Variant report

Variant	rs2054601
Chromosome Location	chr15:72184968-72184969
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	chr15:72183241..72185017-chr15:72188166..72190098,2	MCF-7	breast:

Extended variants
information (count: 130 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:118)

rs_ID	r²[population]
rs10518979	0.95[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1074330	0.94[CEU][hapmap];0.95[CHB][hapmap];0.98[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[TSI][hapmap];0.95[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs11072338	0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs11072339	0.84[CEU][hapmap];0.90[CHB][hapmap];1.00[JPT][hapmap];0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs11072346	0.87[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs11852789	0.95[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs11853268	0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12050895	0.84[AMR][1000 genomes];0.88[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs12439494	0.83[CEU][hapmap]
rs12439900	0.86[AMR][1000 genomes];0.92[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs12591426	0.86[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs12592044	0.86[EUR][1000 genomes]
rs12592364	0.95[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs12593134	0.95[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs12593908	0.85[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs12595228	0.95[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs12595464	0.95[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs12899485	0.97[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs12901580	0.91[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs12901886	0.89[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs12902006	0.94[CEU][hapmap];0.95[CHB][hapmap];0.98[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[TSI][hapmap];0.95[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs12903484	0.86[AMR][1000 genomes];0.95[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs12903980	0.99[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs12906711	0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12908300	0.85[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs12908882	0.81[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs12911154	0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12913042	0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12914070	0.84[ASW][hapmap];0.94[CEU][hapmap];0.95[CHB][hapmap];0.98[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[TSI][hapmap];0.94[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs12916694	0.95[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs12916951	0.94[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.86[LWK][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.86[AMR][1000 genomes];0.95[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs12917428	0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1384007	0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1481860	0.81[EUR][1000 genomes]
rs1481861	0.82[EUR][1000 genomes]
rs16956241	0.86[EUR][1000 genomes]
rs16956302	0.90[EUR][1000 genomes]
rs16956328	0.98[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs16956381	0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs16956444	0.84[AMR][1000 genomes];0.95[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs16956452	0.95[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2035379	0.95[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2200056	0.95[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2246225	0.92[ASW][hapmap];0.80[CEU][hapmap];0.95[CHB][hapmap];0.88[CHD][hapmap];0.94[GIH][hapmap];0.94[JPT][hapmap];0.81[ASN][1000 genomes]
rs2279283	0.92[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2291278	0.91[CHB][hapmap];0.89[JPT][hapmap]
rs2306488	0.95[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2306490	0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2306576	0.83[TSI][hapmap]
rs2415128	0.82[MEX][hapmap];0.85[TSI][hapmap]
rs2415130	0.88[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2625529	0.81[CHB][hapmap];0.85[GIH][hapmap]
rs2625530	0.90[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs2723342	0.81[EUR][1000 genomes]
rs2723343	0.84[ASW][hapmap];0.80[CEU][hapmap];0.91[CHB][hapmap];0.82[CHD][hapmap];0.87[GIH][hapmap];0.94[JPT][hapmap];0.81[TSI][hapmap];0.80[EUR][1000 genomes]
rs2723356	0.81[EUR][1000 genomes]
rs2742323	0.87[CEU][hapmap];0.95[CHB][hapmap];0.84[CHD][hapmap];0.90[GIH][hapmap];0.94[JPT][hapmap];0.89[TSI][hapmap];0.90[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs2899773	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2929518	0.83[TSI][hapmap]
rs2929528	0.81[EUR][1000 genomes]
rs2957373	0.83[CEU][hapmap]
rs2957725	0.83[CEU][hapmap];0.82[MEX][hapmap];0.90[TSI][hapmap];0.81[EUR][1000 genomes]
rs2957734	0.82[CEU][hapmap];0.83[TSI][hapmap]
rs2957735	0.83[TSI][hapmap]
rs2957737	0.83[CEU][hapmap];0.82[MEX][hapmap];0.90[TSI][hapmap];0.81[EUR][1000 genomes]
rs34085279	0.83[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs34137768	0.94[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs34189331	0.80[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs34514871	0.94[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs35021156	0.94[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs35115747	0.95[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs35167572	0.92[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs35186252	0.91[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs35258998	0.82[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs35673773	0.87[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs3784309	0.80[CEU][hapmap];0.87[GIH][hapmap];0.82[JPT][hapmap];0.86[MEX][hapmap]
rs4131630	0.92[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs4238447	0.90[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs4238449	0.82[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs4411469	0.81[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs4445848	0.92[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs4776579	0.85[AMR][1000 genomes];0.90[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs4776581	0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4776584	0.95[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs4776586	0.85[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs4777464	0.84[AMR][1000 genomes];0.90[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs4777467	0.87[EUR][1000 genomes]
rs4777469	0.91[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4777471	0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4777474	0.95[ASN][1000 genomes]
rs4777477	0.95[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4777478	0.95[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4777480	0.86[AMR][1000 genomes];0.94[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs4777484	0.92[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs4777489	0.82[ASN][1000 genomes]
rs55854204	0.85[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs62023342	0.99[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs62025574	0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6494973	0.81[TSI][hapmap]
rs6494975	0.83[CEU][hapmap]
rs71395051	0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7170461	0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7170754	0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7172309	0.92[ASW][hapmap];0.94[CEU][hapmap];0.95[CHB][hapmap];0.98[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[TSI][hapmap];0.92[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs7177242	0.83[CEU][hapmap];0.82[MEX][hapmap];0.90[TSI][hapmap];0.85[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs7183748	0.84[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs7183749	0.92[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs7403191	0.83[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs7497104	0.83[TSI][hapmap]
rs8025504	0.86[AMR][1000 genomes];0.95[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs8028115	0.83[TSI][hapmap]
rs8028532	0.92[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs8032038	0.92[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs8747	0.80[CEU][hapmap];0.91[CHB][hapmap];0.97[GIH][hapmap];0.89[JPT][hapmap]
rs9120	0.87[CEU][hapmap];0.90[CHB][hapmap];0.88[JPT][hapmap];0.83[EUR][1000 genomes]
rs972028	0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs972029	0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs982752	0.83[CEU][hapmap];0.87[TSI][hapmap]

Variant overlapped rSNPs/rCNVs (count:12 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	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
2	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
3	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
4	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
5	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
6	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
7	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
8	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
9	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
10	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
11	nsv457195	chr15:72177659-72250741	Weak transcription Strong transcription Enhancers ZNF genes & repeats Genic enhancers Active TSS Flanking Active TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	2 gene(s)	inside rSNPs	diseases
12	nsv569909	chr15:72177659-72250741	Strong transcription Weak transcription Enhancers ZNF genes & repeats Genic enhancers Active TSS Flanking Active TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	2 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs2054601	PARP6	cis	parietal	SCAN
rs2054601	MYO9A	Cis_1M	lymphoblastoid	RTeQTL
rs2054601	SENP8	cis	cerebellum	SCAN
rs2054601	TIPIN	cis	parietal	SCAN

Chromatin state (count:114 , 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	chr15:72142600-72189600	Weak transcription	NHLF	lung
8	chr15:72142600-72199200	Weak transcription	Hela-S3	cervix
9	chr15:72142800-72190200	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
10	chr15:72143000-72190600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
11	chr15:72143000-72190600	Weak transcription	Colonic Mucosa	Colon
12	chr15:72144600-72223400	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
13	chr15:72145400-72190600	Weak transcription	Spleen	Spleen
14	chr15:72149200-72186000	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
15	chr15:72153200-72189600	Weak transcription	Rectal Smooth Muscle	rectum
16	chr15:72161000-72211000	Weak transcription	Small Intestine	intestine
17	chr15:72162600-72187600	Strong transcription	Placenta	Placenta
18	chr15:72164000-72190600	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
19	chr15:72164000-72190600	Weak transcription	Aorta	Aorta
20	chr15:72164000-72218400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
21	chr15:72165400-72190800	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
22	chr15:72167000-72197800	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
23	chr15:72168800-72190800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
24	chr15:72170200-72194000	Weak transcription	Fetal Intestine Small	intestine
25	chr15:72171200-72192600	Weak transcription	Primary T killer memory cells from peripheral blood	blood
26	chr15:72172400-72192000	Weak transcription	Thymus	Thymus
27	chr15:72172600-72185200	Weak transcription	Cortex derived primary cultured neurospheres	brain
28	chr15:72172600-72190200	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
29	chr15:72172800-72186000	Weak transcription	Muscle Satellite Cultured Cells	--
30	chr15:72172800-72190000	Weak transcription	Duodenum Mucosa	Duodenum
31	chr15:72172800-72190800	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
32	chr15:72172800-72190800	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
33	chr15:72173000-72190000	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
34	chr15:72173000-72200600	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
35	chr15:72173200-72190000	Weak transcription	HUVEC	blood vessel
36	chr15:72173200-72190600	Weak transcription	Dnd41	blood
37	chr15:72174800-72189800	Weak transcription	Fetal Brain Male	brain
38	chr15:72175400-72185200	Weak transcription	Sigmoid Colon	Sigmoid Colon
39	chr15:72175400-72185400	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
40	chr15:72175600-72185200	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
41	chr15:72175600-72185200	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
42	chr15:72175600-72190200	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
43	chr15:72175600-72190200	Weak transcription	Placenta Amnion	Placenta Amnion
44	chr15:72176000-72189600	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
45	chr15:72176000-72189800	Weak transcription	Skeletal Muscle Male	skeletal muscle
46	chr15:72176000-72190000	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
47	chr15:72176000-72193400	Weak transcription	Psoas Muscle	Psoas
48	chr15:72176200-72185200	Weak transcription	Primary hematopoietic stem cells short term culture	blood
49	chr15:72176200-72185200	Weak transcription	Fetal Stomach	stomach
50	chr15:72177400-72192400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived

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