Variant report

Variant	rs17751682
Chromosome Location	chr6:56560530-56560531
allele	C/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	JUND	chr6:56560388-56560978	SK-N-SH	brain:	n/a	chr6:56560676-56560688 chr6:56560686-56560697 chr6:56560677-56560687 chr6:56560678-56560686 chr6:56560677-56560687 chr6:56560677-56560687
2	FOSL2	chr6:56560360-56560948	A549	lung:	n/a	chr6:56560676-56560688 chr6:56560686-56560697 chr6:56560677-56560687 chr6:56560678-56560686 chr6:56560677-56560687 chr6:56560677-56560687
3	EP300	chr6:56560301-56560895	SK-N-SH_RA	brain:	n/a	n/a
4	FOS	chr6:56560520-56560810	MCF10A-Er-Src	breast:	n/a	chr6:56560676-56560688 chr6:56560686-56560697 chr6:56560676-56560687 chr6:56560677-56560687 chr6:56560678-56560686 chr6:56560677-56560687 chr6:56560677-56560687
5	TCF12	chr6:56560213-56561000	SK-N-SH	brain:	n/a	n/a
6	JUND	chr6:56560368-56560976	SK-N-SH	brain:	n/a	chr6:56560676-56560688 chr6:56560686-56560697 chr6:56560677-56560687 chr6:56560678-56560686 chr6:56560677-56560687 chr6:56560677-56560687
7	GATA3	chr6:56560173-56561066	SK-N-SH	brain:	n/a	chr6:56560745-56560761 chr6:56560748-56560758 chr6:56560679-56560688 chr6:56560749-56560756 chr6:56560749-56560756 chr6:56560695-56560708 chr6:56560742-56560763 chr6:56560749-56560756
8	GATA3	chr6:56560126-56561051	SK-N-SH	brain:	n/a	chr6:56560745-56560761 chr6:56560748-56560758 chr6:56560679-56560688 chr6:56560749-56560756 chr6:56560749-56560756 chr6:56560695-56560708 chr6:56560742-56560763 chr6:56560749-56560756
9	FOSL2	chr6:56560383-56560978	SK-N-SH	brain:	n/a	chr6:56560676-56560688 chr6:56560686-56560697 chr6:56560677-56560687 chr6:56560678-56560686 chr6:56560677-56560687 chr6:56560677-56560687
10	MAFF	chr6:56560465-56560822	K562	blood:	n/a	n/a
11	PBX3	chr6:56560431-56560918	SK-N-SH	brain:	n/a	n/a
12	NFIC	chr6:56560372-56560986	SK-N-SH	brain:	n/a	n/a
13	MAFK	chr6:56560525-56560821	IMR90	lung:	n/a	n/a
14	TCF12	chr6:56560343-56560985	SK-N-SH	brain:	n/a	n/a
15	GATA3	chr6:56560379-56560966	A549	lung:	n/a	chr6:56560745-56560761 chr6:56560748-56560758 chr6:56560679-56560688 chr6:56560749-56560756 chr6:56560749-56560756 chr6:56560695-56560708 chr6:56560742-56560763 chr6:56560749-56560756
16	EP300	chr6:56560524-56560870	Hela-S3	cervix:	n/a	n/a
17	PBX3	chr6:56560274-56560924	SK-N-SH	brain:	n/a	n/a
18	FOS	chr6:56560512-56560855	MCF10A-Er-Src	breast:	n/a	chr6:56560676-56560688 chr6:56560686-56560697 chr6:56560676-56560687 chr6:56560677-56560687 chr6:56560678-56560686 chr6:56560677-56560687 chr6:56560677-56560687
19	FOS	chr6:56560476-56560774	MCF10A-Er-Src	breast:	n/a	chr6:56560676-56560688 chr6:56560686-56560697 chr6:56560676-56560687 chr6:56560677-56560687 chr6:56560678-56560686 chr6:56560677-56560687 chr6:56560677-56560687
20	EP300	chr6:56560374-56561049	SK-N-SH	brain:	n/a	n/a
21	POLR2A	chr6:56560472-56560882	SK-N-SH	brain:	n/a	n/a
22	FOS	chr6:56560475-56560830	HUVEC	blood vessel:	n/a	chr6:56560676-56560688 chr6:56560686-56560697 chr6:56560676-56560687 chr6:56560677-56560687 chr6:56560678-56560686 chr6:56560677-56560687 chr6:56560677-56560687

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr2:113506967..113507634-chr6:56560436..56561222,2	MCF-7	breast:
2	chr6:56559575..56561733-chr6:56563230..56565614,2	MCF-7	breast:

Variant related genes	Relation type
DST	TF binding region

Extended variants
information (count: 104 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:100)

rs_ID	r²[population]
rs1024195	1.00[LWK][hapmap]
rs10498811	1.00[CEU][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs11961141	0.83[EUR][1000 genomes]
rs11961342	0.85[EUR][1000 genomes]
rs11968575	0.85[GIH][hapmap];0.81[MEX][hapmap];0.94[TSI][hapmap];0.83[EUR][1000 genomes]
rs11970648	0.81[MEX][hapmap]
rs13191164	1.00[EUR][1000 genomes]
rs13192037	1.00[CEU][hapmap];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs13192478	0.83[EUR][1000 genomes]
rs13192567	0.83[EUR][1000 genomes]
rs13196211	1.00[CEU][hapmap];1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs13198399	0.83[EUR][1000 genomes]
rs13198938	0.83[EUR][1000 genomes]
rs13200166	0.88[MEX][hapmap]
rs13203000	0.83[EUR][1000 genomes]
rs13205013	1.00[EUR][1000 genomes]
rs13206849	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs13207768	0.89[MEX][hapmap]
rs13210876	0.83[EUR][1000 genomes]
rs13213878	0.83[EUR][1000 genomes]
rs13217390	0.83[EUR][1000 genomes]
rs13218913	0.89[MEX][hapmap]
rs13219546	0.83[EUR][1000 genomes]
rs13219942	0.85[EUR][1000 genomes]
rs16888118	1.00[EUR][1000 genomes]
rs16888124	1.00[EUR][1000 genomes]
rs16888126	0.97[EUR][1000 genomes]
rs16888128	0.98[EUR][1000 genomes]
rs16888130	1.00[CEU][hapmap];0.98[EUR][1000 genomes]
rs16888133	0.97[EUR][1000 genomes]
rs16888135	0.83[EUR][1000 genomes]
rs17684511	0.98[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs17684553	1.00[CEU][hapmap];0.89[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs17684571	0.89[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs17684802	0.89[MEX][hapmap]
rs17751695	1.00[CEU][hapmap];0.87[GIH][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2967960	0.82[EUR][1000 genomes]
rs2967963	0.81[EUR][1000 genomes]
rs3002003	0.83[EUR][1000 genomes]
rs3002004	0.83[EUR][1000 genomes]
rs3002006	0.83[EUR][1000 genomes]
rs3002007	0.81[EUR][1000 genomes]
rs3002008	0.83[EUR][1000 genomes]
rs3002009	0.83[EUR][1000 genomes]
rs3002010	0.83[EUR][1000 genomes]
rs3002011	0.83[EUR][1000 genomes]
rs34138864	1.00[EUR][1000 genomes]
rs34429594	0.84[EUR][1000 genomes]
rs34455199	0.83[EUR][1000 genomes]
rs34465210	0.83[EUR][1000 genomes]
rs34566275	0.83[EUR][1000 genomes]
rs34576803	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs34587484	0.83[EUR][1000 genomes]
rs34623351	0.83[EUR][1000 genomes]
rs34724718	1.00[EUR][1000 genomes]
rs34803237	0.83[EUR][1000 genomes]
rs34812826	0.83[EUR][1000 genomes]
rs34824960	0.83[EUR][1000 genomes]
rs34832779	0.82[EUR][1000 genomes]
rs35206656	0.98[EUR][1000 genomes]
rs35326806	0.85[EUR][1000 genomes]
rs35408048	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs35494794	0.85[EUR][1000 genomes]
rs35619924	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs35637749	1.00[EUR][1000 genomes]
rs35668437	0.98[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs35687635	0.98[EUR][1000 genomes]
rs35876418	0.83[EUR][1000 genomes]
rs35920751	0.83[EUR][1000 genomes]
rs36068365	0.85[EUR][1000 genomes]
rs4072271	0.98[EUR][1000 genomes]
rs4073960	0.95[EUR][1000 genomes]
rs4074101	1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs4074102	1.00[CEU][hapmap];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs4074103	0.94[CEU][hapmap];0.97[EUR][1000 genomes]
rs41267675	0.83[EUR][1000 genomes]
rs4262190	0.91[EUR][1000 genomes]
rs4275049	0.83[EUR][1000 genomes]
rs4299824	0.89[MEX][hapmap]
rs4415160	0.89[MEX][hapmap]
rs4640889	0.83[EUR][1000 genomes]
rs5024547	1.00[CEU][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs55742092	0.89[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs56101897	0.98[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs59085778	0.83[EUR][1000 genomes]
rs59247267	0.83[EUR][1000 genomes]
rs60498201	0.83[EUR][1000 genomes]
rs62412526	0.86[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs62412528	0.98[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs62412531	0.98[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs62412532	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs62412556	0.83[EUR][1000 genomes]
rs6901176	1.00[EUR][1000 genomes]
rs6924375	1.00[CEU][hapmap];1.00[EUR][1000 genomes]
rs6926134	0.83[EUR][1000 genomes]
rs6938003	0.82[EUR][1000 genomes]
rs71564848	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs71564849	1.00[AFR][1000 genomes];0.87[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs7761501	0.89[MEX][hapmap]
rs7767128	1.00[CEU][hapmap];1.00[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv491933	chr6:56177722-57171010	Active TSS Enhancers Strong transcription Weak transcription Genic enhancers Flanking Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	51 gene(s)	inside rSNPs	diseases
2	nsv934026	chr6:56382056-57184218	Flanking Bivalent TSS/Enh Strong transcription Weak transcription Enhancers Transcr. at gene 5' and 3' Flanking Active TSS Genic enhancers Bivalent/Poised TSS Active TSS ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	49 gene(s)	inside rSNPs	diseases
3	nsv533050	chr6:56504480-57297586	Active TSS Enhancers Weak transcription Strong transcription Genic enhancers Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	44 gene(s)	inside rSNPs	diseases
4	nsv432888	chr6:56507489-56560764	Weak transcription Flanking Active TSS Strong transcription Genic enhancers Enhancers Transcr. at gene 5' and 3' Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs17751682	BMP5	cis	cerebellum	SCAN
rs17751682	LRRC1	cis	cerebellum	SCAN
rs17751682	DST	cis	cerebellum	SCAN

Chromatin state (count:74 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:56546200-56564800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
2	chr6:56547400-56561600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
3	chr6:56549600-56573600	Weak transcription	iPS-18 Cell Line	embryonic stem cell
4	chr6:56549800-56578000	Weak transcription	Gastric	stomach
5	chr6:56554000-56560600	Weak transcription	Placenta Amnion	Placenta Amnion
6	chr6:56554000-56574600	Weak transcription	iPS-15b Cell Line	embryonic stem cell
7	chr6:56555400-56574600	Weak transcription	H1 Cell Line	embryonic stem cell
8	chr6:56555800-56561200	Enhancers	HUVEC	blood vessel
9	chr6:56555800-56561800	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
10	chr6:56555800-56573600	Weak transcription	HUES48 Cell Line	embryonic stem cell
11	chr6:56556000-56568400	Weak transcription	HUES6 Cell Line	embryonic stem cell
12	chr6:56556200-56573600	Weak transcription	iPS-20b Cell Line	embryonic stem cell
13	chr6:56556200-56574400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
14	chr6:56556400-56561800	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
15	chr6:56556400-56568000	Weak transcription	HUES64 Cell Line	embryonic stem cell
16	chr6:56558200-56561200	Weak transcription	Left Ventricle	heart
17	chr6:56558200-56561800	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
18	chr6:56558200-56562000	Weak transcription	H9 Cell Line	embryonic stem cell
19	chr6:56558200-56563400	Weak transcription	Primary monocytes fromperipheralblood	blood
20	chr6:56558200-56563600	Weak transcription	Monocytes-CD14+_RO01746	blood
21	chr6:56558200-56569800	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
22	chr6:56558200-56573400	Weak transcription	Stomach Mucosa	stomach
23	chr6:56558200-56578200	Weak transcription	Aorta	Aorta
24	chr6:56558400-56561000	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
25	chr6:56558400-56561000	Enhancers	Hela-S3	cervix
26	chr6:56558400-56561200	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
27	chr6:56558400-56561800	Weak transcription	Breast Myoepithelial Primary Cells	Breast
28	chr6:56558400-56561800	Weak transcription	Psoas Muscle	Psoas
29	chr6:56558400-56561800	Weak transcription	Skeletal Muscle Female	skeletal muscle
30	chr6:56558400-56562200	Weak transcription	Skeletal Muscle Male	skeletal muscle
31	chr6:56558400-56562400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
32	chr6:56558400-56563400	Weak transcription	Brain Angular Gyrus	brain
33	chr6:56558400-56563600	Weak transcription	Cortex derived primary cultured neurospheres	brain
34	chr6:56558400-56563600	Weak transcription	Stomach Smooth Muscle	stomach
35	chr6:56558400-56566400	Weak transcription	Colon Smooth Muscle	Colon
36	chr6:56558400-56567000	Weak transcription	Duodenum Smooth Muscle	Duodenum
37	chr6:56558400-56571600	Weak transcription	Fetal Stomach	stomach
38	chr6:56558400-56573200	Weak transcription	Adipose Nuclei	Adipose
39	chr6:56558400-56577800	Weak transcription	Ovary	ovary
40	chr6:56558400-56579400	Weak transcription	Right Ventricle	heart
41	chr6:56558600-56561000	Enhancers	Muscle Satellite Cultured Cells	--
42	chr6:56558600-56562000	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
43	chr6:56558600-56566400	Weak transcription	Rectal Smooth Muscle	rectum
44	chr6:56558600-56577800	Weak transcription	Fetal Heart	heart
45	chr6:56559200-56560600	Enhancers	Fetal Intestine Large	intestine
46	chr6:56559200-56563000	Genic enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
47	chr6:56559400-56560600	Enhancers	HMEC	breast
48	chr6:56559400-56562000	Genic enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
49	chr6:56559400-56563000	Strong transcription	HSMMtube	muscle
50	chr6:56559400-56563800	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell

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