Variant report

Variant	rs538238
Chromosome Location	chr15:43585520-43585521
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr15:43584770..43587744-chr15:43618210..43620882,2	MCF-7	breast:
2	chr15:43582742..43587018-chr15:43587403..43593084,5	K562	blood:
3	chr15:43477092..43479943-chr15:43584228..43585873,3	K562	blood:
4	chr15:43585058..43586868-chr15:43621413..43623111,2	K562	blood:
5	chr15:43578993..43581997-chr15:43583826..43586143,3	K562	blood:
6	chr15:43577270..43578995-chr15:43583941..43586463,2	K562	blood:
7	chr15:43585264..43587919-chr15:43621418..43624239,2	K562	blood:

Variant related genes	Relation type
ENSG00000168806	Chromatin interaction
ENSG00000168803	Chromatin interaction
ENSG00000166946	Chromatin interaction
ENSG00000261687	Chromatin interaction

Extended variants
information (count: 89 )
Associated
traits (count: 14 )

rSNPs within LD-proxies of this variant (count:86)

rs_ID	r²[population]
rs1079309	1.00[ASW][hapmap];0.91[CEU][hapmap];1.00[LWK][hapmap];0.83[TSI][hapmap]
rs1095386	0.84[CHD][hapmap]
rs11070399	0.87[EUR][1000 genomes]
rs1133395	0.87[EUR][1000 genomes]
rs12102205	0.89[EUR][1000 genomes]
rs12148735	0.90[AFR][1000 genomes];0.94[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs12905772	0.91[CEU][hapmap];0.87[EUR][1000 genomes]
rs1549525	0.86[CHD][hapmap]
rs1814323	0.86[JPT][hapmap];0.84[MKK][hapmap]
rs1837960	0.84[CHD][hapmap]
rs2244981	1.00[ASW][hapmap];0.91[CEU][hapmap];0.94[MKK][hapmap];0.83[TSI][hapmap]
rs2278856	0.89[EUR][1000 genomes]
rs2278857	1.00[ASW][hapmap];0.96[CEU][hapmap];0.84[CHD][hapmap];0.88[TSI][hapmap];0.89[EUR][1000 genomes]
rs2278860	0.86[CHD][hapmap]
rs2412779	0.86[CHD][hapmap]
rs2412780	0.86[CHD][hapmap]
rs2412781	1.00[ASW][hapmap];0.91[CEU][hapmap];0.86[CHD][hapmap];1.00[LWK][hapmap];0.88[TSI][hapmap];0.86[EUR][1000 genomes]
rs2467738	0.91[CEU][hapmap]
rs2467745	0.91[CEU][hapmap];0.83[TSI][hapmap]
rs2584700	0.81[EUR][1000 genomes]
rs2602141	0.91[CEU][hapmap];0.83[TSI][hapmap]
rs28702649	0.83[EUR][1000 genomes]
rs2899082	0.86[CHD][hapmap]
rs3742969	0.84[CHD][hapmap]
rs3742971	0.86[CHD][hapmap]
rs3809482	1.00[ASW][hapmap];0.91[CEU][hapmap];0.86[CHD][hapmap];1.00[LWK][hapmap];0.88[TSI][hapmap];0.87[EUR][1000 genomes]
rs4075674	0.86[CHD][hapmap]
rs4296223	0.91[CEU][hapmap];0.86[CHD][hapmap];0.88[TSI][hapmap];0.87[EUR][1000 genomes]
rs4401024	0.87[EUR][1000 genomes]
rs4547312	0.96[CEU][hapmap];0.86[CHD][hapmap];0.88[TSI][hapmap];0.89[EUR][1000 genomes]
rs471122	0.86[JPT][hapmap]
rs473554	0.81[JPT][hapmap]
rs478028	1.00[CEU][hapmap];0.90[EUR][1000 genomes]
rs478104	0.82[CHB][hapmap];0.84[CHD][hapmap];0.82[JPT][hapmap];0.84[ASN][1000 genomes]
rs484846	0.82[ASN][1000 genomes]
rs485148	0.90[EUR][1000 genomes]
rs488756	0.86[CHD][hapmap]
rs491800	0.92[EUR][1000 genomes]
rs493177	0.86[JPT][hapmap]
rs493377	0.91[CEU][hapmap];0.83[TSI][hapmap]
rs499035	0.81[ASN][1000 genomes]
rs501884	0.86[JPT][hapmap]
rs504417	0.86[JPT][hapmap];0.84[MKK][hapmap]
rs507178	1.00[CEU][hapmap];0.90[EUR][1000 genomes]
rs510108	0.90[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs512431	0.86[JPT][hapmap]
rs512628	0.90[EUR][1000 genomes]
rs513970	0.91[JPT][hapmap]
rs524527	0.82[CHB][hapmap];0.86[CHD][hapmap];0.82[JPT][hapmap]
rs524547	0.86[JPT][hapmap]
rs526450	0.82[CHB][hapmap];0.84[CHD][hapmap];0.82[JPT][hapmap]
rs530683	0.81[JPT][hapmap]
rs531910	0.86[JPT][hapmap]
rs536313	0.91[CEU][hapmap];0.83[TSI][hapmap]
rs546722	0.86[JPT][hapmap]
rs552701	0.88[EUR][1000 genomes]
rs554001	0.86[JPT][hapmap]
rs555001	0.86[JPT][hapmap]
rs560134	0.86[JPT][hapmap]
rs567357	0.86[JPT][hapmap]
rs572959	0.86[JPT][hapmap]
rs573615	1.00[ASW][hapmap];1.00[CEU][hapmap];0.86[CHD][hapmap];0.88[TSI][hapmap];0.90[EUR][1000 genomes]
rs574065	0.86[JPT][hapmap]
rs576557	0.92[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs6493083	1.00[ASW][hapmap];0.91[CEU][hapmap];0.86[CHD][hapmap];1.00[LWK][hapmap];0.88[TSI][hapmap];0.87[EUR][1000 genomes]
rs6493084	0.87[EUR][1000 genomes]
rs6493085	0.86[CHD][hapmap]
rs6493086	0.86[EUR][1000 genomes]
rs689767	0.91[CEU][hapmap]
rs690276	0.91[CEU][hapmap];0.83[TSI][hapmap]
rs690367	1.00[ASW][hapmap];0.91[CEU][hapmap];0.94[MKK][hapmap];0.83[TSI][hapmap]
rs690512	0.91[CEU][hapmap]
rs693510	0.91[CEU][hapmap]
rs694725	0.91[CEU][hapmap];0.83[TSI][hapmap]
rs7163288	1.00[ASW][hapmap];0.91[CEU][hapmap];0.83[CHD][hapmap];0.85[TSI][hapmap]
rs7166812	0.87[EUR][1000 genomes]
rs7167882	0.83[EUR][1000 genomes]
rs7170152	0.85[EUR][1000 genomes]
rs7172374	0.85[EUR][1000 genomes]
rs8039638	0.84[CHD][hapmap]
rs8042688	0.87[EUR][1000 genomes]
rs825739	0.82[JPT][hapmap];0.80[ASN][1000 genomes]
rs825740	0.82[JPT][hapmap];0.80[ASN][1000 genomes]
rs884704	0.84[CHD][hapmap]
rs9920879	1.00[ASW][hapmap];0.91[CEU][hapmap];0.86[CHD][hapmap];0.94[MKK][hapmap];0.88[TSI][hapmap];0.87[EUR][1000 genomes]
rs999047	0.84[CHD][hapmap]

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	nsv1044522	chr15:43115348-43658417	Strong transcription Weak transcription Flanking Active TSS Transcr. at gene 5' and 3' Enhancers Active TSS Genic enhancers Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	47 gene(s)	inside rSNPs	diseases
2	nsv1044508	chr15:43270637-43658417	Weak transcription Genic enhancers Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Active TSS Active TSS Enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	43 gene(s)	inside rSNPs	diseases
3	esv3324196	chr15:43584885-43587433	Flanking Active TSS Bivalent Enhancer Active TSS Enhancers Weak transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS	Chromatin interactive region	4 gene(s)	inside rSNPs	diseases

mRNA abundance (count:14)

SNP	Gene	Cis/trans	Tissue	Source
rs538238	TGM5	Cis_1M	lymphoblastoid	RTeQTL
rs538238	TGM5	cis	multi-tissue	Pritchard
rs538238	AC011330.5	cis	Thyroid	GTEx
rs538238	TP53BP1	cis	parietal	SCAN
rs538238	ZSCAN29	cis	multi-tissue	Pritchard
rs538238	TGM5	cis	lymphoblastoid	seeQTL
rs538238	ADAL	cis	lung	GTEx
rs538238	ZSCAN29	cis	Thyroid	GTEx
rs538238	LRRC57	cis	cerebellum	SCAN
rs538238	ADAL	cis	parietal	SCAN
rs538238	ADAL	cis	Nerve Tibial	GTEx
rs538238	STRCP1	cis	Esophagus Muscularis	GTEx
rs538238	TGM7	cis	Esophagus Mucosa	GTEx
rs538238	WDR76	cis	parietal	SCAN

Chromatin state (count:24 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:43584600-43585600	Enhancers	Adipose Nuclei	Adipose
2	chr15:43584800-43585800	Bivalent Enhancer	Foreskin Fibroblast Primary Cells skin02	Skin
3	chr15:43584800-43586000	Bivalent Enhancer	IMR90 fetal lung fibroblasts Cell Line	lung
4	chr15:43584800-43586000	Bivalent Enhancer	Fetal Adrenal Gland	Adrenal Gland
5	chr15:43584800-43586400	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
6	chr15:43585000-43585800	Bivalent Enhancer	ES-WA7 Cell Line	embryonic stem cell
7	chr15:43585000-43586600	Enhancers	iPS DF 6.9 Cell Line	embryonic stem cell
8	chr15:43585200-43585600	Flanking Bivalent TSS/Enh	iPS-15b Cell Line	embryonic stem cell
9	chr15:43585200-43585600	Bivalent Enhancer	Skeletal Muscle Male	skeletal muscle
10	chr15:43585200-43585800	Flanking Bivalent TSS/Enh	HepG2	liver
11	chr15:43585400-43585600	Bivalent/Poised TSS	ES-I3 Cell Line	embryonic stem cell
12	chr15:43585400-43585600	Enhancers	H1 Cell Line	embryonic stem cell
13	chr15:43585400-43585600	Flanking Bivalent TSS/Enh	HUES64 Cell Line	embryonic stem cell
14	chr15:43585400-43585600	Flanking Bivalent TSS/Enh	iPS-18 Cell Line	embryonic stem cell
15	chr15:43585400-43585600	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
16	chr15:43585400-43585600	Bivalent Enhancer	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
17	chr15:43585400-43585600	Enhancers	Breast Myoepithelial Primary Cells	Breast
18	chr15:43585400-43585600	Bivalent Enhancer	Primary T cells from cord blood	blood
19	chr15:43585400-43585800	Flanking Active TSS	HUES48 Cell Line	embryonic stem cell
20	chr15:43585400-43585800	Bivalent/Poised TSS	iPS-20b Cell Line	embryonic stem cell
21	chr15:43585400-43585800	Bivalent Enhancer	Fetal Muscle Leg	muscle
22	chr15:43585400-43586000	Active TSS	H9 Cell Line	embryonic stem cell
23	chr15:43585400-43586000	Bivalent Enhancer	Fetal Muscle Trunk	muscle
24	chr15:43585400-43586000	Bivalent Enhancer	Skeletal Muscle Female	skeletal muscle

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