Variant report

Variant	rs1398241
Chromosome Location	chr15:77153386-77153387
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr15:77151146..77154145-chr15:77195611..77198369,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000140386	Chromatin interaction

Extended variants
information (count: 64 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:57)

rs_ID	r²[population]
rs10431768	0.86[AMR][1000 genomes];0.96[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs10851890	0.81[EUR][1000 genomes]
rs1114717	0.81[AMR][1000 genomes];0.87[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs12593107	0.83[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs1813479	0.83[AFR][1000 genomes];0.87[EUR][1000 genomes]
rs1913001	0.93[EUR][1000 genomes]
rs2011635	0.86[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs2046415	0.91[CHB][hapmap];0.83[CHD][hapmap];1.00[GIH][hapmap];0.90[JPT][hapmap];0.88[MEX][hapmap];1.00[TSI][hapmap];0.87[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs2063542	0.98[AFR][1000 genomes];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2170998	0.91[CHB][hapmap];0.83[CHD][hapmap];1.00[GIH][hapmap];0.90[JPT][hapmap];1.00[TSI][hapmap];0.82[EUR][1000 genomes]
rs2585730	0.80[ASW][hapmap];0.91[CHB][hapmap];0.83[CHD][hapmap];1.00[GIH][hapmap];0.90[JPT][hapmap];0.88[MEX][hapmap];1.00[TSI][hapmap]
rs2629034	0.85[AFR][1000 genomes];0.83[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs280001	0.91[CHB][hapmap];0.83[CHD][hapmap];1.00[GIH][hapmap];0.90[JPT][hapmap];0.88[MEX][hapmap];1.00[TSI][hapmap];0.82[EUR][1000 genomes]
rs280005	0.82[EUR][1000 genomes]
rs280008	0.82[EUR][1000 genomes]
rs280009	0.81[EUR][1000 genomes]
rs280012	0.91[CHB][hapmap];0.90[JPT][hapmap]
rs280013	0.91[CHB][hapmap];0.83[CHD][hapmap];1.00[GIH][hapmap];0.90[JPT][hapmap];0.88[MEX][hapmap];1.00[TSI][hapmap]
rs280024	1.00[ASW][hapmap];0.91[CHB][hapmap];0.83[CHD][hapmap];1.00[GIH][hapmap];0.90[JPT][hapmap];0.86[LWK][hapmap];0.88[MEX][hapmap];0.86[MKK][hapmap];1.00[TSI][hapmap];0.86[AFR][1000 genomes];0.83[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs280028	0.91[CHB][hapmap];0.90[JPT][hapmap];0.86[AFR][1000 genomes];0.83[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs280029	0.87[EUR][1000 genomes]
rs280030	0.89[CHB][hapmap];0.90[JPT][hapmap];0.91[YRI][hapmap];0.87[EUR][1000 genomes]
rs280033	0.85[EUR][1000 genomes]
rs2930681	1.00[ASW][hapmap];0.91[CHB][hapmap];0.83[CHD][hapmap];1.00[GIH][hapmap];0.90[JPT][hapmap];0.84[LWK][hapmap];0.88[MEX][hapmap];0.84[MKK][hapmap];1.00[TSI][hapmap]
rs3099134	0.91[CHB][hapmap];0.90[JPT][hapmap];0.86[AMR][1000 genomes];0.97[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs3099137	0.92[AFR][1000 genomes];0.88[AMR][1000 genomes];0.92[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs3099138	0.92[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs3099140	0.89[AFR][1000 genomes];0.88[AMR][1000 genomes];0.92[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs3099142	0.92[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs3099143	0.88[EUR][1000 genomes]
rs3102709	0.90[AFR][1000 genomes];0.83[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs3102710	0.90[CHB][hapmap];0.90[JPT][hapmap];0.88[AFR][1000 genomes];0.83[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs3102712	0.87[EUR][1000 genomes]
rs3102714	0.82[AFR][1000 genomes];0.83[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs3102716	0.83[AFR][1000 genomes];0.83[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs3106375	0.96[AFR][1000 genomes];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs3106377	0.94[AFR][1000 genomes];0.94[AMR][1000 genomes];0.93[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs3106378	0.92[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs3106380	0.90[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs3110378	0.94[AFR][1000 genomes];0.94[AMR][1000 genomes];0.92[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs3110379	0.91[CHB][hapmap];0.90[JPT][hapmap];0.91[AFR][1000 genomes];0.86[AMR][1000 genomes];0.88[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs3110381	0.90[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs3110384	0.95[AFR][1000 genomes];0.89[AMR][1000 genomes];0.99[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs35373913	0.95[AFR][1000 genomes];0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs35645941	0.94[AFR][1000 genomes];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs3764244	0.88[CHD][hapmap];1.00[GIH][hapmap]
rs4243043	0.92[EUR][1000 genomes]
rs4541044	0.91[CHB][hapmap];0.88[JPT][hapmap];0.87[YRI][hapmap];0.87[AFR][1000 genomes];0.83[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs4583202	0.86[AMR][1000 genomes];0.96[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs4886831	0.92[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs4886832	0.91[CHB][hapmap];0.83[CHD][hapmap];1.00[GIH][hapmap];0.90[JPT][hapmap];1.00[TSI][hapmap];0.83[AMR][1000 genomes];0.92[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs4886838	0.91[CHB][hapmap];0.90[JPT][hapmap]
rs6495222	0.85[AFR][1000 genomes];0.83[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs7172639	0.98[AFR][1000 genomes];0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs7174048	0.98[AFR][1000 genomes];0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs7178759	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]
rs901008	0.90[AFR][1000 genomes];0.88[AMR][1000 genomes];0.90[EUR][1000 genomes];0.81[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:7 , 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
7	esv1803942	chr15:77151005-77210457	Active TSS Weak transcription ZNF genes & repeats Enhancers Flanking Active TSS Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	5 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs1398241	C15orf60	cis	parietal	SCAN

Chromatin state (count:69 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:77111600-77174200	Weak transcription	Primary T helper naive cells from peripheral blood	blood
2	chr15:77112200-77196000	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
3	chr15:77120400-77158400	Weak transcription	Colon Smooth Muscle	Colon
4	chr15:77125800-77175400	Weak transcription	Sigmoid Colon	Sigmoid Colon
5	chr15:77131200-77155600	Weak transcription	Left Ventricle	heart
6	chr15:77133200-77196800	Weak transcription	Rectal Mucosa Donor 31	rectum
7	chr15:77139800-77155600	Weak transcription	Skeletal Muscle Male	skeletal muscle
8	chr15:77139800-77158400	Weak transcription	Rectal Smooth Muscle	rectum
9	chr15:77140000-77153600	Weak transcription	Brain Cingulate Gyrus	brain
10	chr15:77140800-77195800	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
11	chr15:77141400-77171600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
12	chr15:77141800-77168000	Weak transcription	Spleen	Spleen
13	chr15:77142000-77158000	Weak transcription	Brain Angular Gyrus	brain
14	chr15:77142000-77167200	Weak transcription	Esophagus	oesophagus
15	chr15:77142000-77167800	Weak transcription	Pancreas	Pancrea
16	chr15:77142000-77175800	Weak transcription	Fetal Brain Male	brain
17	chr15:77142000-77195800	Weak transcription	Right Ventricle	heart
18	chr15:77142200-77167600	Weak transcription	Lung	lung
19	chr15:77142800-77166400	Weak transcription	Thymus	Thymus
20	chr15:77144800-77179000	Weak transcription	Cortex derived primary cultured neurospheres	brain
21	chr15:77145000-77158000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
22	chr15:77145200-77158200	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
23	chr15:77145200-77158400	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
24	chr15:77146000-77153800	Weak transcription	Primary T helper cells PMA-I stimulated	--
25	chr15:77146000-77155600	Weak transcription	Psoas Muscle	Psoas
26	chr15:77146200-77156000	Weak transcription	Ovary	ovary
27	chr15:77146200-77158000	Weak transcription	Brain Hippocampus Middle	brain
28	chr15:77146200-77175400	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
29	chr15:77146400-77153400	Weak transcription	Fetal Thymus	thymus
30	chr15:77146400-77153600	Weak transcription	Primary neutrophils fromperipheralblood	blood
31	chr15:77146400-77158000	Weak transcription	Skeletal Muscle Female	skeletal muscle
32	chr15:77146400-77158200	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
33	chr15:77146400-77158400	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
34	chr15:77146400-77168000	Weak transcription	Primary T cells from cord blood	blood
35	chr15:77146400-77168200	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
36	chr15:77146400-77196400	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
37	chr15:77146600-77154200	Weak transcription	Fetal Muscle Trunk	muscle
38	chr15:77146600-77166000	Weak transcription	Fetal Intestine Small	intestine
39	chr15:77146600-77167800	Weak transcription	Aorta	Aorta
40	chr15:77146800-77167600	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
41	chr15:77147200-77166200	Weak transcription	Fetal Stomach	stomach
42	chr15:77147800-77173800	Weak transcription	Primary monocytes fromperipheralblood	blood
43	chr15:77147800-77177200	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
44	chr15:77148000-77167400	Weak transcription	Liver	Liver
45	chr15:77148200-77156000	Weak transcription	Brain Inferior Temporal Lobe	brain
46	chr15:77148200-77169200	Weak transcription	Primary B cells from cord blood	blood
47	chr15:77148200-77175200	Weak transcription	Fetal Muscle Leg	muscle
48	chr15:77148400-77153400	Weak transcription	Primary hematopoietic stem cells	blood
49	chr15:77148400-77154600	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
50	chr15:77148400-77174800	Weak transcription	Duodenum Smooth Muscle	Duodenum

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