Variant report

Variant	rs3786839
Chromosome Location	chr19:39182565-39182566
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	chr19:39181974..39184740-chr19:39331353..39332941,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000104824	Chromatin interaction

Extended variants
information (count: 53 )
Associated
traits (count: 8 )

rSNPs within LD-proxies of this variant (count:46)

rs_ID	r²[population]
rs10403540	0.94[EUR][1000 genomes]
rs10405232	1.00[YRI][hapmap]
rs10405261	1.00[YRI][hapmap]
rs10406778	0.83[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs10413936	1.00[LWK][hapmap];1.00[YRI][hapmap]
rs10415219	1.00[CEU][hapmap];0.90[JPT][hapmap];0.84[MEX][hapmap];0.93[TSI][hapmap];0.82[EUR][1000 genomes]
rs10415646	0.97[EUR][1000 genomes]
rs10420476	1.00[YRI][hapmap]
rs10421087	1.00[YRI][hapmap]
rs10421560	1.00[CEU][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];0.87[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs11083475	1.00[CEU][hapmap];0.90[JPT][hapmap];0.98[EUR][1000 genomes]
rs12460849	1.00[CEU][hapmap];0.95[JPT][hapmap];0.83[EUR][1000 genomes]
rs12462270	1.00[CEU][hapmap];0.85[JPT][hapmap];0.94[EUR][1000 genomes]
rs13343794	0.96[EUR][1000 genomes]
rs13344413	0.86[ASW][hapmap];0.92[CEU][hapmap];1.00[LWK][hapmap];0.90[MKK][hapmap];0.93[TSI][hapmap];1.00[YRI][hapmap]
rs16972767	1.00[CEU][hapmap];0.87[GIH][hapmap];0.90[JPT][hapmap];0.84[MEX][hapmap];0.93[TSI][hapmap];0.82[EUR][1000 genomes]
rs2279144	0.96[CEU][hapmap];1.00[GIH][hapmap];0.84[JPT][hapmap];1.00[TSI][hapmap];0.94[EUR][1000 genomes]
rs2287734	1.00[LWK][hapmap];1.00[YRI][hapmap]
rs2303040	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.90[MKK][hapmap];0.93[TSI][hapmap];1.00[YRI][hapmap];0.85[AMR][1000 genomes];0.85[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs2368477	1.00[LWK][hapmap]
rs28488032	0.95[EUR][1000 genomes]
rs28624276	0.81[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs3745859	1.00[CEU][hapmap];1.00[GIH][hapmap];0.85[JPT][hapmap];1.00[TSI][hapmap];0.95[EUR][1000 genomes]
rs3786835	1.00[CEU][hapmap];0.90[JPT][hapmap];0.82[EUR][1000 genomes]
rs3786837	0.83[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs3786845	1.00[CEU][hapmap];1.00[GIH][hapmap];0.85[JPT][hapmap];1.00[TSI][hapmap];0.94[EUR][1000 genomes]
rs3786848	0.94[EUR][1000 genomes]
rs3786851	1.00[CEU][hapmap];1.00[GIH][hapmap];0.90[JPT][hapmap];1.00[TSI][hapmap];0.93[EUR][1000 genomes]
rs4802887	0.86[ASW][hapmap]
rs55876653	0.83[EUR][1000 genomes]
rs55945853	0.80[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs56113315	0.86[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs56365761	0.84[EUR][1000 genomes]
rs62120083	0.80[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs62121814	0.82[EUR][1000 genomes]
rs62121816	0.80[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs62121818	0.83[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs7251903	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7252589	0.85[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs7254100	1.00[CEU][hapmap];0.89[JPT][hapmap];0.81[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs8107416	0.92[CEU][hapmap];0.89[CHD][hapmap];1.00[GIH][hapmap];0.82[JPT][hapmap];0.88[MEX][hapmap];0.98[TSI][hapmap];0.81[EUR][1000 genomes]
rs8111746	0.90[EUR][1000 genomes]
rs883394	0.88[AFR][1000 genomes];0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs883433	1.00[CEU][hapmap];1.00[GIH][hapmap];0.90[JPT][hapmap];1.00[TSI][hapmap];0.94[EUR][1000 genomes]
rs979971	1.00[CEU][hapmap];0.87[GIH][hapmap];0.90[JPT][hapmap];0.84[MEX][hapmap];0.93[TSI][hapmap];0.83[EUR][1000 genomes]
rs979972	1.00[CEU][hapmap];0.90[JPT][hapmap];0.84[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:7 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv833826	chr19:38945106-39184547	Strong transcription Genic enhancers Enhancers Weak transcription Active TSS Flanking Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	37 gene(s)	inside rSNPs	diseases
2	nsv833827	chr19:38993054-39184547	Transcr. at gene 5' and 3' Genic enhancers Weak transcription Enhancers Flanking Active TSS Active TSS Bivalent/Poised TSS Strong transcription Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	35 gene(s)	inside rSNPs	diseases
3	nsv833828	chr19:39084759-39257979	Enhancers Strong transcription Genic enhancers Weak transcription Active TSS Flanking Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	32 gene(s)	inside rSNPs	diseases
4	nsv1057899	chr19:39088319-39475493	Flanking Active TSS Flanking Bivalent TSS/Enh Genic enhancers Weak transcription Transcr. at gene 5' and 3' Enhancers Bivalent Enhancer Active TSS Strong transcription Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	82 gene(s)	inside rSNPs	diseases
5	nsv817834	chr19:39174332-39237950	Enhancers Flanking Active TSS Genic enhancers Strong transcription Weak transcription Bivalent Enhancer Bivalent/Poised TSS Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	14 gene(s)	inside rSNPs	diseases
6	nsv911668	chr19:39174669-39291771	Genic enhancers Enhancers Bivalent Enhancer Strong transcription Flanking Active TSS Weak transcription Bivalent/Poised TSS Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	19 gene(s)	inside rSNPs	diseases
7	esv1826260	chr19:39178364-39248836	Genic enhancers Weak transcription Strong transcription Flanking Active TSS Enhancers Bivalent Enhancer Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	12 gene(s)	inside rSNPs	diseases

mRNA abundance (count:8)

SNP	Gene	Cis/trans	Tissue	Source
rs3786839	ZNF526	cis	cerebellum	SCAN
rs3786839	ERCC1	cis	cerebellum	SCAN
rs3786839	PSG3	cis	parietal	SCAN
rs3786839	TMEM145	cis	parietal	SCAN
rs3786839	LGALS17A	cis	cerebellum	SCAN
rs3786839	RPS16	cis	parietal	SCAN
rs3786839	CAPN12	cis	Esophagus Muscularis	GTEx
rs3786839	MEGF8	cis	parietal	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr19:39164400-39200200	Genic enhancers	Fetal Intestine Small	intestine
2	chr19:39164800-39183800	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
3	chr19:39170000-39183400	Enhancers	Placenta	Placenta
4	chr19:39174800-39182800	Weak transcription	Dnd41	blood
5	chr19:39175600-39182800	Genic enhancers	NHEK	skin
6	chr19:39176400-39182600	Weak transcription	Ovary	ovary
7	chr19:39176800-39182800	Genic enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
8	chr19:39177000-39183000	Weak transcription	Fetal Brain Female	brain
9	chr19:39177200-39182600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
10	chr19:39177200-39195000	Weak transcription	Pancreatic Islets	Pancreatic Islet
11	chr19:39177400-39182600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
12	chr19:39177400-39182600	Genic enhancers	Breast Myoepithelial Primary Cells	Breast
13	chr19:39177400-39183400	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
14	chr19:39177600-39182600	Weak transcription	Colonic Mucosa	Colon
15	chr19:39177600-39182800	Weak transcription	iPS-18 Cell Line	embryonic stem cell
16	chr19:39177600-39182800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
17	chr19:39177600-39182800	Weak transcription	Primary T cells from cord blood	blood
18	chr19:39177800-39182800	Weak transcription	H1 Cell Line	embryonic stem cell
19	chr19:39178000-39182600	Weak transcription	Fetal Thymus	thymus
20	chr19:39178000-39183600	Genic enhancers	Muscle Satellite Cultured Cells	--
21	chr19:39178600-39183200	Weak transcription	HUES64 Cell Line	embryonic stem cell
22	chr19:39178600-39187800	Enhancers	Left Ventricle	heart
23	chr19:39178600-39190600	Enhancers	Skeletal Muscle Female	skeletal muscle
24	chr19:39178600-39198200	Genic enhancers	Fetal Intestine Large	intestine
25	chr19:39178800-39182600	Weak transcription	Primary T killer memory cells from peripheral blood	blood
26	chr19:39179000-39189400	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
27	chr19:39179400-39184400	Enhancers	Placenta Amnion	Placenta Amnion
28	chr19:39179600-39182600	Weak transcription	Primary B cells from peripheral blood	blood
29	chr19:39179600-39182600	Weak transcription	GM12878-XiMat	blood
30	chr19:39179600-39183400	Weak transcription	Primary B cells from cord blood	blood
31	chr19:39179600-39183600	Genic enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
32	chr19:39179600-39205800	Genic enhancers	Fetal Adrenal Gland	Adrenal Gland
33	chr19:39179800-39183800	Genic enhancers	Primary Natural Killer cells fromperipheralblood	blood
34	chr19:39180000-39182600	Weak transcription	Rectal Mucosa Donor 31	rectum
35	chr19:39180000-39182800	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
36	chr19:39180000-39182800	Weak transcription	iPS-20b Cell Line	embryonic stem cell
37	chr19:39180000-39182800	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
38	chr19:39180000-39183200	Genic enhancers	Primary hematopoietic stem cells short term culture	blood
39	chr19:39180000-39183800	Genic enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
40	chr19:39180000-39184800	Genic enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
41	chr19:39180000-39186000	Genic enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
42	chr19:39180000-39191600	Genic enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
43	chr19:39180000-39192400	Genic enhancers	Lung	lung
44	chr19:39180200-39182600	Genic enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
45	chr19:39180200-39182600	Weak transcription	Fetal Kidney	kidney
46	chr19:39180200-39182600	Genic enhancers	A549	lung
47	chr19:39180200-39182600	Weak transcription	HSMM	muscle
48	chr19:39180200-39182600	Weak transcription	HSMMtube	muscle
49	chr19:39180200-39182800	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
50	chr19:39180200-39183000	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast

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