Variant report

Variant	rs11072511
Chromosome Location	chr15:75159433-75159434
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr15:75153777..75156294-chr15:75158618..75161224,2	K562	blood:
2	chr15:75157220..75162664-chr15:75181204..75183708,6	MCF-7	breast:
3	chr15:75158451..75161193-chr15:75161527..75164480,2	MCF-7	breast:
4	chr15:75156545..75159476-chr15:75183223..75185437,3	MCF-7	breast:
5	chr15:75152352..75156342-chr15:75158618..75163297,4	K562	blood:
6	chr15:75156504..75159434-chr15:75228735..75231326,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000178802	Chromatin interaction
ENSG00000178741	Chromatin interaction

Extended variants
information (count: 55 )
Associated
traits (count: 11 )

rSNPs within LD-proxies of this variant (count:53)

rs_ID	r²[population]
rs11072512	0.96[CEU][hapmap];0.93[TSI][hapmap];0.91[EUR][1000 genomes]
rs11072513	0.92[CEU][hapmap]
rs11072514	0.92[CEU][hapmap];0.82[EUR][1000 genomes]
rs1127796	0.96[CEU][hapmap];0.93[TSI][hapmap];0.91[EUR][1000 genomes]
rs1130741	0.88[ASW][hapmap];0.96[CEU][hapmap];0.88[CHB][hapmap];0.85[CHD][hapmap];0.96[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.96[MEX][hapmap];0.98[MKK][hapmap];0.95[TSI][hapmap];0.96[YRI][hapmap];0.95[AFR][1000 genomes];0.90[AMR][1000 genomes];0.92[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs1133322	0.92[CEU][hapmap];0.93[TSI][hapmap];0.88[EUR][1000 genomes]
rs1133323	0.92[CEU][hapmap];0.84[TSI][hapmap];0.80[EUR][1000 genomes]
rs11630918	0.92[CEU][hapmap];0.85[TSI][hapmap];0.86[EUR][1000 genomes]
rs11633472	0.96[CEU][hapmap];0.85[TSI][hapmap];0.85[EUR][1000 genomes]
rs11638130	0.96[CEU][hapmap];0.85[TSI][hapmap];0.83[EUR][1000 genomes]
rs11854704	0.92[CEU][hapmap];0.93[TSI][hapmap];0.88[EUR][1000 genomes]
rs11856413	0.96[CEU][hapmap];0.85[TSI][hapmap];0.84[EUR][1000 genomes]
rs11857695	0.94[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12439641	0.91[YRI][hapmap];0.83[AFR][1000 genomes]
rs12441499	0.95[LWK][hapmap];0.96[YRI][hapmap];0.86[AFR][1000 genomes]
rs12487	0.88[CEU][hapmap]
rs12898539	0.83[EUR][1000 genomes]
rs12899430	0.83[EUR][1000 genomes]
rs12899787	0.88[EUR][1000 genomes]
rs12900662	0.95[EUR][1000 genomes]
rs12901190	0.92[CEU][hapmap];0.85[TSI][hapmap];0.80[EUR][1000 genomes]
rs12902515	0.94[AFR][1000 genomes];0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12903205	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12903370	0.82[EUR][1000 genomes]
rs12904326	0.81[EUR][1000 genomes]
rs12904897	0.90[AFR][1000 genomes];0.88[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs12907898	0.90[EUR][1000 genomes]
rs12908365	0.88[EUR][1000 genomes]
rs12909335	0.92[CEU][hapmap];0.85[TSI][hapmap];0.81[EUR][1000 genomes]
rs12911254	0.88[EUR][1000 genomes]
rs12912839	0.82[EUR][1000 genomes]
rs12913293	0.97[AFR][1000 genomes];0.91[AMR][1000 genomes];0.93[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2415251	0.88[CEU][hapmap];0.83[TSI][hapmap]
rs3935818	0.95[LWK][hapmap];0.91[YRI][hapmap];0.86[AFR][1000 genomes]
rs4643278	0.95[EUR][1000 genomes]
rs4886608	0.89[AFR][1000 genomes];0.99[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4886632	0.96[EUR][1000 genomes]
rs4886636	0.88[ASW][hapmap];0.92[CEU][hapmap];0.88[CHB][hapmap];0.96[GIH][hapmap];1.00[JPT][hapmap];0.95[LWK][hapmap];1.00[MEX][hapmap];0.98[MKK][hapmap];0.93[TSI][hapmap];0.96[YRI][hapmap];0.95[AFR][1000 genomes];0.90[AMR][1000 genomes];0.91[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs4886639	0.82[EUR][1000 genomes]
rs56671860	0.86[AFR][1000 genomes]
rs59945415	0.88[EUR][1000 genomes]
rs60494786	0.86[AFR][1000 genomes]
rs62029167	0.89[EUR][1000 genomes]
rs6495122	0.85[CEU][hapmap]
rs7179093	0.95[LWK][hapmap];0.91[YRI][hapmap];0.86[AFR][1000 genomes]
rs729263	0.95[LWK][hapmap];0.96[YRI][hapmap];0.86[AFR][1000 genomes]
rs7495664	0.82[EUR][1000 genomes]
rs7495739	0.88[ASW][hapmap];0.96[CEU][hapmap];0.88[CHB][hapmap];0.85[CHD][hapmap];0.96[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.98[MKK][hapmap];0.95[TSI][hapmap];0.96[YRI][hapmap];0.97[AFR][1000 genomes];0.94[AMR][1000 genomes];0.93[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs7497026	0.81[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs7497393	0.96[CEU][hapmap];0.87[EUR][1000 genomes]
rs8025447	0.94[AFR][1000 genomes];0.90[AMR][1000 genomes];0.91[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs8032473	0.81[AFR][1000 genomes]
rs9672491	0.83[AFR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv833055	chr15:74988344-75166288	Weak transcription Active TSS Genic enhancers Flanking Active TSS Strong transcription Enhancers Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	46 gene(s)	inside rSNPs	diseases
2	nsv904381	chr15:75108636-75242155	Weak transcription Genic enhancers Enhancers Flanking Active TSS Active TSS Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	55 gene(s)	inside rSNPs	diseases

mRNA abundance (count:11)

SNP	Gene	Cis/trans	Tissue	Source
rs11072511	SCAMP2	cis	Esophagus Mucosa	GTEx
rs11072511	SCAMP2	Cis_1M	lymphoblastoid	RTeQTL
rs11072511	SCAMP5	cis	Artery Tibial	GTEx
rs11072511	ZNF572	trans	cerebellum	SCAN
rs11072511	SCAMP2	cis	Whole Blood	GTEx
rs11072511	ULK3	cis	parietal	SCAN
rs11072511	COX5A	Cis_1M	lymphoblastoid	RTeQTL
rs11072511	MPI	Cis_1M	lymphoblastoid	RTeQTL
rs11072511	SCAMP2	cis	parietal	SCAN
rs11072511	TLE3	cis	cerebellum	SCAN
rs11072511	MPI	cis	lymphoblastoid	seeQTL

Chromatin state (count:126 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:75136200-75160000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
2	chr15:75136200-75161800	Weak transcription	Fetal Kidney	kidney
3	chr15:75136600-75163000	Weak transcription	Fetal Brain Male	brain
4	chr15:75137000-75164800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
5	chr15:75143600-75163000	Weak transcription	iPS-15b Cell Line	embryonic stem cell
6	chr15:75145000-75160000	Weak transcription	HUES64 Cell Line	embryonic stem cell
7	chr15:75146000-75164800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
8	chr15:75146200-75163200	Weak transcription	iPS-20b Cell Line	embryonic stem cell
9	chr15:75146400-75160400	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
10	chr15:75146400-75161800	Weak transcription	Fetal Lung	lung
11	chr15:75146400-75163200	Weak transcription	H1 Cell Line	embryonic stem cell
12	chr15:75146600-75160000	Weak transcription	HUES6 Cell Line	embryonic stem cell
13	chr15:75146600-75163000	Weak transcription	H9 Cell Line	embryonic stem cell
14	chr15:75146600-75164600	Weak transcription	iPS-18 Cell Line	embryonic stem cell
15	chr15:75146800-75159800	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
16	chr15:75147000-75159600	Weak transcription	Fetal Brain Female	brain
17	chr15:75147000-75160000	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
18	chr15:75147000-75164800	Weak transcription	Ovary	ovary
19	chr15:75147200-75164800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
20	chr15:75150000-75160000	Weak transcription	Rectal Smooth Muscle	rectum
21	chr15:75150000-75160200	Weak transcription	Cortex derived primary cultured neurospheres	brain
22	chr15:75150200-75160200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
23	chr15:75150400-75159600	Weak transcription	Dnd41	blood
24	chr15:75150400-75161800	Weak transcription	Aorta	Aorta
25	chr15:75150600-75159600	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
26	chr15:75150600-75159600	Weak transcription	K562	blood
27	chr15:75150600-75160200	Weak transcription	Brain Germinal Matrix	brain
28	chr15:75151000-75160000	Weak transcription	Stomach Smooth Muscle	stomach
29	chr15:75151200-75161800	Weak transcription	Brain Angular Gyrus	brain
30	chr15:75151800-75160200	Weak transcription	Brain Substantia Nigra	brain
31	chr15:75151800-75161800	Weak transcription	Brain Inferior Temporal Lobe	brain
32	chr15:75152200-75162200	Weak transcription	Brain Cingulate Gyrus	brain
33	chr15:75152400-75160200	Weak transcription	Brain Anterior Caudate	brain
34	chr15:75152400-75160200	Weak transcription	Fetal Muscle Trunk	muscle
35	chr15:75152400-75161800	Weak transcription	Brain Hippocampus Middle	brain
36	chr15:75152800-75159800	Weak transcription	Colon Smooth Muscle	Colon
37	chr15:75153600-75162200	Enhancers	Primary T helper cells fromperipheralblood	blood
38	chr15:75154800-75160400	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
39	chr15:75155000-75159800	Enhancers	Primary T helper cells PMA-I stimulated	--
40	chr15:75155000-75160000	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
41	chr15:75155000-75160400	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
42	chr15:75155000-75162000	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
43	chr15:75155200-75160000	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
44	chr15:75155600-75159800	Enhancers	Primary T helper naive cells from peripheral blood	blood
45	chr15:75155800-75164400	Genic enhancers	Fetal Intestine Small	intestine
46	chr15:75156000-75164800	Enhancers	Fetal Intestine Large	intestine
47	chr15:75156600-75163800	Enhancers	Stomach Mucosa	stomach
48	chr15:75156800-75159600	Enhancers	Placenta	Placenta
49	chr15:75156800-75159800	Genic enhancers	Primary hematopoietic stem cells short term culture	blood
50	chr15:75156800-75160000	Enhancers	Rectal Mucosa Donor 31	rectum

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