Variant report

Variant	rs3794543
Chromosome Location	chr15:52441524-52441525
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	chr15:52421802..52423616-chr15:52441108..52442630,2	MCF-7	breast:
2	chr15:52310489..52312428-chr15:52441270..52443572,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000069956	Chromatin interaction
ENSG00000259438	Chromatin interaction

Extended variants
information (count: 62 )
Associated
traits (count: 3 )

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

rs_ID	r²[population]
rs11070882	0.91[ASN][1000 genomes]
rs11855672	0.80[MEX][hapmap]
rs11856177	0.91[ASN][1000 genomes]
rs12438169	1.00[CEU][hapmap];0.85[CHB][hapmap];0.85[AMR][1000 genomes];0.98[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs12438190	0.82[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs12438194	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12438743	0.82[ASW][hapmap];0.91[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];0.87[TSI][hapmap];0.86[AFR][1000 genomes];0.91[AMR][1000 genomes];0.81[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12438937	1.00[CEU][hapmap];0.85[CHB][hapmap];0.81[CHD][hapmap];0.96[GIH][hapmap];1.00[TSI][hapmap];0.87[AMR][1000 genomes];0.98[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs12440354	0.81[ASN][1000 genomes]
rs12440956	0.94[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs12441074	0.81[ASN][1000 genomes]
rs12593041	1.00[CEU][hapmap];0.85[CHB][hapmap];0.96[GIH][hapmap];1.00[TSI][hapmap];0.87[AMR][1000 genomes];0.97[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs12594679	0.92[ASN][1000 genomes]
rs12595160	0.92[CHB][hapmap];0.93[CHD][hapmap];1.00[JPT][hapmap];0.85[MEX][hapmap];0.92[ASN][1000 genomes]
rs12899030	1.00[CEU][hapmap];0.96[GIH][hapmap]
rs12899343	1.00[CEU][hapmap];0.96[GIH][hapmap]
rs12901354	0.94[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs12901730	0.91[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[AMR][1000 genomes];0.81[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12901891	0.91[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[AFR][1000 genomes];0.91[AMR][1000 genomes];0.81[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12902073	1.00[CEU][hapmap];0.91[AMR][1000 genomes];0.83[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12902522	1.00[CEU][hapmap];0.81[AMR][1000 genomes];0.81[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs12903769	0.91[AMR][1000 genomes];0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12904831	0.86[AFR][1000 genomes];0.91[AMR][1000 genomes];0.86[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs12904889	0.87[AMR][1000 genomes];0.84[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12905698	0.81[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs12907835	1.00[CEU][hapmap];0.92[CHB][hapmap];1.00[JPT][hapmap];0.91[AMR][1000 genomes];0.86[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12908742	0.89[AMR][1000 genomes];0.83[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12908833	0.93[ASN][1000 genomes]
rs12909161	0.82[ASW][hapmap];1.00[CEU][hapmap];0.92[CHB][hapmap];0.89[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.81[TSI][hapmap];0.91[AMR][1000 genomes];0.86[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12909184	0.84[ASW][hapmap];0.91[CEU][hapmap];0.85[CHB][hapmap];0.93[GIH][hapmap];0.87[TSI][hapmap];0.81[AMR][1000 genomes];0.81[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs12909880	0.89[AMR][1000 genomes];0.82[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs12910052	0.81[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs12910398	0.81[AMR][1000 genomes];0.82[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs12912428	0.82[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs12916557	0.91[ASN][1000 genomes]
rs2227308	1.00[LWK][hapmap]
rs2398	0.92[CHB][hapmap];0.96[CHD][hapmap];0.96[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.93[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs2414130	0.89[GIH][hapmap]
rs2414132	0.93[GIH][hapmap]
rs34283892	0.92[ASN][1000 genomes]
rs35709612	0.85[AMR][1000 genomes];0.98[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs35827106	0.91[ASN][1000 genomes]
rs3794540	1.00[CEU][hapmap];1.00[JPT][hapmap];0.86[AFR][1000 genomes];0.91[AMR][1000 genomes];0.86[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs4238384	0.85[CHB][hapmap];0.81[GIH][hapmap]
rs4636859	1.00[CEU][hapmap];0.86[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4638520	1.00[CEU][hapmap];0.96[GIH][hapmap];0.85[TSI][hapmap];0.81[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs4774608	0.86[AFR][1000 genomes];0.94[AMR][1000 genomes];0.91[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4776003	0.90[CHD][hapmap];0.96[GIH][hapmap];1.00[JPT][hapmap];0.86[MEX][hapmap];0.88[ASN][1000 genomes]
rs4776007	0.91[CEU][hapmap];0.85[CHB][hapmap];0.81[AMR][1000 genomes];0.81[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs4776010	0.80[MEX][hapmap]
rs4776011	0.80[AMR][1000 genomes]
rs62014721	0.87[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs62014722	0.87[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs7166799	0.85[CHB][hapmap]
rs7177248	0.91[CHB][hapmap]
rs8034097	1.00[CEU][hapmap];0.92[CHB][hapmap];1.00[JPT][hapmap];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv471244	chr15:52305463-52511465	Enhancers Strong transcription Weak transcription Active TSS Flanking Bivalent TSS/Enh Flanking Active TSS Genic enhancers ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	52 gene(s)	inside rSNPs	diseases
2	nsv984198	chr15:52319726-52481137	Weak transcription Enhancers Genic enhancers ZNF genes & repeats Flanking Active TSS Active TSS Strong transcription Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	23 gene(s)	inside rSNPs	diseases
3	nsv1054372	chr15:52369078-52579464	Weak transcription Genic enhancers Enhancers Flanking Active TSS Strong transcription Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	27 gene(s)	inside rSNPs	diseases
4	nsv542387	chr15:52369078-52579464	Enhancers Strong transcription Genic enhancers Weak transcription Active TSS Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	27 gene(s)	inside rSNPs	diseases
5	nsv833005	chr15:52389869-52541330	Bivalent/Poised TSS Strong transcription Genic enhancers Flanking Active TSS Weak transcription Enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	23 gene(s)	inside rSNPs	diseases
6	nsv1047647	chr15:52425879-52469181	Enhancers Flanking Active TSS Weak transcription Strong transcription Active TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs3794543	GNB5	Cis_1M	lymphoblastoid	RTeQTL
rs3794543	KIAA1370	cis	parietal	SCAN
rs3794543	ARPP19	cis	parietal	SCAN

Chromatin state (count:116 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:52407600-52441600	Weak transcription	Fetal Lung	lung
2	chr15:52410200-52441600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
3	chr15:52422600-52457600	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
4	chr15:52423000-52458200	Weak transcription	Dnd41	blood
5	chr15:52427400-52441600	Weak transcription	Esophagus	oesophagus
6	chr15:52429000-52446400	Strong transcription	Breast Myoepithelial Primary Cells	Breast
7	chr15:52429000-52447200	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
8	chr15:52429200-52447400	Strong transcription	Primary T cells from cord blood	blood
9	chr15:52429800-52470200	Weak transcription	Fetal Brain Male	brain
10	chr15:52430000-52442800	Weak transcription	Fetal Heart	heart
11	chr15:52430000-52445800	Weak transcription	Small Intestine	intestine
12	chr15:52430200-52441800	Weak transcription	Rectal Mucosa Donor 31	rectum
13	chr15:52430200-52442800	Strong transcription	Primary B cells from peripheral blood	blood
14	chr15:52430200-52442800	Weak transcription	Right Ventricle	heart
15	chr15:52430200-52444800	Weak transcription	Left Ventricle	heart
16	chr15:52430200-52446600	Strong transcription	Primary T helper cells fromperipheralblood	blood
17	chr15:52430200-52457800	Weak transcription	Fetal Intestine Large	intestine
18	chr15:52431000-52446200	Strong transcription	Primary B cells from cord blood	blood
19	chr15:52431400-52446600	Strong transcription	Primary T helper naive cells fromperipheralblood	blood
20	chr15:52432200-52443000	Weak transcription	Primary monocytes fromperipheralblood	blood
21	chr15:52432200-52445400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
22	chr15:52432200-52453800	Weak transcription	Fetal Muscle Trunk	muscle
23	chr15:52432200-52455200	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
24	chr15:52432200-52455200	Weak transcription	Colonic Mucosa	Colon
25	chr15:52432600-52441600	Weak transcription	Brain Angular Gyrus	brain
26	chr15:52434800-52446400	Strong transcription	Primary T cells fromperipheralblood	blood
27	chr15:52435000-52446600	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
28	chr15:52435400-52444200	Strong transcription	Fetal Stomach	stomach
29	chr15:52435400-52445600	Strong transcription	HUES48 Cell Line	embryonic stem cell
30	chr15:52435400-52446200	Strong transcription	Brain Germinal Matrix	brain
31	chr15:52435400-52446200	Strong transcription	Fetal Brain Female	brain
32	chr15:52435600-52445600	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
33	chr15:52435800-52443800	Strong transcription	Brain Inferior Temporal Lobe	brain
34	chr15:52435800-52445800	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
35	chr15:52436000-52444000	Strong transcription	Liver	Liver
36	chr15:52436000-52445600	Strong transcription	Primary T helper 17 cells PMA-I stimulated	--
37	chr15:52436600-52442400	Strong transcription	iPS-20b Cell Line	embryonic stem cell
38	chr15:52436600-52444200	Strong transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
39	chr15:52436800-52446400	Weak transcription	Placenta	Placenta
40	chr15:52436800-52457200	Weak transcription	GM12878-XiMat	blood
41	chr15:52437200-52441600	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
42	chr15:52437200-52442200	Strong transcription	HUES64 Cell Line	embryonic stem cell
43	chr15:52437200-52444000	Strong transcription	Primary hematopoietic stem cells short term culture	blood
44	chr15:52437200-52444200	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
45	chr15:52437200-52445400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
46	chr15:52437200-52456800	Weak transcription	HSMM	muscle
47	chr15:52437400-52441800	Weak transcription	HMEC	breast
48	chr15:52437400-52442800	Weak transcription	Rectal Smooth Muscle	rectum
49	chr15:52437400-52443600	Weak transcription	HUVEC	blood vessel
50	chr15:52437400-52444400	Weak transcription	Osteobl	bone

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