Variant report

Variant	rs1504439
Chromosome Location	chr13:90166539-90166540
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 46 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:38)

rs_ID	r²[population]
rs1113478	0.80[EUR][1000 genomes]
rs1158015	0.82[EUR][1000 genomes]
rs1158016	0.82[EUR][1000 genomes]
rs1199479	0.81[EUR][1000 genomes]
rs12584227	0.82[EUR][1000 genomes]
rs12874844	0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1394321	0.92[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1504437	0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1504438	0.94[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs17395268	0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2047905	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34294912	0.81[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs35003959	0.90[EUR][1000 genomes]
rs3736408	0.92[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs4773474	0.80[EUR][1000 genomes]
rs515212	0.96[CEU][hapmap];0.86[CHB][hapmap];1.00[JPT][hapmap]
rs572497	0.93[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs574402	0.81[EUR][1000 genomes]
rs617470	0.96[CEU][hapmap];0.86[CHB][hapmap];0.93[CHD][hapmap];1.00[JPT][hapmap];0.93[TSI][hapmap]
rs618484	0.96[CEU][hapmap];0.86[CHB][hapmap];1.00[JPT][hapmap]
rs620909	0.81[EUR][1000 genomes]
rs633976	0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs657998	0.94[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs669093	0.94[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7318774	0.82[EUR][1000 genomes]
rs7332656	0.94[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7996556	0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs8001088	0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs8001305	0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs9555901	0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs9555902	0.95[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs9555906	0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9560339	0.82[EUR][1000 genomes]
rs9560340	0.82[EUR][1000 genomes]
rs9560341	0.90[EUR][1000 genomes]
rs9560355	0.94[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs9560356	0.93[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs9560374	0.81[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[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	nsv1048574	chr13:89650680-90232894	Enhancers Weak transcription Flanking Active TSS Active TSS Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases
2	nsv1044807	chr13:89991827-90263328	Enhancers Weak transcription Flanking Active TSS Genic enhancers ZNF genes & repeats Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
3	nsv1039775	chr13:89995537-90260944	Enhancers Weak transcription ZNF genes & repeats Flanking Active TSS Active TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
4	nsv900860	chr13:90008941-90259291	Weak transcription Enhancers Flanking Active TSS Active TSS ZNF genes & repeats Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
5	nsv533455	chr13:90041897-90255725	Enhancers Weak transcription Flanking Active TSS Active TSS ZNF genes & repeats Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
6	nsv1053657	chr13:90100510-90578568	Enhancers Weak transcription Flanking Active TSS Active TSS ZNF genes & repeats Genic enhancers Bivalent Enhancer Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
7	nsv900864	chr13:90110725-90173515	Enhancers Weak transcription Flanking Active TSS Active TSS ZNF genes & repeats	TF binding region Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	n/a
8	esv3433367	chr13:90162000-90184090	Enhancers Weak transcription Flanking Active TSS Active TSS ZNF genes & repeats	Chromatin interactive region	n/a	inside rSNPs	n/a

No data

Chromatin state (count:26 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr13:90164200-90167000	Weak transcription	Fetal Lung	lung
2	chr13:90165200-90168000	Enhancers	HUES48 Cell Line	embryonic stem cell
3	chr13:90165200-90168000	Enhancers	HUES64 Cell Line	embryonic stem cell
4	chr13:90165400-90166600	Flanking Active TSS	A549	lung
5	chr13:90165400-90166800	Enhancers	iPS-20b Cell Line	embryonic stem cell
6	chr13:90165400-90167800	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
7	chr13:90165400-90167800	Enhancers	iPS-18 Cell Line	embryonic stem cell
8	chr13:90165600-90167600	Enhancers	iPS-15b Cell Line	embryonic stem cell
9	chr13:90165600-90167600	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
10	chr13:90165600-90167800	Enhancers	ES-I3 Cell Line	embryonic stem cell
11	chr13:90165800-90166800	Weak transcription	Cortex derived primary cultured neurospheres	brain
12	chr13:90165800-90167000	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
13	chr13:90165800-90167800	Enhancers	HUES6 Cell Line	embryonic stem cell
14	chr13:90165800-90168000	Enhancers	NHEK	skin
15	chr13:90166000-90167800	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
16	chr13:90166000-90167800	Enhancers	Muscle Satellite Cultured Cells	--
17	chr13:90166000-90168000	Enhancers	Hela-S3	cervix
18	chr13:90166000-90170400	Weak transcription	H9 Cell Line	embryonic stem cell
19	chr13:90166200-90167800	Enhancers	H1 Cell Line	embryonic stem cell
20	chr13:90166200-90168000	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
21	chr13:90166400-90166600	Flanking Active TSS	HUVEC	blood vessel
22	chr13:90166400-90167600	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
23	chr13:90166400-90167600	Enhancers	Fetal Adrenal Gland	Adrenal Gland
24	chr13:90166400-90167800	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
25	chr13:90166400-90167800	Enhancers	Fetal Heart	heart
26	chr13:90166400-90167800	Enhancers	HMEC	breast

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