Variant report

Variant	rs3816197
Chromosome Location	chr15:74282880-74282881
allele	C/T
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	chr15:74282759-74283356	K562	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr15:74282640..74284615-chr15:74313984..74316844,2	MCF-7	breast:
2	chr15:74281335..74284539-chr15:74284801..74290369,7	MCF-7	breast:
3	chr15:74272863..74275185-chr15:74282100..74283789,2	K562	blood:

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

Extended variants
information (count: 16 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:12)

rs_ID	r²[population]
rs1078555	0.83[CHB][hapmap]
rs11072460	0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11072468	1.00[CHB][hapmap];0.85[CHD][hapmap];0.90[GIH][hapmap];1.00[JPT][hapmap];0.93[ASN][1000 genomes]
rs1550434	0.83[CHB][hapmap]
rs16869	0.93[ASN][1000 genomes]
rs2415188	0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3816198	0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4993000	1.00[CEU][hapmap];0.95[MEX][hapmap];0.85[TSI][hapmap];0.87[EUR][1000 genomes]
rs7171694	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[YRI][hapmap];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7174985	0.84[EUR][1000 genomes]
rs7182319	0.97[ASN][1000 genomes]
rs9630436	0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][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	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

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs3816197	BBS4	cis	parietal	SCAN
rs3816197	STOML1	cis	cerebellum	SCAN
rs3816197	UACA	cis	parietal	SCAN
rs3816197	CYP11A1	cis	cerebellum	SCAN

Chromatin state (count:106 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:74272600-74283800	Weak transcription	Pancreatic Islets	Pancreatic Islet
2	chr15:74273800-74283600	Enhancers	HMEC	breast
3	chr15:74273800-74283600	Enhancers	NHDF-Ad	bronchial
4	chr15:74273800-74283800	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
5	chr15:74274600-74284000	Weak transcription	Ovary	ovary
6	chr15:74274800-74283800	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
7	chr15:74275000-74283600	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
8	chr15:74275000-74284000	Weak transcription	Aorta	Aorta
9	chr15:74276000-74283400	Weak transcription	Cortex derived primary cultured neurospheres	brain
10	chr15:74276200-74283000	Weak transcription	Primary T helper naive cells from peripheral blood	blood
11	chr15:74276600-74283000	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
12	chr15:74277600-74283000	Weak transcription	Fetal Lung	lung
13	chr15:74277600-74283400	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
14	chr15:74277800-74283400	Weak transcription	Monocytes-CD14+_RO01746	blood
15	chr15:74277800-74283600	Weak transcription	Primary neutrophils fromperipheralblood	blood
16	chr15:74277800-74283600	Weak transcription	Primary T helper cells PMA-I stimulated	--
17	chr15:74278000-74283400	Weak transcription	Primary T cells fromperipheralblood	blood
18	chr15:74278400-74283000	Weak transcription	Fetal Heart	heart
19	chr15:74278400-74283000	Weak transcription	Rectal Mucosa Donor 29	rectum
20	chr15:74278600-74283000	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
21	chr15:74278600-74283600	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
22	chr15:74279200-74283000	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
23	chr15:74279200-74283400	Enhancers	HUVEC	blood vessel
24	chr15:74279400-74283800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
25	chr15:74279600-74283200	Weak transcription	Primary T helper cells fromperipheralblood	blood
26	chr15:74279600-74283800	Enhancers	NH-A	brain
27	chr15:74279800-74283800	Enhancers	Stomach Mucosa	stomach
28	chr15:74280000-74283000	Weak transcription	Liver	Liver
29	chr15:74280200-74283600	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
30	chr15:74280200-74283800	Enhancers	Esophagus	oesophagus
31	chr15:74280200-74284000	Enhancers	Sigmoid Colon	Sigmoid Colon
32	chr15:74280400-74283000	Genic enhancers	Skeletal Muscle Male	skeletal muscle
33	chr15:74280600-74283400	Enhancers	Right Atrium	heart
34	chr15:74280800-74283000	Strong transcription	Thymus	Thymus
35	chr15:74280800-74283600	Enhancers	Colonic Mucosa	Colon
36	chr15:74280800-74284200	Enhancers	Small Intestine	intestine
37	chr15:74281000-74283000	Enhancers	NHLF	lung
38	chr15:74281000-74283400	Weak transcription	Primary B cells from cord blood	blood
39	chr15:74281000-74283400	Weak transcription	Primary B cells from peripheral blood	blood
40	chr15:74281000-74283400	Weak transcription	Primary hematopoietic stem cells	blood
41	chr15:74281000-74283600	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
42	chr15:74281000-74283600	Enhancers	Right Ventricle	heart
43	chr15:74281000-74284000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
44	chr15:74281200-74283000	Enhancers	K562	blood
45	chr15:74281200-74283400	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
46	chr15:74281200-74283600	Enhancers	Lung	lung
47	chr15:74281400-74283600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
48	chr15:74281400-74283600	Weak transcription	Primary T cells from cord blood	blood
49	chr15:74281400-74283800	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
50	chr15:74281400-74283800	Enhancers	Rectal Mucosa Donor 31	rectum

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