[ASN][1000 genomes]
rs13313455	0.84[ASN][1000 genomes]
rs2169465	0.93[ASN][1000 genomes]
rs2169466	0.83[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2414494	0.84[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2615231	0.84[ASN][1000 genomes]
rs2733307	0.92[ASN][1000 genomes]
rs2733332	0.82[ASN][1000 genomes]
rs28414972	0.83[ASN][1000 genomes]
rs28514688	0.83[ASN][1000 genomes]
rs28648502	0.84[ASN][1000 genomes]
rs2927189	0.82[ASN][1000 genomes]
rs2957591	0.83[ASN][1000 genomes]
rs4774910	0.80[AFR][1000 genomes];0.85[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6493901	0.85[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7168387	0.83[ASN][1000 genomes]
rs8037901	0.93[ASN][1000 genomes]
rs967514	0.84[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1042486	chr15:57094598-57505992	Strong transcription Weak transcription Enhancers Flanking Active TSS Active TSS ZNF genes & repeats 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	21 gene(s)	inside rSNPs	diseases
2	nsv904251	chr15:57241970-57575916	Enhancers Weak transcription Strong transcription ZNF genes & repeats Flanking Active TSS Genic enhancers Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	8 gene(s)	inside rSNPs	diseases
3	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

No data

Chromatin state (count:102 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:57372800-57410200	Weak transcription	Muscle Satellite Cultured Cells	--
2	chr15:57374800-57409600	Weak transcription	Osteobl	bone
3	chr15:57374800-57414600	Weak transcription	Fetal Kidney	kidney
4	chr15:57381000-57412400	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
5	chr15:57382600-57423800	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
6	chr15:57382800-57419600	Weak transcription	K562	blood
7	chr15:57384600-57410400	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
8	chr15:57386200-57410200	Weak transcription	Ovary	ovary
9	chr15:57386400-57426600	Weak transcription	Primary T cells fromperipheralblood	blood
10	chr15:57386600-57424600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
11	chr15:57387000-57430000	Weak transcription	Placenta	Placenta
12	chr15:57387200-57425400	Weak transcription	Primary T helper cells fromperipheralblood	blood
13	chr15:57387600-57442400	Weak transcription	Fetal Intestine Large	intestine
14	chr15:57391200-57410200	Weak transcription	HMEC	breast
15	chr15:57391400-57409600	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
16	chr15:57397800-57416600	Weak transcription	Fetal Stomach	stomach
17	chr15:57398000-57415800	Weak transcription	Fetal Intestine Small	intestine
18	chr15:57399400-57409600	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
19	chr15:57399400-57410000	Weak transcription	NH-A	brain
20	chr15:57399400-57424600	Weak transcription	Primary T helper cells PMA-I stimulated	--
21	chr15:57399600-57410000	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
22	chr15:57399600-57410200	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
23	chr15:57399600-57416200	Weak transcription	Primary T cells from cord blood	blood
24	chr15:57401600-57410200	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
25	chr15:57402000-57410200	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
26	chr15:57402600-57414600	Weak transcription	Primary B cells from cord blood	blood
27	chr15:57403000-57424600	Weak transcription	Primary T helper naive cells from peripheral blood	blood
28	chr15:57403800-57425200	Weak transcription	H9 Cell Line	embryonic stem cell
29	chr15:57404600-57409800	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
30	chr15:57404600-57410200	Weak transcription	iPS-15b Cell Line	embryonic stem cell
31	chr15:57404600-57410200	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
32	chr15:57404600-57425000	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
33	chr15:57404800-57409800	Weak transcription	iPS-18 Cell Line	embryonic stem cell
34	chr15:57404800-57410200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
35	chr15:57404800-57410200	Weak transcription	H1 Cell Line	embryonic stem cell
36	chr15:57404800-57410200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
37	chr15:57404800-57410200	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
38	chr15:57404800-57410200	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
39	chr15:57404800-57410200	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
40	chr15:57404800-57410200	Strong transcription	Fetal Thymus	thymus
41	chr15:57404800-57410200	Weak transcription	Skeletal Muscle Male	skeletal muscle
42	chr15:57404800-57410200	Weak transcription	HSMM	muscle
43	chr15:57404800-57410200	Weak transcription	NHEK	skin
44	chr15:57404800-57411200	Weak transcription	Spleen	Spleen
45	chr15:57404800-57415600	Weak transcription	Thymus	Thymus
46	chr15:57405000-57410200	Weak transcription	Skeletal Muscle Female	skeletal muscle
47	chr15:57405400-57410200	Weak transcription	HSMMtube	muscle
48	chr15:57405600-57410200	Weak transcription	iPS-20b Cell Line	embryonic stem cell
49	chr15:57405600-57410200	Weak transcription	Breast Myoepithelial Primary Cells	Breast
50	chr15:57406000-57410600	Enhancers	Duodenum Mucosa	Duodenum

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