Variant report

Variant	rs12438925
Chromosome Location	chr15:29998521-29998522
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	chr15:29993453..29996171-chr15:29998499..30000876,2	K562	blood:

Extended variants
information (count: 64 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:56)

rs_ID	r²[population]
rs10152681	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs10775231	1.00[CEU][hapmap];0.91[EUR][1000 genomes]
rs11073205	0.87[AMR][1000 genomes];1.00[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs11073218	0.88[CHB][hapmap];0.90[JPT][hapmap]
rs11632848	0.81[ASN][1000 genomes]
rs11636849	0.83[CEU][hapmap];0.93[GIH][hapmap];0.81[TSI][hapmap];0.81[EUR][1000 genomes]
rs12440211	0.93[EUR][1000 genomes]
rs12440708	0.86[EUR][1000 genomes]
rs12441554	0.84[EUR][1000 genomes]
rs1383315	0.94[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.96[GIH][hapmap];1.00[JPT][hapmap];0.88[MKK][hapmap];1.00[TSI][hapmap];0.93[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs1480503	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.96[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.88[MKK][hapmap];1.00[TSI][hapmap];0.93[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs1552077	0.94[CEU][hapmap];0.89[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.84[MEX][hapmap];0.83[TSI][hapmap];0.83[ASN][1000 genomes]
rs1585900	1.00[CEU][hapmap];0.93[GIH][hapmap];1.00[MEX][hapmap];0.89[TSI][hapmap];0.89[EUR][1000 genomes]
rs1679647	0.98[ASN][1000 genomes]
rs17750802	0.88[CHB][hapmap]
rs1871678	0.86[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2032	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs2229518	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.88[MKK][hapmap];1.00[TSI][hapmap];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2306437	0.88[CHB][hapmap]
rs2337167	0.89[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.92[AFR][1000 genomes];0.93[AMR][1000 genomes];0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs260528	0.87[ASN][1000 genomes]
rs260529	0.87[ASN][1000 genomes]
rs260531	1.00[CHB][hapmap];0.89[CHD][hapmap];0.90[JPT][hapmap];0.87[ASN][1000 genomes]
rs260532	1.00[CHB][hapmap];0.90[JPT][hapmap];0.87[ASN][1000 genomes]
rs260533	1.00[CHB][hapmap];0.89[CHD][hapmap];0.90[JPT][hapmap];0.87[ASN][1000 genomes]
rs260534	1.00[CHB][hapmap];0.89[CHD][hapmap];0.90[JPT][hapmap];0.87[ASN][1000 genomes]
rs260535	1.00[CHB][hapmap];0.90[JPT][hapmap];0.87[ASN][1000 genomes]
rs260538	0.90[ASN][1000 genomes]
rs28675809	0.86[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs2878893	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.88[MKK][hapmap];1.00[TSI][hapmap];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2878905	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs3809503	0.88[CHB][hapmap]
rs4073316	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.90[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4362339	0.83[ASW][hapmap];0.94[CEU][hapmap];0.89[CHB][hapmap];0.94[CHD][hapmap];1.00[JPT][hapmap];0.84[MEX][hapmap];0.88[MKK][hapmap];0.83[TSI][hapmap];0.83[YRI][hapmap];0.83[AMR][1000 genomes];0.87[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4779670	0.94[CEU][hapmap];0.88[CHB][hapmap];1.00[JPT][hapmap];0.80[ASN][1000 genomes]
rs4780258	0.82[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs4780259	1.00[CEU][hapmap];0.89[CHB][hapmap];1.00[CHD][hapmap];0.96[GIH][hapmap];1.00[JPT][hapmap];0.94[MEX][hapmap];0.88[MKK][hapmap];1.00[TSI][hapmap];0.82[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4780260	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.96[GIH][hapmap];0.90[JPT][hapmap];0.94[MEX][hapmap];0.88[MKK][hapmap];0.96[TSI][hapmap];0.90[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs4780263	0.84[EUR][1000 genomes]
rs6495890	0.82[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs6495914	0.93[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs6495927	0.90[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs6495935	0.90[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs6495945	1.00[CEU][hapmap];0.84[EUR][1000 genomes]
rs7166786	0.84[EUR][1000 genomes]
rs7168919	0.94[CEU][hapmap];0.93[GIH][hapmap];1.00[MEX][hapmap];0.85[TSI][hapmap];0.86[EUR][1000 genomes]
rs7170406	1.00[CEU][hapmap];0.93[GIH][hapmap];0.94[MEX][hapmap];0.89[TSI][hapmap];0.91[EUR][1000 genomes]
rs7171815	0.89[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs7175819	0.82[EUR][1000 genomes]
rs7176476	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.96[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.91[MKK][hapmap];1.00[TSI][hapmap];0.90[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs7176594	0.89[CEU][hapmap];0.84[CHB][hapmap];1.00[JPT][hapmap];0.83[ASN][1000 genomes]
rs7180387	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.96[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.91[MKK][hapmap];1.00[TSI][hapmap];0.87[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs767514	1.00[CHB][hapmap];0.95[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.88[MKK][hapmap];1.00[TSI][hapmap];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs785445	0.83[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[ASN][1000 genomes]
rs785446	0.83[CEU][hapmap]
rs8027827	0.80[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:8 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv456736	chr15:29327352-30208654	Weak transcription Active TSS Enhancers ZNF genes & repeats Strong transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Flanking Active TSS Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	31 gene(s)	inside rSNPs	diseases
2	nsv568675	chr15:29327352-30208654	Flanking Active TSS Strong transcription Active TSS Enhancers Weak transcription Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	31 gene(s)	inside rSNPs	diseases
3	nsv903747	chr15:29361126-30008977	Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Enhancers Weak transcription Flanking Active TSS Strong transcription Genic enhancers Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	15 gene(s)	inside rSNPs	diseases
4	nsv995038	chr15:29744279-30366124	Weak transcription Enhancers Strong transcription Flanking Bivalent TSS/Enh Flanking Active TSS Active TSS Bivalent/Poised TSS ZNF genes & repeats Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	27 gene(s)	inside rSNPs	diseases
5	nsv1038495	chr15:29825859-30351687	Weak transcription Bivalent Enhancer Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Enhancers Strong transcription Genic enhancers Active TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	26 gene(s)	inside rSNPs	diseases
6	nsv542293	chr15:29825859-30351687	Weak transcription Enhancers Active TSS Strong transcription Bivalent Enhancer Bivalent/Poised TSS Flanking Active TSS ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	26 gene(s)	inside rSNPs	diseases
7	nsv832944	chr15:29861062-30082057	Weak transcription ZNF genes & repeats Strong transcription Enhancers Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent/Poised TSS Genic enhancers Bivalent Enhancer Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	9 gene(s)	inside rSNPs	diseases
8	nsv832945	chr15:29932599-30123721	Genic enhancers Weak transcription Strong transcription Enhancers Active TSS Flanking Active TSS ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	18 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:97 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:29987000-29999400	Weak transcription	Brain Germinal Matrix	brain
2	chr15:29988800-29999400	Weak transcription	Fetal Brain Male	brain
3	chr15:29989000-30014800	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
4	chr15:29989200-29999200	Weak transcription	Spleen	Spleen
5	chr15:29989600-30002400	Strong transcription	Fetal Muscle Leg	muscle
6	chr15:29989600-30013400	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
7	chr15:29989600-30021200	Strong transcription	Duodenum Smooth Muscle	Duodenum
8	chr15:29989600-30027200	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
9	chr15:29989800-30000600	Strong transcription	Adipose Nuclei	Adipose
10	chr15:29990000-30014200	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
11	chr15:29990000-30016600	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
12	chr15:29990200-30000600	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
13	chr15:29990200-30013600	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
14	chr15:29990200-30016200	Strong transcription	Left Ventricle	heart
15	chr15:29990200-30028400	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
16	chr15:29990400-30014200	Strong transcription	Breast Myoepithelial Primary Cells	Breast
17	chr15:29990400-30014400	Strong transcription	Fetal Muscle Trunk	muscle
18	chr15:29990400-30014400	Strong transcription	Placenta	Placenta
19	chr15:29990400-30026400	Strong transcription	Stomach Smooth Muscle	stomach
20	chr15:29990600-30004800	Strong transcription	Fetal Intestine Large	intestine
21	chr15:29990600-30014200	Strong transcription	iPS-20b Cell Line	embryonic stem cell
22	chr15:29990800-30014400	Strong transcription	HUES48 Cell Line	embryonic stem cell
23	chr15:29991000-30014200	Strong transcription	HUES6 Cell Line	embryonic stem cell
24	chr15:29991200-30003600	Strong transcription	HSMM	muscle
25	chr15:29991200-30013800	Strong transcription	NH-A	brain
26	chr15:29991200-30014200	Strong transcription	HUES64 Cell Line	embryonic stem cell
27	chr15:29991200-30014400	Strong transcription	iPS-18 Cell Line	embryonic stem cell
28	chr15:29991200-30014400	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
29	chr15:29991200-30014600	Strong transcription	Osteobl	bone
30	chr15:29991200-30020200	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
31	chr15:29991200-30022400	Strong transcription	Skeletal Muscle Female	skeletal muscle
32	chr15:29991400-30005800	Strong transcription	H1 Cell Line	embryonic stem cell
33	chr15:29991600-30003200	Strong transcription	Muscle Satellite Cultured Cells	--
34	chr15:29991600-30014400	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
35	chr15:29992000-30026600	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
36	chr15:29992200-30014800	Weak transcription	Small Intestine	intestine
37	chr15:29992600-30004200	Weak transcription	Pancreatic Islets	Pancreatic Islet
38	chr15:29993200-30003200	Strong transcription	Foreskin Fibroblast Primary Cells skin01	Skin
39	chr15:29993200-30003200	Strong transcription	Ovary	ovary
40	chr15:29993200-30019600	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
41	chr15:29993800-30003200	Strong transcription	Brain Substantia Nigra	brain
42	chr15:29994200-30003200	Strong transcription	Duodenum Mucosa	Duodenum
43	chr15:29994400-30003200	Strong transcription	Fetal Intestine Small	intestine
44	chr15:29994400-30003200	Strong transcription	HUVEC	blood vessel
45	chr15:29994400-30004000	Strong transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
46	chr15:29994400-30004000	Strong transcription	Fetal Stomach	stomach
47	chr15:29994600-30003200	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
48	chr15:29994600-30003400	Strong transcription	HepG2	liver
49	chr15:29995000-30001600	Strong transcription	A549	lung
50	chr15:29995400-30002400	Strong transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived

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