Variant report

Variant	rs9302260
Chromosome Location	chr15:72174611-72174612
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	chr15:72173982..72176259-chr15:72181202..72184060,3	K562	blood:

Extended variants
information (count: 104 )
Associated
traits (count: 7 )

rSNPs within LD-proxies of this variant (count:93)

rs_ID	r²[population]
rs1074330	0.83[CEU][hapmap];0.82[TSI][hapmap]
rs10851847	0.92[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs11633167	1.00[CEU][hapmap];0.86[CHB][hapmap];0.95[JPT][hapmap];0.86[AMR][1000 genomes];0.99[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs11634608	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];0.95[JPT][hapmap];0.97[TSI][hapmap];0.82[AMR][1000 genomes];0.91[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs12050794	0.86[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs12148078	0.86[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs12161990	0.82[ASN][1000 genomes]
rs12439494	0.94[CEU][hapmap];0.82[CHB][hapmap];0.82[JPT][hapmap];0.93[AMR][1000 genomes];0.91[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs12898728	0.87[AMR][1000 genomes];0.83[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs12898868	0.86[AMR][1000 genomes];0.83[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs12902006	0.83[CEU][hapmap];0.82[TSI][hapmap]
rs12912771	0.90[AMR][1000 genomes];0.92[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs12914070	0.83[CEU][hapmap];0.82[TSI][hapmap]
rs12916951	0.83[CEU][hapmap];0.82[TSI][hapmap]
rs1481860	0.82[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs1481861	0.81[AMR][1000 genomes];0.83[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs1481862	0.85[AMR][1000 genomes];0.90[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs1552134	0.84[ASN][1000 genomes]
rs16956273	0.89[CEU][hapmap];0.89[GIH][hapmap];0.80[TSI][hapmap]
rs16956369	0.86[AMR][1000 genomes];0.98[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2054601	0.82[TSI][hapmap]
rs2128112	0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2278987	0.80[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs2306489	0.82[AMR][1000 genomes];0.86[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2306576	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.86[MKK][hapmap];1.00[TSI][hapmap];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2415120	1.00[CEU][hapmap];0.92[GIH][hapmap];0.93[MEX][hapmap];0.92[TSI][hapmap];0.93[EUR][1000 genomes]
rs2415121	0.92[AMR][1000 genomes];0.91[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2415126	0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2415128	0.94[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.86[MEX][hapmap];0.97[TSI][hapmap];0.84[AMR][1000 genomes];0.91[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs28650442	0.92[AMR][1000 genomes];0.94[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs28717020	0.90[AMR][1000 genomes];0.91[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2899775	0.80[AMR][1000 genomes];0.87[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2899776	0.82[AMR][1000 genomes];0.91[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2929508	0.93[CEU][hapmap];0.80[CHB][hapmap];0.89[JPT][hapmap];0.90[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2929509	0.88[AMR][1000 genomes];0.91[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2929510	0.90[AMR][1000 genomes];0.90[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2929511	0.92[AMR][1000 genomes];0.91[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2929513	0.84[AMR][1000 genomes];0.90[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2929517	0.89[EUR][1000 genomes]
rs2929518	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.93[MEX][hapmap];1.00[TSI][hapmap]
rs2929525	0.85[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2929526	0.86[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2929527	0.80[AMR][1000 genomes];0.87[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2929528	0.83[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2929532	0.82[AMR][1000 genomes];0.87[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2930069	0.88[AMR][1000 genomes];0.90[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2957361	0.80[AMR][1000 genomes];0.87[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2957365	0.82[AMR][1000 genomes];0.86[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2957368	0.81[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2957373	0.94[CEU][hapmap];0.86[CHB][hapmap];0.82[JPT][hapmap];0.82[ASN][1000 genomes]
rs2957724	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[AMR][1000 genomes];0.89[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2957725	0.94[CEU][hapmap];0.86[CHB][hapmap];0.86[CHD][hapmap];0.92[GIH][hapmap];0.82[JPT][hapmap];0.86[MEX][hapmap];0.92[TSI][hapmap];0.82[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2957728	0.90[AMR][1000 genomes];0.90[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2957734	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.93[MEX][hapmap];1.00[TSI][hapmap];0.82[AMR][1000 genomes];0.91[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2957735	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.93[MEX][hapmap];1.00[TSI][hapmap];0.81[AMR][1000 genomes];0.90[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2957736	0.80[AMR][1000 genomes];0.90[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2957737	0.94[CEU][hapmap];0.86[CHB][hapmap];0.86[CHD][hapmap];0.89[GIH][hapmap];0.82[JPT][hapmap];0.86[MEX][hapmap];0.92[TSI][hapmap];0.82[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2957740	0.90[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2957742	0.81[AMR][1000 genomes];0.90[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2957743	0.82[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs2957745	0.80[AMR][1000 genomes];0.89[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2957746	0.85[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2957750	0.82[AMR][1000 genomes];0.89[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs3759820	0.82[AMR][1000 genomes];0.90[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs3784310	0.89[CEU][hapmap];0.93[MEX][hapmap]
rs3784313	0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4454922	0.81[EUR][1000 genomes]
rs4511483	0.82[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs4526973	0.90[AMR][1000 genomes];0.94[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs4777466	0.92[AMR][1000 genomes];0.91[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs62023343	0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6494973	1.00[CEU][hapmap];0.86[CHB][hapmap];0.88[CHD][hapmap];0.87[GIH][hapmap];0.95[JPT][hapmap];1.00[MEX][hapmap];0.97[TSI][hapmap];0.85[AMR][1000 genomes];0.95[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs6494975	0.94[CEU][hapmap];0.86[CHB][hapmap];0.82[JPT][hapmap];0.82[YRI][hapmap];0.93[AMR][1000 genomes];0.89[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs6494992	0.84[EUR][1000 genomes]
rs7162299	0.80[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs7164780	0.86[EUR][1000 genomes]
rs7173626	0.86[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs7175373	0.90[AMR][1000 genomes];0.89[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7177242	0.94[CEU][hapmap];0.86[CHB][hapmap];0.86[CHD][hapmap];0.92[GIH][hapmap];0.82[JPT][hapmap];0.86[MEX][hapmap];0.92[TSI][hapmap];0.85[YRI][hapmap];0.81[AFR][1000 genomes];0.87[AMR][1000 genomes];0.86[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7183055	0.82[AMR][1000 genomes];0.85[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs7183748	0.86[AMR][1000 genomes];0.87[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs7403191	0.87[AMR][1000 genomes];0.87[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs7496582	1.00[CEU][hapmap];0.86[CHB][hapmap];0.95[JPT][hapmap];0.85[AMR][1000 genomes];0.95[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs7497104	1.00[CEU][hapmap];0.90[CHB][hapmap];0.92[CHD][hapmap];0.97[GIH][hapmap];0.95[JPT][hapmap];1.00[TSI][hapmap];0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs8027164	0.80[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs8028115	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];0.90[JPT][hapmap];0.93[MEX][hapmap];1.00[TSI][hapmap];0.80[AMR][1000 genomes];0.86[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs8030815	0.86[EUR][1000 genomes]
rs8036307	0.94[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs8037381	0.82[EUR][1000 genomes]
rs8040216	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.89[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs8178	0.89[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[AMR][1000 genomes];0.81[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs8557	0.94[CEU][hapmap];0.91[CHB][hapmap];0.85[JPT][hapmap];0.87[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs982752	0.94[CEU][hapmap];0.86[CHB][hapmap];0.86[CHD][hapmap];0.89[GIH][hapmap];0.86[JPT][hapmap];0.89[LWK][hapmap];1.00[MEX][hapmap];0.89[MKK][hapmap];0.95[TSI][hapmap];0.93[YRI][hapmap];0.87[AFR][1000 genomes];0.93[AMR][1000 genomes];0.91[EUR][1000 genomes];0.83[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:11 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv904334	chr15:71737376-72177659	Strong transcription Active TSS Enhancers Weak transcription Flanking Bivalent TSS/Enh Genic enhancers ZNF genes & repeats Flanking Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases
2	nsv1036938	chr15:71948106-72272855	Weak transcription Strong transcription Flanking Active TSS ZNF genes & repeats Enhancers Genic enhancers Active TSS 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 target site	11 gene(s)	inside rSNPs	diseases
3	esv3331306	chr15:72049818-72427559	Strong transcription ZNF genes & repeats Active TSS Weak transcription Enhancers Flanking Active TSS Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	34 gene(s)	inside rSNPs	diseases
4	esv3433206	chr15:72049838-72427529	Enhancers Strong transcription Weak transcription Flanking Active TSS ZNF genes & repeats Active TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	34 gene(s)	inside rSNPs	diseases
5	nsv569906	chr15:72126034-72218036	Strong transcription Weak transcription Active TSS Enhancers ZNF genes & repeats Genic enhancers Flanking Active TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	3 gene(s)	inside rSNPs	diseases
6	nsv516871	chr15:72126034-72325595	Weak transcription Strong transcription Active TSS ZNF genes & repeats Enhancers Genic enhancers Flanking Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	5 gene(s)	inside rSNPs	diseases
7	nsv1042740	chr15:72128799-72482239	Weak transcription Enhancers Strong transcription Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Active TSS Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	30 gene(s)	inside rSNPs	diseases
8	nsv542426	chr15:72128799-72482239	Flanking Active TSS Strong transcription Weak transcription Enhancers Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Active TSS Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	30 gene(s)	inside rSNPs	diseases
9	nsv904336	chr15:72145937-72329906	Strong transcription Weak transcription Enhancers ZNF genes & repeats Active TSS Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	5 gene(s)	inside rSNPs	diseases
10	nsv569907	chr15:72154000-72215065	Weak transcription Strong transcription Enhancers Active TSS ZNF genes & repeats Genic enhancers Flanking Active TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	2 gene(s)	inside rSNPs	diseases
11	nsv569908	chr15:72154000-72218036	Weak transcription Strong transcription Enhancers ZNF genes & repeats Active TSS Flanking Active TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	2 gene(s)	inside rSNPs	diseases

mRNA abundance (count:7)

SNP	Gene	Cis/trans	Tissue	Source
rs9302260	PARP6	cis	lymphoblastoid	seeQTL
rs9302260	SENP8	cis	cerebellum	SCAN
rs9302260	TIPIN	cis	parietal	SCAN
rs9302260	PARP6	cis	parietal	SCAN
rs9302260	TPK1	trans	lymphoblastoid	seeQTL
rs9302260	MYO9A	Cis_1M	lymphoblastoid	RTeQTL
rs9302260	AAGAB	cis	cerebellum	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:72114600-72190600	Weak transcription	Pancreas	Pancrea
2	chr15:72122200-72189400	Weak transcription	Right Ventricle	heart
3	chr15:72122400-72195000	Weak transcription	NHEK	skin
4	chr15:72122600-72185200	Weak transcription	Esophagus	oesophagus
5	chr15:72122600-72195800	Weak transcription	Gastric	stomach
6	chr15:72131800-72192800	Weak transcription	Primary T helper naive cells from peripheral blood	blood
7	chr15:72142600-72183400	Weak transcription	Brain Angular Gyrus	brain
8	chr15:72142600-72189600	Weak transcription	NHLF	lung
9	chr15:72142600-72199200	Weak transcription	Hela-S3	cervix
10	chr15:72142800-72176000	Weak transcription	HUES48 Cell Line	embryonic stem cell
11	chr15:72142800-72184800	Weak transcription	A549	lung
12	chr15:72142800-72190200	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
13	chr15:72143000-72190600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
14	chr15:72143000-72190600	Weak transcription	Colonic Mucosa	Colon
15	chr15:72144600-72223400	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
16	chr15:72145400-72190600	Weak transcription	Spleen	Spleen
17	chr15:72145600-72182800	Weak transcription	Brain Cingulate Gyrus	brain
18	chr15:72145600-72184800	Weak transcription	Lung	lung
19	chr15:72149200-72186000	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
20	chr15:72153200-72189600	Weak transcription	Rectal Smooth Muscle	rectum
21	chr15:72160800-72177000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
22	chr15:72161000-72211000	Weak transcription	Small Intestine	intestine
23	chr15:72162600-72187600	Strong transcription	Placenta	Placenta
24	chr15:72164000-72190600	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
25	chr15:72164000-72190600	Weak transcription	Aorta	Aorta
26	chr15:72164000-72218400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
27	chr15:72165400-72190800	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
28	chr15:72166200-72181800	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
29	chr15:72166800-72175600	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
30	chr15:72167000-72197800	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
31	chr15:72167200-72175400	Weak transcription	GM12878-XiMat	blood
32	chr15:72167600-72181600	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
33	chr15:72168400-72176000	Strong transcription	Fetal Muscle Trunk	muscle
34	chr15:72168800-72176600	Strong transcription	Primary T helper cells fromperipheralblood	blood
35	chr15:72168800-72180400	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
36	chr15:72168800-72190800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
37	chr15:72169000-72180400	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
38	chr15:72169600-72176000	Strong transcription	Fetal Lung	lung
39	chr15:72169600-72176000	Strong transcription	Skeletal Muscle Female	skeletal muscle
40	chr15:72169800-72175000	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
41	chr15:72169800-72176000	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
42	chr15:72169800-72176000	Strong transcription	Stomach Smooth Muscle	stomach
43	chr15:72169800-72176200	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
44	chr15:72169800-72176200	Strong transcription	Osteobl	bone
45	chr15:72170000-72176000	Strong transcription	Fetal Brain Female	brain
46	chr15:72170000-72176800	Strong transcription	Breast Myoepithelial Primary Cells	Breast
47	chr15:72170200-72194000	Weak transcription	Fetal Intestine Small	intestine
48	chr15:72170400-72174800	Strong transcription	HSMM	muscle
49	chr15:72171200-72192600	Weak transcription	Primary T killer memory cells from peripheral blood	blood
50	chr15:72171400-72180200	Strong transcription	Rectal Mucosa Donor 31	rectum

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