Variant report

Variant	rs2025405
Chromosome Location	chr13:38170523-38170524
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 44 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:39)

rs_ID	r²[population]
rs1003062	0.87[CEU][hapmap];0.91[JPT][hapmap];0.90[TSI][hapmap];0.81[EUR][1000 genomes]
rs10161932	0.93[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.93[TSI][hapmap];0.85[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1041019	0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1535775	0.81[CEU][hapmap];1.00[JPT][hapmap];0.89[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs1570612	0.87[CEU][hapmap];0.91[JPT][hapmap];0.90[TSI][hapmap];0.81[EUR][1000 genomes]
rs17056378	0.87[CEU][hapmap];0.91[JPT][hapmap];0.85[EUR][1000 genomes]
rs1886165	0.87[CEU][hapmap];0.95[JPT][hapmap];0.90[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs1924296	0.94[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];1.00[TSI][hapmap];0.90[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1924306	0.94[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.96[TSI][hapmap];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1951894	0.90[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1977278	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28407779	0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3812842	0.94[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4341641	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4368050	0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4943523	0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7319022	0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7319663	0.83[EUR][1000 genomes]
rs7320832	0.94[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.96[TSI][hapmap];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7330467	0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7335776	0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7336380	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7338118	0.85[CEU][hapmap];0.83[EUR][1000 genomes]
rs7338244	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.82[LWK][hapmap];1.00[MEX][hapmap];0.82[MKK][hapmap];1.00[TSI][hapmap];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7984226	0.87[CEU][hapmap];0.91[JPT][hapmap];0.90[TSI][hapmap]
rs7996934	0.86[CEU][hapmap];0.91[JPT][hapmap];0.81[EUR][1000 genomes]
rs8000496	0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs8001321	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9315504	0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9532087	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9566239	0.89[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9576302	0.91[AMR][1000 genomes];0.92[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9576310	0.94[CEU][hapmap];0.95[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];0.95[JPT][hapmap];1.00[MEX][hapmap];0.96[TSI][hapmap];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9576319	0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9576320	0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs9603225	0.91[AMR][1000 genomes];0.92[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9603240	0.92[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs9603241	0.87[CEU][hapmap];0.89[CHB][hapmap];1.00[JPT][hapmap];0.92[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs9603247	0.81[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	nsv948975	chr13:37281203-38280430	Enhancers Flanking Active TSS Weak transcription Strong transcription Active TSS Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	50 gene(s)	inside rSNPs	diseases
2	nsv1038850	chr13:37820489-38209571	Strong transcription Enhancers Active TSS Weak transcription Flanking Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
3	esv34109	chr13:37843819-38276391	Weak transcription Enhancers Strong transcription Flanking Active TSS ZNF genes & repeats Active TSS 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	4 gene(s)	inside rSNPs	diseases
4	nsv1045716	chr13:37952062-38394595	Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Strong transcription Genic enhancers Active TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	4 gene(s)	inside rSNPs	diseases
5	nsv832583	chr13:38030752-38202000	Enhancers Weak transcription Genic enhancers Active TSS Strong transcription Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs2025405	STARD13	cis	parietal	SCAN

Chromatin state (count:35 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr13:38139000-38171000	Weak transcription	Fetal Kidney	kidney
2	chr13:38150000-38171000	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
3	chr13:38150200-38171400	Weak transcription	Colon Smooth Muscle	Colon
4	chr13:38152600-38171200	Weak transcription	Stomach Smooth Muscle	stomach
5	chr13:38163200-38171200	Weak transcription	Duodenum Smooth Muscle	Duodenum
6	chr13:38165800-38182400	Weak transcription	Placenta	Placenta
7	chr13:38167600-38171200	Transcr. at gene 5' and 3'	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
8	chr13:38168800-38171000	Enhancers	NHDF-Ad	bronchial
9	chr13:38168800-38171400	Transcr. at gene 5' and 3'	Osteobl	bone
10	chr13:38168800-38173400	Active TSS	Fetal Muscle Trunk	muscle
11	chr13:38169200-38173000	Active TSS	NH-A	brain
12	chr13:38169400-38170600	Enhancers	H9 Cell Line	embryonic stem cell
13	chr13:38169400-38173600	Active TSS	NHLF	lung
14	chr13:38169600-38172800	Weak transcription	H1 Cell Line	embryonic stem cell
15	chr13:38169800-38170800	Weak transcription	Right Atrium	heart
16	chr13:38169800-38171000	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
17	chr13:38169800-38171600	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
18	chr13:38169800-38171800	Weak transcription	HUES64 Cell Line	embryonic stem cell
19	chr13:38169800-38171800	Weak transcription	iPS-18 Cell Line	embryonic stem cell
20	chr13:38169800-38172600	Weak transcription	iPS-15b Cell Line	embryonic stem cell
21	chr13:38169800-38172600	Weak transcription	iPS-20b Cell Line	embryonic stem cell
22	chr13:38169800-38172800	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
23	chr13:38169800-38175600	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
24	chr13:38169800-38175600	Weak transcription	HUES6 Cell Line	embryonic stem cell
25	chr13:38170000-38171200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
26	chr13:38170000-38171600	Weak transcription	HUES48 Cell Line	embryonic stem cell
27	chr13:38170000-38172800	Weak transcription	HUVEC	blood vessel
28	chr13:38170200-38170600	Flanking Active TSS	Breast Myoepithelial Primary Cells	Breast
29	chr13:38170200-38170600	Transcr. at gene 5' and 3'	Fetal Muscle Leg	muscle
30	chr13:38170400-38170600	Enhancers	ES-WA7 Cell Line	embryonic stem cell
31	chr13:38170400-38170800	Flanking Active TSS	Muscle Satellite Cultured Cells	--
32	chr13:38170400-38171200	Transcr. at gene 5' and 3'	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
33	chr13:38170400-38171200	Flanking Active TSS	Fetal Lung	lung
34	chr13:38170400-38173400	Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
35	chr13:38170400-38173600	Active TSS	Fetal Stomach	stomach

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