Variant report

Variant	rs7178759
Chromosome Location	chr15:77143513-77143514
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 71 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:65)

rs_ID	r²[population]
rs10431768	0.86[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs10851890	0.82[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs1114717	0.86[AMR][1000 genomes];0.88[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12593107	0.94[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs1398241	0.91[CHB][hapmap];0.83[CHD][hapmap];0.86[GIH][hapmap];0.90[JPT][hapmap];0.90[TSI][hapmap];0.89[AMR][1000 genomes];0.99[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs166794	0.81[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs1813479	0.88[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs1905694	0.81[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs1913001	0.95[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2011635	0.86[AMR][1000 genomes];0.99[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs203753	0.81[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2046415	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.86[GIH][hapmap];1.00[JPT][hapmap];0.90[TSI][hapmap];0.88[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2063542	0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2170998	0.83[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.86[GIH][hapmap];1.00[JPT][hapmap];0.88[LWK][hapmap];0.89[MEX][hapmap];0.95[MKK][hapmap];0.90[TSI][hapmap];0.83[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2585730	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.86[GIH][hapmap];1.00[JPT][hapmap];0.90[TSI][hapmap];0.81[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2629021	0.81[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2629034	0.83[AMR][1000 genomes];0.88[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs279997	0.85[ASN][1000 genomes]
rs279999	0.81[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs280001	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.86[GIH][hapmap];1.00[JPT][hapmap];0.90[TSI][hapmap];0.83[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs280005	0.83[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs280008	0.83[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs280009	0.82[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs280012	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs280013	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.86[GIH][hapmap];1.00[JPT][hapmap];0.90[TSI][hapmap];0.81[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs280014	0.81[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs280024	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.85[GIH][hapmap];1.00[JPT][hapmap];0.90[TSI][hapmap];0.83[AMR][1000 genomes];0.88[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs280028	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[AMR][1000 genomes];0.88[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs280029	0.88[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs280030	1.00[CEU][hapmap];0.89[CHB][hapmap];0.91[JPT][hapmap];0.88[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs280033	0.86[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2930681	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.86[GIH][hapmap];1.00[JPT][hapmap];0.90[TSI][hapmap];0.81[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs3099134	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3099137	0.88[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3099138	0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3099140	0.88[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3099142	0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs3099143	0.89[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs3102709	0.83[AMR][1000 genomes];0.88[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs3102710	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[AMR][1000 genomes];0.87[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs3102712	0.88[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs3102713	0.88[ASN][1000 genomes]
rs3102714	0.83[AMR][1000 genomes];0.83[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs3102716	0.83[AMR][1000 genomes];0.88[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs3106375	0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs3106377	0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs3106378	0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3106380	0.91[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs3110378	1.00[CEU][hapmap];0.94[AMR][1000 genomes];0.93[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs3110379	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[AMR][1000 genomes];0.90[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs3110381	0.91[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs3110384	0.89[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35373913	0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs35645941	0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs3764244	0.87[CEU][hapmap];0.96[CHD][hapmap];0.86[GIH][hapmap];0.89[MEX][hapmap]
rs4243043	0.89[AMR][1000 genomes];0.93[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs4541044	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[AMR][1000 genomes];0.95[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs4583202	0.86[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4886831	1.00[CEU][hapmap];0.86[AMR][1000 genomes];0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4886832	0.83[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.86[GIH][hapmap];1.00[JPT][hapmap];0.93[LWK][hapmap];0.89[MEX][hapmap];0.98[MKK][hapmap];0.90[TSI][hapmap];0.86[AFR][1000 genomes];0.94[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4886838	0.92[CHB][hapmap];1.00[JPT][hapmap];0.80[ASN][1000 genomes]
rs6495222	0.83[AMR][1000 genomes];0.95[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs7172639	0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7174048	0.82[CEU][hapmap];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs901008	0.88[AMR][1000 genomes];0.91[EUR][1000 genomes];0.97[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	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
2	esv3440794	chr15:76764595-77571114	Weak transcription Enhancers Strong transcription Active TSS Flanking Active TSS Genic enhancers ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	25 gene(s)	inside rSNPs	diseases
3	esv2830013	chr15:76863023-77176158	Weak transcription ZNF genes & repeats Strong transcription Enhancers Flanking Active TSS Genic enhancers Active TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA	4 gene(s)	inside rSNPs	diseases
4	nsv1046137	chr15:76892097-77196336	ZNF genes & repeats Strong transcription Weak transcription Enhancers Flanking Active TSS Genic enhancers Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
5	nsv542442	chr15:76892097-77196336	ZNF genes & repeats Strong transcription Weak transcription Enhancers Genic enhancers Flanking Active TSS Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
6	esv3367577	chr15:77015618-77442634	Genic enhancers Weak transcription Strong transcription Enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Flanking Active TSS Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	20 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs7178759	C15orf60	cis	parietal	SCAN

Chromatin state (count:85 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:77111600-77144000	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
2	chr15:77111600-77174200	Weak transcription	Primary T helper naive cells from peripheral blood	blood
3	chr15:77112200-77196000	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
4	chr15:77115400-77144600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
5	chr15:77116800-77144000	Weak transcription	Brain Inferior Temporal Lobe	brain
6	chr15:77120400-77158400	Weak transcription	Colon Smooth Muscle	Colon
7	chr15:77123200-77144800	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
8	chr15:77123200-77153200	Weak transcription	Muscle Satellite Cultured Cells	--
9	chr15:77124400-77149600	Weak transcription	HepG2	liver
10	chr15:77125800-77175400	Weak transcription	Sigmoid Colon	Sigmoid Colon
11	chr15:77126000-77145600	Weak transcription	Aorta	Aorta
12	chr15:77130200-77143600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
13	chr15:77130600-77147400	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
14	chr15:77131200-77155600	Weak transcription	Left Ventricle	heart
15	chr15:77131400-77148000	Weak transcription	Placenta	Placenta
16	chr15:77131800-77144000	Weak transcription	HSMM	muscle
17	chr15:77133200-77147600	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
18	chr15:77133200-77196800	Weak transcription	Rectal Mucosa Donor 31	rectum
19	chr15:77133800-77143600	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
20	chr15:77137000-77144000	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
21	chr15:77139600-77144000	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
22	chr15:77139800-77145600	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
23	chr15:77139800-77155600	Weak transcription	Skeletal Muscle Male	skeletal muscle
24	chr15:77139800-77158400	Weak transcription	Rectal Smooth Muscle	rectum
25	chr15:77140000-77144800	Weak transcription	NHLF	lung
26	chr15:77140000-77153600	Weak transcription	Brain Cingulate Gyrus	brain
27	chr15:77140400-77144400	Weak transcription	Brain Anterior Caudate	brain
28	chr15:77140400-77144800	Weak transcription	Brain Hippocampus Middle	brain
29	chr15:77140800-77195800	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
30	chr15:77141000-77144800	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
31	chr15:77141200-77143800	Weak transcription	Fetal Lung	lung
32	chr15:77141200-77144200	ZNF genes & repeats	Brain Germinal Matrix	brain
33	chr15:77141200-77146400	ZNF genes & repeats	GM12878-XiMat	blood
34	chr15:77141400-77143600	Strong transcription	Primary T cells from cord blood	blood
35	chr15:77141400-77143800	Strong transcription	Primary B cells from peripheral blood	blood
36	chr15:77141400-77144000	Strong transcription	Breast Myoepithelial Primary Cells	Breast
37	chr15:77141400-77171600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
38	chr15:77141600-77143800	Strong transcription	Fetal Muscle Trunk	muscle
39	chr15:77141600-77143800	Strong transcription	Monocytes-CD14+_RO01746	blood
40	chr15:77141600-77144000	Strong transcription	Duodenum Smooth Muscle	Duodenum
41	chr15:77141600-77144800	Strong transcription	Fetal Thymus	thymus
42	chr15:77141600-77146800	ZNF genes & repeats	Ganglion Eminence derived primary cultured neurospheres	brain
43	chr15:77141800-77143800	Strong transcription	Cortex derived primary cultured neurospheres	brain
44	chr15:77141800-77144200	Strong transcription	Fetal Intestine Large	intestine
45	chr15:77141800-77147400	Weak transcription	Fetal Kidney	kidney
46	chr15:77141800-77168000	Weak transcription	Spleen	Spleen
47	chr15:77142000-77143600	Strong transcription	Primary B cells from cord blood	blood
48	chr15:77142000-77148200	Weak transcription	Gastric	stomach
49	chr15:77142000-77158000	Weak transcription	Brain Angular Gyrus	brain
50	chr15:77142000-77167200	Weak transcription	Esophagus	oesophagus

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