Variant report

Variant	rs6494973
Chromosome Location	chr15:72145728-72145729
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	MAFK	chr15:72145454-72145742	HepG2	liver:	n/a	n/a

Variant related genes	Relation type
MYO9A	TF binding region

Extended variants
information (count: 94 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:86)

rs_ID	r²[population]
rs1074330	0.83[CEU][hapmap];0.81[TSI][hapmap]
rs10851847	0.84[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs1109744	0.82[YRI][hapmap]
rs11633167	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.93[AFR][1000 genomes];0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs11634608	1.00[CEU][hapmap];0.87[CHB][hapmap];0.88[CHD][hapmap];0.85[GIH][hapmap];0.90[JPT][hapmap];0.95[TSI][hapmap];0.90[EUR][1000 genomes]
rs12050794	0.87[AFR][1000 genomes];0.96[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs12148078	0.85[EUR][1000 genomes]
rs12439494	0.94[CEU][hapmap];0.83[AMR][1000 genomes];0.93[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs12898728	0.85[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs12898868	0.83[AMR][1000 genomes];0.85[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs12902006	0.83[CEU][hapmap];0.81[TSI][hapmap]
rs12912771	0.87[AMR][1000 genomes];0.91[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs12914070	0.83[CEU][hapmap];0.80[TSI][hapmap]
rs12916951	0.83[CEU][hapmap];0.81[TSI][hapmap]
rs1481860	0.81[EUR][1000 genomes]
rs1481861	0.82[EUR][1000 genomes]
rs1481862	0.82[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs16956273	0.89[CEU][hapmap]
rs16956369	0.93[AFR][1000 genomes];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2054601	0.81[TSI][hapmap]
rs2128112	0.89[AMR][1000 genomes];0.96[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2306489	0.85[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs2306576	1.00[CEU][hapmap];0.87[CHB][hapmap];0.88[CHD][hapmap];0.90[GIH][hapmap];0.95[JPT][hapmap];0.94[MEX][hapmap];0.97[TSI][hapmap];0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2415120	1.00[CEU][hapmap];0.94[MEX][hapmap];0.95[TSI][hapmap];0.93[EUR][1000 genomes]
rs2415121	0.91[AMR][1000 genomes];0.93[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2415126	0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2415128	0.94[CEU][hapmap];0.87[CHB][hapmap];0.90[CHD][hapmap];0.85[GIH][hapmap];0.95[JPT][hapmap];0.88[MEX][hapmap];0.95[TSI][hapmap];0.82[AMR][1000 genomes];0.91[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs28650442	0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs28717020	0.87[AMR][1000 genomes];0.90[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2899775	0.88[EUR][1000 genomes]
rs2899776	0.91[EUR][1000 genomes]
rs2929508	0.93[CEU][hapmap];0.95[CHB][hapmap];0.94[JPT][hapmap];0.85[AMR][1000 genomes];0.89[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2929509	0.83[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs2929510	0.85[AMR][1000 genomes];0.91[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs2929511	0.84[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs2929513	0.81[AFR][1000 genomes];0.92[AMR][1000 genomes];0.89[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2929517	0.83[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs2929518	1.00[CEU][hapmap];0.87[CHB][hapmap];0.88[CHD][hapmap];0.85[GIH][hapmap];0.95[JPT][hapmap];0.94[MEX][hapmap];0.97[TSI][hapmap]
rs2929525	0.85[EUR][1000 genomes]
rs2929526	0.86[EUR][1000 genomes]
rs2929527	0.88[EUR][1000 genomes]
rs2929528	0.82[EUR][1000 genomes]
rs2929532	0.87[EUR][1000 genomes]
rs2930069	0.89[AMR][1000 genomes];0.89[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs2957361	0.87[EUR][1000 genomes]
rs2957365	0.85[EUR][1000 genomes]
rs2957368	0.81[EUR][1000 genomes]
rs2957373	0.94[CEU][hapmap]
rs2957724	1.00[CEU][hapmap];0.87[CHB][hapmap];0.95[JPT][hapmap];0.88[EUR][1000 genomes]
rs2957725	0.94[CEU][hapmap];0.88[MEX][hapmap];0.90[TSI][hapmap];0.81[EUR][1000 genomes]
rs2957728	0.85[AMR][1000 genomes];0.91[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs2957734	1.00[CEU][hapmap];0.87[CHB][hapmap];0.88[CHD][hapmap];0.85[GIH][hapmap];0.95[JPT][hapmap];0.94[MEX][hapmap];0.97[TSI][hapmap];0.90[EUR][1000 genomes]
rs2957735	1.00[CEU][hapmap];0.87[CHB][hapmap];0.88[CHD][hapmap];0.84[GIH][hapmap];0.95[JPT][hapmap];0.94[MEX][hapmap];0.97[TSI][hapmap];0.91[EUR][1000 genomes]
rs2957736	0.91[EUR][1000 genomes]
rs2957737	0.94[CEU][hapmap];0.88[MEX][hapmap];0.90[TSI][hapmap];0.81[EUR][1000 genomes]
rs2957740	0.89[EUR][1000 genomes]
rs2957742	0.89[EUR][1000 genomes]
rs2957745	0.89[EUR][1000 genomes]
rs2957746	0.85[EUR][1000 genomes]
rs2957750	0.88[EUR][1000 genomes]
rs3759820	0.89[EUR][1000 genomes]
rs3784310	0.89[ASW][hapmap];0.89[CEU][hapmap];0.86[CHD][hapmap];0.85[GIH][hapmap];0.80[JPT][hapmap];1.00[LWK][hapmap];0.94[MEX][hapmap];0.89[MKK][hapmap];1.00[YRI][hapmap];0.85[AMR][1000 genomes]
rs3784313	0.89[AMR][1000 genomes];0.95[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs4511483	0.87[AFR][1000 genomes];0.96[AMR][1000 genomes];0.92[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs4526973	0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs4777466	0.91[AMR][1000 genomes];0.93[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs62023343	0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs6494975	0.94[CEU][hapmap];0.83[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs7164780	0.83[EUR][1000 genomes]
rs7173626	0.93[AFR][1000 genomes];0.96[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs7175373	0.87[AMR][1000 genomes];0.90[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs7177242	0.94[CEU][hapmap];0.88[MEX][hapmap];0.90[TSI][hapmap];0.85[EUR][1000 genomes]
rs7183055	0.84[EUR][1000 genomes]
rs7183748	0.86[EUR][1000 genomes]
rs7402085	0.82[YRI][hapmap]
rs7403191	0.86[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs7496582	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7497104	1.00[CEU][hapmap];0.85[CHB][hapmap];0.84[GIH][hapmap];0.89[JPT][hapmap];0.97[TSI][hapmap];0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs8028115	1.00[CEU][hapmap];0.88[CHD][hapmap];0.85[GIH][hapmap];0.85[JPT][hapmap];0.94[MEX][hapmap];0.97[TSI][hapmap];0.85[EUR][1000 genomes]
rs8030815	0.83[EUR][1000 genomes]
rs8036307	0.86[AMR][1000 genomes];0.95[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs8040216	1.00[CEU][hapmap];0.85[CHB][hapmap];0.94[JPT][hapmap];0.81[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs8178	0.89[CEU][hapmap];0.86[CHB][hapmap];0.95[JPT][hapmap];0.83[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs8557	0.94[CEU][hapmap];0.85[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs9302260	0.85[AMR][1000 genomes];0.95[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs982752	0.94[CEU][hapmap];0.81[JPT][hapmap];1.00[MEX][hapmap];0.92[TSI][hapmap];0.85[AMR][1000 genomes];0.93[EUR][1000 genomes];0.83[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:4)

SNP	Gene	Cis/trans	Tissue	Source
rs6494973	AAGAB	cis	cerebellum	SCAN
rs6494973	PARP6	cis	parietal	SCAN
rs6494973	TIPIN	cis	parietal	SCAN
rs6494973	SENP8	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	chr15:72115800-72147000	Weak transcription	HUES6 Cell Line	embryonic stem cell
3	chr15:72116400-72147000	Weak transcription	Pancreatic Islets	Pancreatic Islet
4	chr15:72119200-72171800	Weak transcription	Psoas Muscle	Psoas
5	chr15:72120600-72147400	Weak transcription	Small Intestine	intestine
6	chr15:72122200-72189400	Weak transcription	Right Ventricle	heart
7	chr15:72122400-72195000	Weak transcription	NHEK	skin
8	chr15:72122600-72171800	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
9	chr15:72122600-72185200	Weak transcription	Esophagus	oesophagus
10	chr15:72122600-72195800	Weak transcription	Gastric	stomach
11	chr15:72124800-72145800	Weak transcription	Fetal Heart	heart
12	chr15:72129200-72148000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
13	chr15:72131200-72148200	Strong transcription	Placenta	Placenta
14	chr15:72131600-72147000	Strong transcription	Fetal Muscle Leg	muscle
15	chr15:72131800-72192800	Weak transcription	Primary T helper naive cells from peripheral blood	blood
16	chr15:72134000-72149000	Strong transcription	Breast Myoepithelial Primary Cells	Breast
17	chr15:72135200-72146600	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
18	chr15:72135200-72147600	Strong transcription	Primary T cells from cord blood	blood
19	chr15:72136200-72148400	Strong transcription	Primary B cells from peripheral blood	blood
20	chr15:72136200-72148400	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
21	chr15:72136200-72149000	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
22	chr15:72136400-72147000	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
23	chr15:72136400-72147000	Strong transcription	Adipose Nuclei	Adipose
24	chr15:72136400-72148400	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
25	chr15:72136600-72146600	Strong transcription	Fetal Muscle Trunk	muscle
26	chr15:72136800-72146400	Strong transcription	Duodenum Smooth Muscle	Duodenum
27	chr15:72136800-72146400	Strong transcription	Monocytes-CD14+_RO01746	blood
28	chr15:72136800-72147000	Strong transcription	Primary B cells from cord blood	blood
29	chr15:72137000-72156400	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
30	chr15:72137800-72146000	Strong transcription	Fetal Lung	lung
31	chr15:72137800-72147000	Strong transcription	Stomach Smooth Muscle	stomach
32	chr15:72138200-72146200	Strong transcription	Primary T helper cells PMA-I stimulated	--
33	chr15:72138200-72172400	Weak transcription	HUVEC	blood vessel
34	chr15:72138400-72145800	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
35	chr15:72138400-72146200	Strong transcription	Sigmoid Colon	Sigmoid Colon
36	chr15:72138400-72146200	Strong transcription	Skeletal Muscle Female	skeletal muscle
37	chr15:72138400-72146400	Strong transcription	Skeletal Muscle Male	skeletal muscle
38	chr15:72138400-72146600	Strong transcription	Primary T helper cells fromperipheralblood	blood
39	chr15:72138400-72147000	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
40	chr15:72138600-72146200	Strong transcription	Left Ventricle	heart
41	chr15:72138600-72147000	Strong transcription	Liver	Liver
42	chr15:72138800-72146200	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
43	chr15:72138800-72146800	Weak transcription	K562	blood
44	chr15:72139600-72146400	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
45	chr15:72139600-72146800	Strong transcription	Duodenum Mucosa	Duodenum
46	chr15:72140200-72171800	Weak transcription	HMEC	breast
47	chr15:72141200-72146400	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
48	chr15:72141400-72174200	Weak transcription	Fetal Brain Male	brain
49	chr15:72141600-72147000	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
50	chr15:72142000-72146400	Strong transcription	Rectal Mucosa Donor 31	rectum

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