Variant report

Variant	rs3920191
Chromosome Location	chr15:99907719-99907720
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 32 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:16)

rs_ID	r²[population]
rs11858067	0.83[CEU][hapmap];0.95[CHB][hapmap];0.93[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.96[MEX][hapmap];0.92[TSI][hapmap];0.94[AMR][1000 genomes];0.87[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12050640	0.81[JPT][hapmap]
rs12050653	0.81[JPT][hapmap]
rs12050904	0.82[JPT][hapmap]
rs1372755	0.92[AFR][1000 genomes];0.90[AMR][1000 genomes];0.85[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1472987	0.83[CHD][hapmap];0.82[JPT][hapmap];0.87[MEX][hapmap]
rs2175226	0.82[JPT][hapmap];0.83[MEX][hapmap]
rs28807370	0.95[CHB][hapmap];0.90[CHD][hapmap];0.91[GIH][hapmap];0.95[JPT][hapmap];0.98[ASN][1000 genomes]
rs3817147	0.86[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.93[AFR][1000 genomes];0.94[AMR][1000 genomes];0.88[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4471660	0.84[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs56679647	0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6598240	0.82[AMR][1000 genomes];0.85[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7162764	0.87[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.89[AMR][1000 genomes];0.92[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7180005	0.88[AMR][1000 genomes];0.81[ASN][1000 genomes]
rs7183514	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs978704	0.84[ASW][hapmap];1.00[CEU][hapmap];0.95[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.91[LWK][hapmap];0.96[MEX][hapmap];0.93[MKK][hapmap];0.97[TSI][hapmap];0.96[YRI][hapmap];0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:16 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1039575	chr15:98982045-99924685	Weak transcription Bivalent Enhancer Enhancers Genic enhancers Flanking Active TSS Active TSS Strong transcription ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	96 gene(s)	inside rSNPs	diseases
2	nsv1055008	chr15:99477144-100019861	Enhancers Weak transcription Strong transcription Flanking Active TSS Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Active TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	46 gene(s)	inside rSNPs	diseases
3	nsv904543	chr15:99513231-99991506	Weak transcription Flanking Active TSS Enhancers Strong transcription Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	45 gene(s)	inside rSNPs	diseases
4	nsv533926	chr15:99519820-99997114	Enhancers Active TSS Weak transcription Bivalent Enhancer Flanking Active TSS Strong transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	45 gene(s)	inside rSNPs	diseases
5	nsv915926	chr15:99519820-100138705	Active TSS Enhancers Weak transcription Flanking Bivalent TSS/Enh Strong transcription Flanking Active TSS Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	55 gene(s)	inside rSNPs	diseases
6	nsv949203	chr15:99621061-99932797	Strong transcription Weak transcription Enhancers Bivalent Enhancer Active TSS Genic enhancers ZNF genes & repeats Flanking Active TSS 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	31 gene(s)	inside rSNPs	diseases
7	nsv817289	chr15:99621061-100138705	Weak transcription Flanking Active TSS Enhancers ZNF genes & repeats Strong transcription Bivalent/Poised TSS Active TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	44 gene(s)	inside rSNPs	diseases
8	nsv431411	chr15:99621061-100143999	Enhancers Flanking Active TSS Weak transcription Active TSS Bivalent/Poised TSS Strong transcription Genic enhancers ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	44 gene(s)	inside rSNPs	diseases
9	nsv570716	chr15:99629901-99916332	Weak transcription Active TSS Transcr. at gene 5' and 3' Strong transcription Enhancers Flanking Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Genic enhancers Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	30 gene(s)	inside rSNPs	diseases
10	nsv904546	chr15:99696046-100166300	Flanking Active TSS Weak transcription Enhancers Bivalent Enhancer Strong transcription Active TSS ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	41 gene(s)	inside rSNPs	diseases
11	nsv1036346	chr15:99752391-100365458	Flanking Bivalent TSS/Enh Flanking Active TSS Strong transcription Enhancers Weak transcription Active TSS Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	47 gene(s)	inside rSNPs	diseases
12	nsv542520	chr15:99752391-100365458	Enhancers Flanking Active TSS Weak transcription Active TSS Strong transcription Genic enhancers ZNF genes & repeats 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	47 gene(s)	inside rSNPs	diseases
13	nsv1051560	chr15:99837102-100124483	Enhancers Flanking Active TSS Weak transcription Active TSS ZNF genes & repeats Strong transcription Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	19 gene(s)	inside rSNPs	diseases
14	nsv817201	chr15:99839238-100537341	Weak transcription Strong transcription Flanking Active TSS Enhancers Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	36 gene(s)	inside rSNPs	diseases
15	nsv1052683	chr15:99869631-99924685	Enhancers Strong transcription Weak transcription ZNF genes & repeats Flanking Active TSS Genic enhancers Active TSS	TF binding region Chromatin interactive region lncRNA miRNA target site	3 gene(s)	inside rSNPs	diseases
16	nsv542521	chr15:99869631-99924685	Weak transcription Strong transcription Enhancers Genic enhancers ZNF genes & repeats Flanking Active TSS Active TSS	TF binding region Chromatin interactive region lncRNA miRNA target site	3 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs3920191	LRRC28	cis	multi-tissue	Pritchard

Chromatin state (count:73 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:99867200-99926600	Weak transcription	NHEK	skin
2	chr15:99872000-99912600	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
3	chr15:99872600-99909000	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
4	chr15:99872800-99911400	Weak transcription	Brain Cingulate Gyrus	brain
5	chr15:99882200-99908600	Weak transcription	Colon Smooth Muscle	Colon
6	chr15:99882600-99908800	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
7	chr15:99882600-99911200	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
8	chr15:99882600-99925200	Weak transcription	Skeletal Muscle Male	skeletal muscle
9	chr15:99882800-99908600	Weak transcription	Placenta	Placenta
10	chr15:99884400-99910400	Weak transcription	Brain Substantia Nigra	brain
11	chr15:99884600-99910800	Weak transcription	Brain Hippocampus Middle	brain
12	chr15:99885400-99911800	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
13	chr15:99885400-99916000	Weak transcription	Fetal Heart	heart
14	chr15:99886600-99911400	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
15	chr15:99886600-99931400	Weak transcription	Esophagus	oesophagus
16	chr15:99890800-99908600	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
17	chr15:99892000-99908400	Weak transcription	Fetal Brain Female	brain
18	chr15:99893600-99925400	Weak transcription	Rectal Mucosa Donor 31	rectum
19	chr15:99893800-99911600	Weak transcription	Primary T helper cells fromperipheralblood	blood
20	chr15:99894000-99908600	Weak transcription	Psoas Muscle	Psoas
21	chr15:99894000-99925200	Weak transcription	Stomach Smooth Muscle	stomach
22	chr15:99894200-99908600	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
23	chr15:99899200-99908600	Weak transcription	Primary T helper cells PMA-I stimulated	--
24	chr15:99900200-99909600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
25	chr15:99900600-99911400	Weak transcription	Right Ventricle	heart
26	chr15:99900800-99908600	Weak transcription	HSMMtube	muscle
27	chr15:99901200-99911400	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
28	chr15:99901400-99910200	Strong transcription	Fetal Intestine Large	intestine
29	chr15:99901600-99910400	Strong transcription	Liver	Liver
30	chr15:99902000-99925600	Weak transcription	Muscle Satellite Cultured Cells	--
31	chr15:99902400-99911400	Weak transcription	Ovary	ovary
32	chr15:99902600-99909000	Weak transcription	Primary neutrophils fromperipheralblood	blood
33	chr15:99903600-99924800	Weak transcription	Left Ventricle	heart
34	chr15:99903600-99925200	Weak transcription	Lung	lung
35	chr15:99903600-99926600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
36	chr15:99903800-99911400	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
37	chr15:99904400-99908600	Weak transcription	Primary T cells fromperipheralblood	blood
38	chr15:99904400-99908800	Weak transcription	Fetal Lung	lung
39	chr15:99905000-99928200	Weak transcription	Pancreas	Pancrea
40	chr15:99906000-99910400	ZNF genes & repeats	GM12878-XiMat	blood
41	chr15:99906200-99908800	ZNF genes & repeats	Fetal Intestine Small	intestine
42	chr15:99906200-99909600	Strong transcription	Duodenum Mucosa	Duodenum
43	chr15:99906200-99909800	ZNF genes & repeats	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
44	chr15:99906200-99910000	ZNF genes & repeats	Primary hematopoietic stem cells G-CSF-mobilized Female	--
45	chr15:99906200-99910000	Strong transcription	Fetal Thymus	thymus
46	chr15:99906200-99910200	ZNF genes & repeats	Breast Myoepithelial Primary Cells	Breast
47	chr15:99906200-99910400	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
48	chr15:99906400-99910200	ZNF genes & repeats	Primary hematopoietic stem cells short term culture	blood
49	chr15:99906400-99910400	ZNF genes & repeats	Primary hematopoietic stem cells G-CSF-mobilized Male	--
50	chr15:99906400-99916200	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived

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