Variant report

Variant	rs11072597
Chromosome Location	chr15:76763514-76763515
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	TCF12	chr15:76762914-76763533	SK-N-SH	brain:	n/a	n/a
2	GATA3	chr15:76763045-76763521	SK-N-SH	brain:	n/a	chr15:76763242-76763250
3	GATA3	chr15:76762856-76763551	SK-N-SH	brain:	n/a	chr15:76763242-76763250

Variant related genes	Relation type
ENSG00000261232	TF binding region

Extended variants
information (count: 80 )
Associated
traits (count: 14 )

rSNPs within LD-proxies of this variant (count:78)

rs_ID	r²[population]
rs10851888	0.95[CEU][hapmap];0.87[CHB][hapmap];0.87[YRI][hapmap]
rs11072591	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs11072598	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11072610	0.95[CEU][hapmap];0.87[CHB][hapmap];0.87[YRI][hapmap]
rs11072612	0.91[CEU][hapmap];0.87[CHB][hapmap]
rs11629888	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs11632222	0.97[AFR][1000 genomes];0.96[AMR][1000 genomes];0.94[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs11634019	0.91[CEU][hapmap];0.95[CHB][hapmap];0.90[JPT][hapmap];0.82[AMR][1000 genomes]
rs11635463	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11637096	0.95[CEU][hapmap];0.86[CHB][hapmap]
rs11637490	0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11638767	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs11855999	0.84[AFR][1000 genomes];0.83[AMR][1000 genomes]
rs11856717	0.87[CHB][hapmap]
rs11857015	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];0.92[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs11857327	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12437981	0.95[CEU][hapmap];0.87[CHB][hapmap]
rs12440965	0.91[CEU][hapmap];0.87[CHB][hapmap];0.87[YRI][hapmap]
rs12591100	0.95[CHB][hapmap];1.00[JPT][hapmap];0.82[ASN][1000 genomes]
rs12898810	0.81[AFR][1000 genomes]
rs12900179	0.93[AMR][1000 genomes];0.91[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12903874	0.93[AMR][1000 genomes];0.92[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs12906143	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];0.96[AMR][1000 genomes];0.93[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs12909656	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs157783	0.95[CHB][hapmap];1.00[JPT][hapmap];0.92[ASN][1000 genomes]
rs1607015	0.95[CEU][hapmap];0.95[CHB][hapmap];0.90[JPT][hapmap];0.87[YRI][hapmap];0.97[AFR][1000 genomes];0.96[AMR][1000 genomes];0.93[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs1607017	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap]
rs2003344	0.81[AMR][1000 genomes]
rs2047504	0.95[CEU][hapmap];0.87[CHB][hapmap]
rs2048856	0.95[AFR][1000 genomes];0.85[AMR][1000 genomes];0.90[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs206205	0.87[ASN][1000 genomes]
rs2164102	0.81[AFR][1000 genomes]
rs2280306	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs2404734	0.91[CEU][hapmap];0.87[CHB][hapmap]
rs2436994	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[AMR][1000 genomes];0.90[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2436996	0.86[AFR][1000 genomes];0.82[AMR][1000 genomes];0.88[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2454450	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[AMR][1000 genomes];0.88[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2454451	0.95[CEU][hapmap];0.87[CHB][hapmap]
rs2454454	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2459361	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[AMR][1000 genomes];0.87[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs2461870	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs2461871	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.81[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2461872	0.84[CEU][hapmap];0.90[CHB][hapmap];0.84[AMR][1000 genomes]
rs2468130	0.95[AFR][1000 genomes];0.84[AMR][1000 genomes];0.91[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2468131	0.95[AFR][1000 genomes];0.85[AMR][1000 genomes];0.91[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2469249	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.86[AMR][1000 genomes];0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs283789	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.88[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs283793	1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs283795	0.95[CHB][hapmap];1.00[JPT][hapmap];0.92[ASN][1000 genomes]
rs284891	0.86[ASN][1000 genomes]
rs284892	0.85[ASN][1000 genomes]
rs284899	0.82[AMR][1000 genomes];0.87[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs284909	0.87[ASN][1000 genomes]
rs2944378	0.86[ASN][1000 genomes]
rs2957614	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.88[AMR][1000 genomes];0.92[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs3765115	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[AMR][1000 genomes];0.91[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs437131	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[AMR][1000 genomes];0.91[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4886488	0.82[JPT][hapmap]
rs4886493	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[AMR][1000 genomes];0.91[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs4886495	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4886798	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.92[AFR][1000 genomes];0.94[AMR][1000 genomes];0.92[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs4886800	0.80[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.90[AFR][1000 genomes];0.81[ASN][1000 genomes]
rs4886805	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4886816	0.95[CEU][hapmap];0.86[CHB][hapmap]
rs4886819	0.95[CEU][hapmap];0.87[CHB][hapmap]
rs56246286	0.93[AMR][1000 genomes];0.92[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs57682236	0.85[AFR][1000 genomes]
rs62028380	0.91[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs62028406	0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs62028423	0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs62028434	0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs71405204	0.83[AMR][1000 genomes]
rs7181506	0.91[CEU][hapmap];0.87[CHB][hapmap]
rs744336	0.95[CHB][hapmap];1.00[JPT][hapmap]
rs8029283	0.95[CEU][hapmap];0.86[CHB][hapmap]
rs8037847	0.95[CEU][hapmap];0.87[CHB][hapmap]
rs908817	0.91[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs965818	0.95[CEU][hapmap];0.87[CHB][hapmap]

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	nsv542438	chr15:76697056-76892157	Weak transcription Strong transcription ZNF genes & repeats Enhancers Flanking Active TSS Genic enhancers Active TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA	3 gene(s)	inside rSNPs	diseases
2	nsv542439	chr15:76762161-77196336	Enhancers Weak transcription Strong transcription ZNF genes & repeats Flanking Active TSS Active TSS Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA	9 gene(s)	inside rSNPs	diseases

mRNA abundance (count:14)

SNP	Gene	Cis/trans	Tissue	Source
rs11072597	SCAPER	cis	Whole Blood	GTEx
rs11072597	SCAPER	cis	Muscle Skeletal	GTEx
rs11072597	SCAPER	cis	Adipose Subcutaneous	GTEx
rs11072597	ISL2	Cis_1M	lymphoblastoid	RTeQTL
rs11072597	ZNF291	cis	uninvolved skin	skin_eQTL
rs11072597	SCAPER	Cis_1M	lymphoblastoid	RTeQTL
rs11072597	SCAPER	cis	Thyroid	GTEx
rs11072597	SCAPER	cis	Esophagus Muscularis	GTEx
rs11072597	SCAPER	cis	Nerve Tibial	GTEx
rs11072597	ZNF291	cis	lesional skin	skin_eQTL
rs11072597	SCAPER	cis	Esophagus Mucosa	GTEx
rs11072597	SCAPER	cis	lung	GTEx
rs11072597	SCAPER	cis	Artery Tibial	GTEx
rs11072597	SCAPER	cis	Skin Sun Exposed Lower leg	GTEx

Chromatin state (count:51 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:76711600-76767200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
2	chr15:76720800-76763600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
3	chr15:76725800-76812600	Weak transcription	Left Ventricle	heart
4	chr15:76750400-76763800	Weak transcription	Placenta	Placenta
5	chr15:76753800-76764400	Weak transcription	Fetal Intestine Large	intestine
6	chr15:76754000-76764400	Weak transcription	Brain Hippocampus Middle	brain
7	chr15:76754200-76763600	Weak transcription	Pancreas	Pancrea
8	chr15:76754400-76763600	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
9	chr15:76754800-76764400	Weak transcription	Fetal Muscle Trunk	muscle
10	chr15:76755600-76764600	Weak transcription	Skeletal Muscle Male	skeletal muscle
11	chr15:76757800-76765200	Weak transcription	Aorta	Aorta
12	chr15:76758400-76765600	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
13	chr15:76758800-76764400	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
14	chr15:76758800-76765000	Weak transcription	Primary T helper cells PMA-I stimulated	--
15	chr15:76758800-76765200	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
16	chr15:76759200-76763800	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
17	chr15:76759200-76764400	Weak transcription	Psoas Muscle	Psoas
18	chr15:76759400-76763600	Strong transcription	Liver	Liver
19	chr15:76759400-76764400	Weak transcription	Fetal Muscle Leg	muscle
20	chr15:76759800-76770400	Weak transcription	Colon Smooth Muscle	Colon
21	chr15:76760000-76772600	Weak transcription	GM12878-XiMat	blood
22	chr15:76760400-76773800	Weak transcription	Primary T helper naive cells from peripheral blood	blood
23	chr15:76760600-76764200	Weak transcription	Primary monocytes fromperipheralblood	blood
24	chr15:76760800-76764200	Strong transcription	Primary T helper cells fromperipheralblood	blood
25	chr15:76761000-76763600	Strong transcription	Primary T cells fromperipheralblood	blood
26	chr15:76761200-76764800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
27	chr15:76761400-76763600	Weak transcription	Brain Anterior Caudate	brain
28	chr15:76761400-76765400	Weak transcription	Sigmoid Colon	Sigmoid Colon
29	chr15:76761800-76764200	Strong transcription	Primary T cells from cord blood	blood
30	chr15:76762000-76771400	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
31	chr15:76762400-76763800	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
32	chr15:76762400-76764000	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
33	chr15:76762400-76765200	Enhancers	Breast Myoepithelial Primary Cells	Breast
34	chr15:76762600-76763800	Enhancers	HSMM	muscle
35	chr15:76762600-76764200	Strong transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
36	chr15:76762800-76764400	Weak transcription	Dnd41	blood
37	chr15:76762800-76764600	Weak transcription	Monocytes-CD14+_RO01746	blood
38	chr15:76762800-76765400	Weak transcription	Rectal Mucosa Donor 29	rectum
39	chr15:76762800-76765600	Weak transcription	Stomach Smooth Muscle	stomach
40	chr15:76762800-76771200	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
41	chr15:76763000-76764600	Weak transcription	Duodenum Smooth Muscle	Duodenum
42	chr15:76763000-76764600	Weak transcription	Rectal Mucosa Donor 31	rectum
43	chr15:76763000-76768200	Weak transcription	Ovary	ovary
44	chr15:76763000-76768600	Weak transcription	Primary hematopoietic stem cells	blood
45	chr15:76763000-76795000	Weak transcription	Primary B cells from cord blood	blood
46	chr15:76763200-76765000	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
47	chr15:76763200-76770200	Weak transcription	Adipose Nuclei	Adipose
48	chr15:76763400-76765000	Weak transcription	Primary B cells from peripheral blood	blood
49	chr15:76763400-76765000	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
50	chr15:76763400-76765000	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood

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