Variant report

Variant	rs7258692
Chromosome Location	chr19:37818829-37818830
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr19:37806423..37808569-chr19:37817496..37819060,2	MCF-7	breast:
2	chr19:37808613..37811422-chr19:37818380..37821776,3	MCF-7	breast:

Variant related genes	Relation type
ENSG00000181666	Chromatin interaction

Extended variants
information (count: 119 )
Associated
traits (count: 12 )

rSNPs within LD-proxies of this variant (count:115)

rs_ID	r²[population]
rs1015848	0.84[EUR][1000 genomes]
rs1015849	1.00[CEU][hapmap];0.81[CHB][hapmap];0.93[CHD][hapmap];0.93[GIH][hapmap];0.84[JPT][hapmap];0.90[TSI][hapmap];0.84[EUR][1000 genomes]
rs1035479	0.84[EUR][1000 genomes]
rs10403582	0.82[EUR][1000 genomes]
rs10403613	0.91[AMR][1000 genomes];0.99[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs10404602	0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10404920	1.00[CEU][hapmap];0.81[CHB][hapmap];0.93[CHD][hapmap];1.00[GIH][hapmap];0.84[JPT][hapmap];0.88[MEX][hapmap];0.95[TSI][hapmap];0.80[YRI][hapmap];0.93[EUR][1000 genomes]
rs10405064	1.00[CEU][hapmap];0.87[CHB][hapmap];0.90[CHD][hapmap];1.00[GIH][hapmap];0.84[JPT][hapmap];0.88[MEX][hapmap];0.95[TSI][hapmap];0.87[AMR][1000 genomes];0.97[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs10405325	0.89[EUR][1000 genomes]
rs10405407	1.00[CEU][hapmap];0.87[GIH][hapmap];0.89[JPT][hapmap];0.95[TSI][hapmap];0.96[EUR][1000 genomes]
rs10406177	1.00[CEU][hapmap];0.80[GIH][hapmap];0.90[JPT][hapmap];0.90[TSI][hapmap];0.82[EUR][1000 genomes]
rs10407084	1.00[CEU][hapmap];0.81[CHB][hapmap];0.93[CHD][hapmap];0.93[GIH][hapmap];0.84[JPT][hapmap];0.90[TSI][hapmap];0.84[EUR][1000 genomes]
rs10409204	1.00[CEU][hapmap];0.81[CHB][hapmap];0.93[CHD][hapmap];0.93[GIH][hapmap];0.84[JPT][hapmap];0.81[MKK][hapmap];0.90[TSI][hapmap];0.86[EUR][1000 genomes]
rs10412043	0.97[EUR][1000 genomes]
rs10413602	0.87[EUR][1000 genomes]
rs10414904	1.00[CEU][hapmap];0.89[JPT][hapmap];0.96[EUR][1000 genomes]
rs10415024	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10415358	0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs10415937	1.00[CEU][hapmap];0.89[JPT][hapmap];0.96[EUR][1000 genomes]
rs10417503	1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];0.95[JPT][hapmap];0.88[MEX][hapmap];0.93[MKK][hapmap];0.95[TSI][hapmap];0.80[YRI][hapmap];0.91[AMR][1000 genomes];0.99[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs10417844	0.93[CEU][hapmap];0.87[GIH][hapmap];0.84[JPT][hapmap];0.95[TSI][hapmap];0.96[EUR][1000 genomes]
rs10420430	0.87[EUR][1000 genomes]
rs10420754	1.00[CEU][hapmap];0.88[JPT][hapmap]
rs10422074	0.87[EUR][1000 genomes]
rs10422423	0.91[AMR][1000 genomes];0.99[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs10422667	0.84[EUR][1000 genomes]
rs10422967	0.91[AMR][1000 genomes];0.99[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs10424574	1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];0.95[JPT][hapmap];0.88[MEX][hapmap];0.93[MKK][hapmap];0.90[TSI][hapmap];0.80[YRI][hapmap];0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs10426297	0.83[AMR][1000 genomes];0.89[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs10426618	0.84[EUR][1000 genomes]
rs10426666	0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs10426699	0.99[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12104380	0.95[EUR][1000 genomes]
rs12104381	0.84[AMR][1000 genomes];0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12709812	0.98[AFR][1000 genomes];0.92[AMR][1000 genomes];0.91[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs12709813	0.96[EUR][1000 genomes]
rs12972252	0.84[EUR][1000 genomes]
rs12979470	0.83[EUR][1000 genomes]
rs12981532	0.87[EUR][1000 genomes]
rs12982333	0.83[AMR][1000 genomes];0.88[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs13343471	1.00[CEU][hapmap];0.81[CHB][hapmap];0.93[CHD][hapmap];0.93[GIH][hapmap];0.84[JPT][hapmap];0.84[MKK][hapmap];0.90[TSI][hapmap];0.86[EUR][1000 genomes]
rs13343485	0.92[EUR][1000 genomes]
rs13343502	1.00[CEU][hapmap];0.81[CHB][hapmap];0.93[CHD][hapmap];0.93[GIH][hapmap];0.84[JPT][hapmap];0.90[TSI][hapmap];0.82[EUR][1000 genomes]
rs13345116	1.00[CEU][hapmap];0.89[JPT][hapmap];0.96[EUR][1000 genomes]
rs13345148	0.98[EUR][1000 genomes]
rs1373991	1.00[CEU][hapmap];0.87[GIH][hapmap];0.89[JPT][hapmap];0.95[TSI][hapmap];0.96[EUR][1000 genomes]
rs1382357	1.00[CEU][hapmap];0.80[GIH][hapmap];0.90[JPT][hapmap];0.90[TSI][hapmap]
rs1529957	0.86[CEU][hapmap];0.89[JPT][hapmap]
rs1559229	1.00[CEU][hapmap];0.89[JPT][hapmap];0.89[EUR][1000 genomes]
rs1823061	0.85[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[AMR][1000 genomes];0.91[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2081096	1.00[CEU][hapmap];0.80[GIH][hapmap];0.90[JPT][hapmap];0.90[TSI][hapmap]
rs2112923	1.00[CEU][hapmap];0.80[GIH][hapmap];0.90[JPT][hapmap];0.90[TSI][hapmap];0.82[EUR][1000 genomes]
rs2126977	0.93[CEU][hapmap];0.80[GIH][hapmap];0.90[JPT][hapmap];0.90[TSI][hapmap]
rs2291004	0.93[CEU][hapmap];0.81[CHB][hapmap];0.87[CHD][hapmap];0.93[GIH][hapmap];0.84[JPT][hapmap];0.82[TSI][hapmap]
rs2303131	1.00[CEU][hapmap];0.81[CHB][hapmap];0.93[CHD][hapmap];0.93[GIH][hapmap];0.84[JPT][hapmap];0.84[MKK][hapmap];0.90[TSI][hapmap];0.86[EUR][1000 genomes]
rs28402338	0.91[AMR][1000 genomes];0.99[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs28538699	0.82[EUR][1000 genomes]
rs28623164	0.83[EUR][1000 genomes]
rs2891699	1.00[CEU][hapmap];0.80[GIH][hapmap];0.90[JPT][hapmap];0.90[TSI][hapmap];0.83[EUR][1000 genomes]
rs34544865	0.85[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs34603719	0.85[EUR][1000 genomes]
rs35085437	0.89[AMR][1000 genomes];0.99[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs35777021	0.86[EUR][1000 genomes]
rs3745765	1.00[CEU][hapmap];0.87[GIH][hapmap];0.89[JPT][hapmap];0.95[TSI][hapmap];0.94[EUR][1000 genomes]
rs3760825	1.00[CEU][hapmap];0.80[GIH][hapmap];0.90[JPT][hapmap];0.90[TSI][hapmap];0.82[EUR][1000 genomes]
rs3803895	0.84[EUR][1000 genomes]
rs4417644	1.00[CEU][hapmap];0.94[CHB][hapmap];0.96[CHD][hapmap];1.00[GIH][hapmap];0.95[JPT][hapmap];0.88[MEX][hapmap];0.93[MKK][hapmap];0.95[TSI][hapmap];0.91[AMR][1000 genomes];0.99[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs4452075	1.00[CEU][hapmap];0.87[GIH][hapmap];0.90[JPT][hapmap];0.95[TSI][hapmap];0.90[EUR][1000 genomes]
rs4801759	1.00[CEU][hapmap];0.81[CHB][hapmap];0.93[CHD][hapmap];0.93[GIH][hapmap];0.84[JPT][hapmap];0.82[MKK][hapmap];0.90[TSI][hapmap];0.84[EUR][1000 genomes]
rs4801803	1.00[CEU][hapmap];0.81[CHB][hapmap];0.90[CHD][hapmap];0.93[GIH][hapmap];0.84[JPT][hapmap];0.84[MKK][hapmap];0.90[TSI][hapmap];0.82[EUR][1000 genomes]
rs4802766	0.80[EUR][1000 genomes]
rs4803229	1.00[CEU][hapmap];0.87[GIH][hapmap];0.90[JPT][hapmap];0.95[TSI][hapmap];0.92[EUR][1000 genomes]
rs4803347	0.96[EUR][1000 genomes]
rs4803460	0.84[EUR][1000 genomes]
rs4803539	0.84[EUR][1000 genomes]
rs4969487	0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs57795776	0.85[EUR][1000 genomes]
rs6508711	0.98[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs6508713	0.89[EUR][1000 genomes]
rs6508714	0.89[EUR][1000 genomes]
rs6508715	0.89[EUR][1000 genomes]
rs6508716	0.97[EUR][1000 genomes]
rs6508719	1.00[CEU][hapmap];0.90[JPT][hapmap];0.89[EUR][1000 genomes]
rs6508732	0.93[CEU][hapmap];0.80[GIH][hapmap];0.90[JPT][hapmap];0.86[TSI][hapmap]
rs6508733	0.93[CEU][hapmap];0.90[JPT][hapmap]
rs67293224	0.88[AMR][1000 genomes];0.91[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs713256	1.00[CEU][hapmap];0.81[CHB][hapmap];0.93[CHD][hapmap];1.00[GIH][hapmap];0.84[JPT][hapmap];0.88[MEX][hapmap];0.85[MKK][hapmap];0.95[TSI][hapmap];0.80[YRI][hapmap];0.87[AMR][1000 genomes];0.95[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs7246657	0.86[CEU][hapmap];0.87[GIH][hapmap];0.95[JPT][hapmap];0.85[TSI][hapmap]
rs7246993	0.87[EUR][1000 genomes]
rs7247259	1.00[CEU][hapmap];0.89[JPT][hapmap];0.96[EUR][1000 genomes]
rs7248733	0.93[CEU][hapmap];0.90[JPT][hapmap];0.82[TSI][hapmap]
rs7252099	0.86[EUR][1000 genomes]
rs7252325	0.83[EUR][1000 genomes]
rs7252346	1.00[CEU][hapmap];0.80[GIH][hapmap];0.90[JPT][hapmap];0.90[TSI][hapmap];0.83[EUR][1000 genomes]
rs7253091	1.00[CEU][hapmap];0.80[GIH][hapmap];0.90[JPT][hapmap];0.90[TSI][hapmap]
rs7253114	0.93[CEU][hapmap];0.80[GIH][hapmap];0.90[TSI][hapmap]
rs7255407	0.83[EUR][1000 genomes]
rs7255952	0.93[CEU][hapmap]
rs7255972	1.00[CEU][hapmap];0.81[CHB][hapmap];0.93[CHD][hapmap];0.93[GIH][hapmap];0.84[JPT][hapmap];0.90[TSI][hapmap];0.86[EUR][1000 genomes]
rs7256130	0.80[EUR][1000 genomes]
rs7257495	0.98[EUR][1000 genomes]
rs7257672	1.00[CEU][hapmap];0.95[JPT][hapmap];0.98[EUR][1000 genomes]
rs7259968	0.98[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs7408133	0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7408446	0.83[AMR][1000 genomes];0.86[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7408563	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs8106839	0.83[ASW][hapmap];1.00[CEU][hapmap];0.81[CHB][hapmap];0.93[CHD][hapmap];0.82[GIH][hapmap];0.84[JPT][hapmap];0.90[TSI][hapmap]
rs8109038	0.93[CEU][hapmap];0.83[CHD][hapmap];0.93[GIH][hapmap];0.84[JPT][hapmap];0.82[TSI][hapmap]
rs8109632	0.83[EUR][1000 genomes]
rs8111782	1.00[CEU][hapmap];0.81[CHB][hapmap];0.84[JPT][hapmap];0.93[EUR][1000 genomes]
rs8112011	1.00[CHB][hapmap]
rs8112610	0.80[EUR][1000 genomes]
rs9304566	1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];0.95[JPT][hapmap];0.88[MEX][hapmap];0.93[MKK][hapmap];0.95[TSI][hapmap];0.80[YRI][hapmap];0.91[AMR][1000 genomes];0.99[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs9676967	0.83[EUR][1000 genomes]
rs9917081	1.00[CEU][hapmap];0.81[CHB][hapmap];0.84[JPT][hapmap];0.80[YRI][hapmap];0.92[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv918028	chr19:37020645-38014526	Weak transcription ZNF genes & repeats Active TSS Enhancers Flanking Active TSS Strong transcription Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	73 gene(s)	inside rSNPs	diseases
2	nsv978811	chr19:37749967-37820517	Weak transcription Active TSS Enhancers Flanking Active TSS Strong transcription ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
3	esv2757695	chr19:37794850-38051606	Genic enhancers Weak transcription ZNF genes & repeats Flanking Active TSS Active TSS Strong transcription Enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	23 gene(s)	inside rSNPs	diseases
4	esv2758759	chr19:37794850-38051606	ZNF genes & repeats Weak transcription Strong transcription Flanking Active TSS Active TSS Bivalent/Poised TSS Enhancers Transcr. at gene 5' and 3' Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	23 gene(s)	inside rSNPs	diseases

mRNA abundance (count:12)

SNP	Gene	Cis/trans	Tissue	Source
rs7258692	PLEKHG2	cis	cerebellum	SCAN
rs7258692	PAFAH1B3	cis	cerebellum	SCAN
rs7258692	EXOSC5	cis	cerebellum	SCAN
rs7258692	LIPE	cis	cerebellum	SCAN
rs7258692	FAM98C	cis	cerebellum	SCAN
rs7258692	CYP2B6	cis	cerebellum	SCAN
rs7258692	DMPK	cis	parietal	SCAN
rs7258692	HIPK4	cis	parietal	SCAN
rs7258692	LTBP4	cis	cerebellum	SCAN
rs7258692	BLVRB	cis	cerebellum	SCAN
rs7258692	MEGF8	cis	cerebellum	SCAN
rs7258692	CBLC	cis	parietal	SCAN

Chromatin state (count:122 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr19:37809200-37824800	Weak transcription	Stomach Mucosa	stomach
2	chr19:37809400-37825000	Weak transcription	Fetal Thymus	thymus
3	chr19:37809400-37825000	Weak transcription	Placenta Amnion	Placenta Amnion
4	chr19:37809600-37819200	Weak transcription	Brain Substantia Nigra	brain
5	chr19:37809600-37819400	Weak transcription	Pancreas	Pancrea
6	chr19:37809600-37824400	Weak transcription	NHDF-Ad	bronchial
7	chr19:37809600-37825000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
8	chr19:37809800-37820000	Weak transcription	HMEC	breast
9	chr19:37810000-37819000	Weak transcription	Fetal Brain Female	brain
10	chr19:37810000-37819400	Weak transcription	Brain Germinal Matrix	brain
11	chr19:37810000-37819400	Weak transcription	NHEK	skin
12	chr19:37810000-37820000	Weak transcription	NHLF	lung
13	chr19:37810000-37825000	Weak transcription	Hela-S3	cervix
14	chr19:37810200-37821800	ZNF genes & repeats	A549	lung
15	chr19:37810400-37821000	Strong transcription	Foreskin Fibroblast Primary Cells skin01	Skin
16	chr19:37810400-37821600	ZNF genes & repeats	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
17	chr19:37810600-37824400	Weak transcription	Small Intestine	intestine
18	chr19:37810600-37824800	Weak transcription	Fetal Heart	heart
19	chr19:37810800-37824200	Weak transcription	Pancreatic Islets	Pancreatic Islet
20	chr19:37811000-37821400	Strong transcription	Fetal Stomach	stomach
21	chr19:37811600-37819200	Weak transcription	Primary T killer memory cells from peripheral blood	blood
22	chr19:37811600-37819200	Weak transcription	HSMM	muscle
23	chr19:37811600-37820200	Weak transcription	NH-A	brain
24	chr19:37811600-37821000	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
25	chr19:37811600-37821200	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
26	chr19:37811600-37825000	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
27	chr19:37811800-37819400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
28	chr19:37811800-37819600	Weak transcription	HepG2	liver
29	chr19:37811800-37821600	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
30	chr19:37812200-37821000	Strong transcription	Primary hematopoietic stem cells short term culture	blood
31	chr19:37812600-37820600	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
32	chr19:37812600-37820800	Strong transcription	Primary T helper cells fromperipheralblood	blood
33	chr19:37812600-37821000	Strong transcription	Primary T cells fromperipheralblood	blood
34	chr19:37813000-37821400	Strong transcription	Stomach Smooth Muscle	stomach
35	chr19:37813200-37821200	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
36	chr19:37813200-37821400	Strong transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
37	chr19:37813200-37821400	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
38	chr19:37813200-37821400	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
39	chr19:37813200-37821400	Strong transcription	Foreskin Fibroblast Primary Cells skin02	Skin
40	chr19:37813200-37821800	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
41	chr19:37813400-37820400	Strong transcription	Primary T helper naive cells fromperipheralblood	blood
42	chr19:37813400-37821600	Strong transcription	Fetal Muscle Trunk	muscle
43	chr19:37813400-37821600	Strong transcription	Skeletal Muscle Female	skeletal muscle
44	chr19:37813400-37821600	Strong transcription	Monocytes-CD14+_RO01746	blood
45	chr19:37813600-37820800	Strong transcription	Primary T helper cells PMA-I stimulated	--
46	chr19:37813600-37821400	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
47	chr19:37813800-37819600	Weak transcription	GM12878-XiMat	blood
48	chr19:37813800-37820200	Strong transcription	Dnd41	blood
49	chr19:37813800-37820600	ZNF genes & repeats	Primary monocytes fromperipheralblood	blood
50	chr19:37813800-37820800	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived

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