Variant report

Variant	rs16970078
Chromosome Location	chr15:74857972-74857973
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr15:74856700..74859617-chr15:74876884..74880128,3	MCF-7	breast:
2	chr15:74855746..74857619-chr15:74857871..74860921,3	MCF-7	breast:
3	chr15:74835921..74837918-chr15:74855388..74858238,2	K562	blood:
4	chr15:74857691..74860080-chr15:74890652..74893317,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000179335	Chromatin interaction
ENSG00000179361	Chromatin interaction

Extended variants
information (count: 12 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:11)

rs_ID	r²[population]
rs11631682	0.82[ASW][hapmap];0.82[YRI][hapmap]
rs11632086	0.82[ASW][hapmap];1.00[LWK][hapmap];0.81[MKK][hapmap];0.90[YRI][hapmap]
rs16970170	1.00[ASW][hapmap];1.00[LWK][hapmap];0.90[YRI][hapmap];0.97[AFR][1000 genomes]
rs17861094	0.85[AFR][1000 genomes]
rs2069519	0.82[ASW][hapmap]
rs2069521	0.82[YRI][hapmap]
rs2069522	0.82[ASW][hapmap]
rs2069525	0.82[ASW][hapmap]
rs2069526	0.82[ASW][hapmap]
rs4646427	0.82[ASW][hapmap];0.82[YRI][hapmap]
rs74025819	0.82[AFR][1000 genomes]

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

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv1809847	chr15:74734500-74948063	Genic enhancers Flanking Active TSS Weak transcription Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Strong transcription Enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	70 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs16970078	SCAMP5	cis	multi-tissue	Pritchard
rs16970078	SCAMP5	cis	lymphoblastoid	seeQTL

Chromatin state (count:108 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:74839000-74863400	Weak transcription	Gastric	stomach
2	chr15:74839000-74863600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
3	chr15:74839200-74859200	Weak transcription	HepG2	liver
4	chr15:74839200-74860800	Weak transcription	Colonic Mucosa	Colon
5	chr15:74839200-74862000	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
6	chr15:74839200-74865200	Weak transcription	Placenta Amnion	Placenta Amnion
7	chr15:74839200-74866400	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
8	chr15:74839200-74866800	Weak transcription	Pancreas	Pancrea
9	chr15:74839400-74865800	Weak transcription	HUVEC	blood vessel
10	chr15:74839400-74880600	Weak transcription	Hela-S3	cervix
11	chr15:74839600-74862400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
12	chr15:74840000-74862000	Weak transcription	Colon Smooth Muscle	Colon
13	chr15:74840600-74890400	Weak transcription	Stomach Mucosa	stomach
14	chr15:74840800-74862200	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
15	chr15:74841000-74862000	Weak transcription	Brain Cingulate Gyrus	brain
16	chr15:74841000-74862000	Weak transcription	Brain Inferior Temporal Lobe	brain
17	chr15:74841200-74859400	Weak transcription	Sigmoid Colon	Sigmoid Colon
18	chr15:74841200-74862000	Weak transcription	Brain Substantia Nigra	brain
19	chr15:74841200-74862200	Weak transcription	Brain Angular Gyrus	brain
20	chr15:74841200-74862400	Weak transcription	Left Ventricle	heart
21	chr15:74841200-74862600	Weak transcription	Right Ventricle	heart
22	chr15:74841400-74861800	Weak transcription	Thymus	Thymus
23	chr15:74842400-74862000	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
24	chr15:74842400-74865000	Weak transcription	Rectal Mucosa Donor 31	rectum
25	chr15:74842600-74862000	Weak transcription	NH-A	brain
26	chr15:74843200-74862000	Weak transcription	Fetal Muscle Trunk	muscle
27	chr15:74843200-74865600	Weak transcription	Esophagus	oesophagus
28	chr15:74843400-74862400	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
29	chr15:74843600-74862000	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
30	chr15:74843800-74862200	Weak transcription	Stomach Smooth Muscle	stomach
31	chr15:74844000-74862200	Weak transcription	HSMMtube	muscle
32	chr15:74844000-74862400	Weak transcription	Brain Germinal Matrix	brain
33	chr15:74844200-74861200	Weak transcription	iPS-15b Cell Line	embryonic stem cell
34	chr15:74844600-74862400	Weak transcription	Duodenum Smooth Muscle	Duodenum
35	chr15:74845000-74863800	Weak transcription	Breast Myoepithelial Primary Cells	Breast
36	chr15:74845400-74859200	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
37	chr15:74845400-74861800	Weak transcription	Primary hematopoietic stem cells	blood
38	chr15:74845400-74880200	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
39	chr15:74845600-74859200	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
40	chr15:74845600-74859400	Weak transcription	Fetal Intestine Large	intestine
41	chr15:74845600-74861800	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
42	chr15:74845600-74862200	Weak transcription	Fetal Lung	lung
43	chr15:74845600-74876200	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
44	chr15:74845800-74859600	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
45	chr15:74845800-74861800	Weak transcription	H1 Cell Line	embryonic stem cell
46	chr15:74845800-74864600	Weak transcription	Dnd41	blood
47	chr15:74845800-74890400	Weak transcription	A549	lung
48	chr15:74846000-74859400	Weak transcription	Liver	Liver
49	chr15:74846000-74861800	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
50	chr15:74846200-74859000	Weak transcription	HUES48 Cell Line	embryonic stem cell

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