Variant report

Variant	rs4526973
Chromosome Location	chr15:72138719-72138720
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr15:72138309..72141068-chr15:72175580..72177408,2	MCF-7	breast:
2	chr15:72137846..72140290-chr15:72140971..72143287,2	K562	blood:

Extended variants
information (count: 86 )
Associated
traits (count: 5 )

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

rs_ID	r²[population]
rs1074330	0.83[CEU][hapmap];0.81[TSI][hapmap]
rs10851847	0.92[AMR][1000 genomes];0.90[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11633167	1.00[CEU][hapmap];0.88[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs11634608	1.00[CEU][hapmap];0.91[CHB][hapmap];0.95[CHD][hapmap];0.92[GIH][hapmap];0.89[JPT][hapmap];0.95[TSI][hapmap];0.82[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs12050794	0.88[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs12148078	0.83[EUR][1000 genomes]
rs12439494	0.94[CEU][hapmap];0.88[AMR][1000 genomes];0.90[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs12898728	0.85[AMR][1000 genomes];0.85[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs12898868	0.82[AFR][1000 genomes];0.86[AMR][1000 genomes];0.85[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs12902006	0.83[CEU][hapmap];0.81[TSI][hapmap]
rs12912771	0.90[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs12914070	0.83[CEU][hapmap];0.80[TSI][hapmap]
rs12916951	0.83[CEU][hapmap];0.81[TSI][hapmap]
rs1481862	0.85[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs16956273	0.89[CEU][hapmap];0.84[GIH][hapmap]
rs16956369	0.88[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs2054601	0.81[TSI][hapmap]
rs2128112	0.93[AMR][1000 genomes];0.92[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2306489	0.82[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs2306576	1.00[CEU][hapmap];0.91[CHB][hapmap];0.95[CHD][hapmap];0.97[GIH][hapmap];0.84[JPT][hapmap];1.00[MEX][hapmap];0.97[TSI][hapmap];0.95[AMR][1000 genomes];0.93[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2415120	1.00[ASW][hapmap];1.00[CEU][hapmap];0.86[CHB][hapmap];0.83[CHD][hapmap];0.92[GIH][hapmap];0.84[JPT][hapmap];0.90[LWK][hapmap];0.87[MEX][hapmap];0.97[MKK][hapmap];0.95[TSI][hapmap];1.00[YRI][hapmap];0.84[AFR][1000 genomes];0.95[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2415121	0.96[AMR][1000 genomes];0.92[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2415126	0.86[AFR][1000 genomes];0.95[AMR][1000 genomes];0.93[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs2415128	0.94[CEU][hapmap];0.91[CHB][hapmap];0.95[CHD][hapmap];0.92[GIH][hapmap];0.84[JPT][hapmap];0.81[MEX][hapmap];0.95[TSI][hapmap];0.85[AMR][1000 genomes];0.88[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs28650442	0.96[AMR][1000 genomes];0.92[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs28717020	0.90[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs2899775	0.80[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs2899776	0.82[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs2929508	0.93[CEU][hapmap];0.87[EUR][1000 genomes]
rs2929509	0.88[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs2929510	0.88[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs2929511	0.89[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs2929513	0.86[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs2929517	0.85[EUR][1000 genomes]
rs2929518	1.00[CEU][hapmap];0.91[CHB][hapmap];0.95[CHD][hapmap];0.92[GIH][hapmap];0.84[JPT][hapmap];0.88[MEX][hapmap];0.97[TSI][hapmap]
rs2929525	0.83[EUR][1000 genomes]
rs2929526	0.84[EUR][1000 genomes]
rs2929527	0.83[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs2929532	0.82[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs2930069	0.91[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs2957361	0.83[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs2957365	0.82[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs2957724	1.00[CEU][hapmap];0.91[CHB][hapmap];0.84[JPT][hapmap];0.80[YRI][hapmap];0.83[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs2957725	0.94[CEU][hapmap];0.82[CHD][hapmap];0.87[GIH][hapmap];0.81[MEX][hapmap];0.90[TSI][hapmap]
rs2957728	0.88[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs2957734	1.00[CEU][hapmap];0.91[CHB][hapmap];0.95[CHD][hapmap];0.92[GIH][hapmap];0.84[JPT][hapmap];0.88[MEX][hapmap];0.97[TSI][hapmap];0.82[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs2957735	1.00[CEU][hapmap];0.91[CHB][hapmap];0.95[CHD][hapmap];0.92[GIH][hapmap];0.84[JPT][hapmap];0.94[MEX][hapmap];0.97[TSI][hapmap];0.81[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs2957736	0.80[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs2957737	0.94[CEU][hapmap];0.82[CHD][hapmap];0.84[GIH][hapmap];0.81[MEX][hapmap];0.90[TSI][hapmap]
rs2957740	0.87[EUR][1000 genomes]
rs2957742	0.81[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs2957745	0.83[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs2957746	0.83[EUR][1000 genomes]
rs2957750	0.82[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs3759820	0.82[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs3784309	0.88[YRI][hapmap]
rs3784310	0.89[CEU][hapmap];0.87[MEX][hapmap]
rs3784313	0.93[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs4511483	0.88[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs4777466	0.96[AMR][1000 genomes];0.92[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs62023343	0.83[AFR][1000 genomes];0.95[AMR][1000 genomes];0.93[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs6494973	1.00[CEU][hapmap];0.83[CHD][hapmap];0.87[GIH][hapmap];0.94[MEX][hapmap];1.00[TSI][hapmap];0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs6494975	0.94[CEU][hapmap];0.86[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs7173626	0.88[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs7175373	0.90[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs7177242	0.94[CEU][hapmap];0.82[CHD][hapmap];0.87[GIH][hapmap];0.81[MEX][hapmap];0.90[TSI][hapmap];0.83[EUR][1000 genomes]
rs7183055	0.82[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs7183748	0.84[EUR][1000 genomes]
rs7403191	0.80[AMR][1000 genomes];0.84[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs7496582	1.00[CEU][hapmap];0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs7497104	1.00[CEU][hapmap];0.90[CHB][hapmap];0.87[CHD][hapmap];0.92[GIH][hapmap];0.84[JPT][hapmap];0.97[TSI][hapmap];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs8028115	0.83[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs8036307	0.89[AMR][1000 genomes];0.94[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs8040216	1.00[CEU][hapmap];0.85[CHB][hapmap];0.88[JPT][hapmap];0.81[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs8178	0.89[CEU][hapmap];0.91[CHB][hapmap];0.84[JPT][hapmap];0.85[AMR][1000 genomes];0.85[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs8557	0.94[CEU][hapmap];1.00[CHB][hapmap];0.90[JPT][hapmap];0.87[AMR][1000 genomes];0.87[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9302260	0.90[AMR][1000 genomes];0.94[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs982752	0.94[CEU][hapmap];0.82[CHD][hapmap];0.84[GIH][hapmap];0.94[MEX][hapmap];0.92[TSI][hapmap];0.91[AMR][1000 genomes];0.90[EUR][1000 genomes];0.82[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:8 , 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

mRNA abundance (count:5)

SNP	Gene	Cis/trans	Tissue	Source
rs4526973	SENP8	cis	cerebellum	SCAN
rs4526973	AAGAB	cis	cerebellum	SCAN
rs4526973	PARP6	cis	parietal	SCAN
rs4526973	TIPIN	cis	parietal	SCAN
rs4526973	MYO9A	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:116 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:72114600-72190600	Weak transcription	Pancreas	Pancrea
2	chr15:72115800-72147000	Weak transcription	HUES6 Cell Line	embryonic stem cell
3	chr15:72116000-72140800	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
4	chr15:72116000-72142000	Weak transcription	Hela-S3	cervix
5	chr15:72116400-72147000	Weak transcription	Pancreatic Islets	Pancreatic Islet
6	chr15:72117000-72142800	Weak transcription	Stomach Mucosa	stomach
7	chr15:72119200-72171800	Weak transcription	Psoas Muscle	Psoas
8	chr15:72119400-72142400	Weak transcription	Fetal Thymus	thymus
9	chr15:72119600-72139000	Weak transcription	iPS-20b Cell Line	embryonic stem cell
10	chr15:72119800-72140800	Weak transcription	HUES48 Cell Line	embryonic stem cell
11	chr15:72119800-72142200	Weak transcription	Spleen	Spleen
12	chr15:72120200-72139000	Weak transcription	Primary monocytes fromperipheralblood	blood
13	chr15:72120400-72142400	Weak transcription	GM12878-XiMat	blood
14	chr15:72120600-72139800	Weak transcription	HMEC	breast
15	chr15:72120600-72147400	Weak transcription	Small Intestine	intestine
16	chr15:72120800-72142200	Weak transcription	Colonic Mucosa	Colon
17	chr15:72122200-72139000	Weak transcription	Fetal Brain Male	brain
18	chr15:72122200-72189400	Weak transcription	Right Ventricle	heart
19	chr15:72122400-72139200	Weak transcription	Fetal Brain Female	brain
20	chr15:72122400-72140200	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
21	chr15:72122400-72141800	Weak transcription	NH-A	brain
22	chr15:72122400-72142200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
23	chr15:72122400-72195000	Weak transcription	NHEK	skin
24	chr15:72122600-72139000	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
25	chr15:72122600-72139000	Weak transcription	Brain Angular Gyrus	brain
26	chr15:72122600-72139600	Weak transcription	Duodenum Mucosa	Duodenum
27	chr15:72122600-72140800	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
28	chr15:72122600-72140800	Weak transcription	Brain Substantia Nigra	brain
29	chr15:72122600-72141000	Weak transcription	Primary hematopoietic stem cells	blood
30	chr15:72122600-72141200	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
31	chr15:72122600-72142200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
32	chr15:72122600-72142200	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
33	chr15:72122600-72142200	Weak transcription	Lung	lung
34	chr15:72122600-72144600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
35	chr15:72122600-72145600	Weak transcription	Thymus	Thymus
36	chr15:72122600-72171800	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
37	chr15:72122600-72185200	Weak transcription	Esophagus	oesophagus
38	chr15:72122600-72195800	Weak transcription	Gastric	stomach
39	chr15:72122800-72139200	Weak transcription	Brain Hippocampus Middle	brain
40	chr15:72122800-72139600	Weak transcription	A549	lung
41	chr15:72122800-72139800	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
42	chr15:72122800-72141400	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
43	chr15:72122800-72142200	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
44	chr15:72123000-72139600	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
45	chr15:72124000-72139600	Weak transcription	Fetal Intestine Large	intestine
46	chr15:72124800-72145800	Weak transcription	Fetal Heart	heart
47	chr15:72129200-72148000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
48	chr15:72131200-72148200	Strong transcription	Placenta	Placenta
49	chr15:72131600-72147000	Strong transcription	Fetal Muscle Leg	muscle
50	chr15:72131800-72192800	Weak transcription	Primary T helper naive cells from peripheral blood	blood

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