Variant report

Variant	rs3784563
Chromosome Location	chr15:74290993-74290994
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr15:74286936-74291631	K562	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr15:74276152..74278081-chr15:74290806..74293651,2	K562	blood:
2	chr15:74286840..74288514-chr15:74288531..74291100,2	MCF-7	breast:

Variant related genes	Relation type
STOML1	TF binding region
ENSG00000067221	Chromatin interaction
ENSG00000140464	Chromatin interaction

Extended variants
information (count: 9 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:4)

rs_ID	r²[population]
rs3825941	0.96[CEU][hapmap];1.00[CHB][hapmap];0.91[CHD][hapmap];1.00[GIH][hapmap];0.90[JPT][hapmap];0.90[MEX][hapmap];0.85[TSI][hapmap];0.91[AMR][1000 genomes];0.88[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4886809	1.00[CHB][hapmap];0.97[CHD][hapmap];0.89[GIH][hapmap];0.89[JPT][hapmap];0.92[ASN][1000 genomes]
rs60822319	0.92[ASN][1000 genomes]
rs8028206	0.92[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv2758387	chr15:74215114-74464916	Enhancers Flanking Active TSS Bivalent/Poised TSS Weak transcription Strong transcription Active TSS Flanking Bivalent TSS/Enh Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	32 gene(s)	inside rSNPs	diseases
2	esv2760040	chr15:74215114-74464916	Weak transcription Enhancers Strong transcription Flanking Bivalent TSS/Enh Active TSS Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	32 gene(s)	inside rSNPs	diseases
3	nsv428308	chr15:74215114-74464916	Transcr. at gene 5' and 3' Enhancers Weak transcription Bivalent Enhancer Bivalent/Poised TSS Strong transcription Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	32 gene(s)	inside rSNPs	diseases
4	nsv833052	chr15:74250378-74377150	Genic enhancers Enhancers Transcr. at gene 5' and 3' Strong transcription Weak transcription Flanking Active TSS Bivalent Enhancer Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	14 gene(s)	inside rSNPs	diseases
5	nsv518316	chr15:74290993-74331083	Strong transcription Weak transcription Enhancers Transcr. at gene 5' and 3' Genic enhancers Flanking Active TSS ZNF genes & repeats Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs3784563	STOML1	cis	parietal	SCAN
rs3784563	ISLR2	cis	cerebellum	SCAN
rs3784563	LARP6	cis	parietal	SCAN
rs3784563	NR2E3	cis	parietal	SCAN

Chromatin state (count:125 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:74288200-74291000	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
2	chr15:74288200-74301800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
3	chr15:74288200-74303000	Weak transcription	A549	lung
4	chr15:74288200-74303800	Weak transcription	Brain Angular Gyrus	brain
5	chr15:74288200-74331000	Weak transcription	Fetal Heart	heart
6	chr15:74289600-74302400	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
7	chr15:74289800-74291400	Enhancers	Primary T killer naive cells fromperipheralblood	blood
8	chr15:74289800-74291600	Weak transcription	Fetal Brain Male	brain
9	chr15:74289800-74292000	Transcr. at gene 5' and 3'	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
10	chr15:74289800-74292000	Transcr. at gene 5' and 3'	GM12878-XiMat	blood
11	chr15:74289800-74293000	Genic enhancers	Primary T cells fromperipheralblood	blood
12	chr15:74289800-74296000	Genic enhancers	Primary T helper cells fromperipheralblood	blood
13	chr15:74289800-74303200	Weak transcription	Brain Substantia Nigra	brain
14	chr15:74289800-74331000	Weak transcription	Pancreatic Islets	Pancreatic Islet
15	chr15:74290000-74291000	Genic enhancers	Fetal Muscle Leg	muscle
16	chr15:74290000-74291000	Genic enhancers	Sigmoid Colon	Sigmoid Colon
17	chr15:74290000-74291200	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
18	chr15:74290000-74291200	Enhancers	Right Atrium	heart
19	chr15:74290000-74291200	Genic enhancers	Spleen	Spleen
20	chr15:74290000-74291400	Genic enhancers	Primary T helper cells PMA-I stimulated	--
21	chr15:74290000-74291400	Enhancers	Primary T killer memory cells from peripheral blood	blood
22	chr15:74290000-74291600	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
23	chr15:74290000-74291600	Genic enhancers	Skeletal Muscle Male	skeletal muscle
24	chr15:74290000-74292000	Genic enhancers	Primary T cells from cord blood	blood
25	chr15:74290000-74292000	Genic enhancers	Primary mononuclear cells fromperipheralblood	Blood
26	chr15:74290000-74295200	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
27	chr15:74290000-74299000	Weak transcription	Stomach Mucosa	stomach
28	chr15:74290000-74303400	Weak transcription	Fetal Kidney	kidney
29	chr15:74290000-74314800	Weak transcription	Brain Cingulate Gyrus	brain
30	chr15:74290200-74291000	Genic enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
31	chr15:74290200-74291000	Strong transcription	iPS DF 6.9 Cell Line	embryonic stem cell
32	chr15:74290200-74291000	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
33	chr15:74290200-74291000	Weak transcription	Primary T helper naive cells from peripheral blood	blood
34	chr15:74290200-74291000	Genic enhancers	Primary Natural Killer cells fromperipheralblood	blood
35	chr15:74290200-74291000	Transcr. at gene 5' and 3'	Foreskin Fibroblast Primary Cells skin01	Skin
36	chr15:74290200-74291000	Weak transcription	Colon Smooth Muscle	Colon
37	chr15:74290200-74291000	Strong transcription	Fetal Intestine Small	intestine
38	chr15:74290200-74291000	Genic enhancers	Placenta	Placenta
39	chr15:74290200-74291000	Genic enhancers	Gastric	stomach
40	chr15:74290200-74291000	Genic enhancers	Lung	lung
41	chr15:74290200-74291000	Genic enhancers	Right Ventricle	heart
42	chr15:74290200-74291200	Transcr. at gene 5' and 3'	Foreskin Keratinocyte Primary Cells skin02	Skin
43	chr15:74290200-74291200	Weak transcription	Rectal Mucosa Donor 31	rectum
44	chr15:74290200-74291400	Strong transcription	Placenta Amnion	Placenta Amnion
45	chr15:74290200-74291600	Genic enhancers	Primary hematopoietic stem cells short term culture	blood
46	chr15:74290200-74291600	Genic enhancers	Fetal Adrenal Gland	Adrenal Gland
47	chr15:74290200-74292000	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
48	chr15:74290200-74292000	Genic enhancers	Primary B cells from cord blood	blood
49	chr15:74290200-74292000	Genic enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
50	chr15:74290200-74292000	Strong transcription	Cortex derived primary cultured neurospheres	brain

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