Variant report

Variant	rs528713
Chromosome Location	chr1:10488555-10488556
allele	A/G
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	RAD21	chr1:10487977-10488573	MCF-7	breast:	n/a	chr1:10488302-10488309 chr1:10488292-10488311
2	RAD21	chr1:10488051-10488556	A549	lung:	n/a	chr1:10488302-10488309 chr1:10488292-10488311
3	CTCF	chr1:10487991-10488576	K562	blood:	n/a	chr1:10488289-10488310 chr1:10488294-10488312 chr1:10488295-10488311
4	RAD21	chr1:10488007-10488592	HCT-116	colon:	n/a	chr1:10488302-10488309 chr1:10488292-10488311
5	TFAP2A	chr1:10487980-10488582	Hela-S3	cervix:	n/a	chr1:10488248-10488263
6	RAD21	chr1:10487915-10488603	ECC-1	luminal epithelium:	n/a	chr1:10488302-10488309 chr1:10488292-10488311
7	CTCF	chr1:10488420-10488570	HUVEC	blood vessel:	n/a	n/a
8	RAD21	chr1:10487901-10488714	HCT-116	colon:	n/a	chr1:10488302-10488309 chr1:10488292-10488311
9	RAD21	chr1:10487886-10488587	A549	lung:	n/a	chr1:10488302-10488309 chr1:10488292-10488311
10	CTCF	chr1:10487892-10488700	A549	lung:	n/a	chr1:10488289-10488310 chr1:10488294-10488312 chr1:10488295-10488311
11	CTCF	chr1:10487872-10488721	SK-N-SH	brain:	n/a	chr1:10488289-10488310 chr1:10488294-10488312 chr1:10488295-10488311
12	CTCF	chr1:10487918-10488587	HCT-116	colon:	n/a	chr1:10488289-10488310 chr1:10488294-10488312 chr1:10488295-10488311
13	TFAP2C	chr1:10487938-10488584	Hela-S3	cervix:	n/a	n/a
14	SMC3	chr1:10487711-10488680	SK-N-SH	brain:	n/a	chr1:10488296-10488310
15	CTCF	chr1:10487918-10488595	HCT-116	colon:	n/a	chr1:10488289-10488310 chr1:10488294-10488312 chr1:10488295-10488311
16	RAD21	chr1:10487877-10488688	SK-N-SH	brain:	n/a	chr1:10488302-10488309 chr1:10488292-10488311

No.	Distal block	Cell Line	Cell type
1	chr1:10437153..10438509-chr1:10487547..10488685,4	MCF-7	breast:
2	chr1:10457794..10460664-chr1:10487844..10492697,5	K562	blood:
3	chr1:10437151..10438144-chr1:10487374..10488787,12	K562	blood:
4	chr1:10488008..10492443-chr1:10531123..10534892,8	K562	blood:
5	chr1:10483316..10484984-chr1:10487772..10489866,2	K562	blood:
6	chr1:10488255..10489166-chr1:10567048..10567550,2	MCF-7	breast:
7	chr1:9686810..9687638-chr1:10488073..10488748,2	K562	blood:
8	chr1:10269993..10270712-chr1:10488254..10488767,2	K562	blood:
9	chr1:10457794..10461321-chr1:10487053..10491931,7	K562	blood:
10	chr1:9687093..9687961-chr1:10487848..10488666,2	MCF-7	breast:

Variant related genes	Relation type
APITD1-CORT	TF binding region
APITD1	TF binding region
ENSG00000142657	Chromatin interaction
ENSG00000142655	Chromatin interaction
ENSG00000160049	Chromatin interaction

Extended variants
information (count: 52 )
Associated
traits (count: 6 )

rSNPs within LD-proxies of this variant (count:45)

rs_ID	r²[population]
rs10746494	0.92[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs11121579	0.96[CEU][hapmap];0.91[CHB][hapmap];0.86[JPT][hapmap]
rs1203122	0.87[EUR][1000 genomes]
rs12565133	0.92[CEU][hapmap];0.91[CHB][hapmap];0.85[CHD][hapmap];0.84[GIH][hapmap];0.86[JPT][hapmap];0.87[MEX][hapmap];0.82[TSI][hapmap]
rs1307485	1.00[CEU][hapmap];0.95[CHB][hapmap];0.85[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.84[MEX][hapmap];1.00[TSI][hapmap];0.84[AMR][1000 genomes];0.98[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1307487	0.89[AFR][1000 genomes];0.85[AMR][1000 genomes];0.96[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs1750349	0.87[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs1760664	0.98[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2483679	1.00[CHB][hapmap];0.98[CHD][hapmap];1.00[JPT][hapmap];0.85[TSI][hapmap]
rs2483684	0.84[AMR][1000 genomes];0.98[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2781233	0.96[CEU][hapmap];0.81[CHD][hapmap];0.91[GIH][hapmap];0.82[JPT][hapmap];0.87[MEX][hapmap];0.93[TSI][hapmap];0.86[EUR][1000 genomes]
rs36013615	0.90[EUR][1000 genomes]
rs475549	0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs481571	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs491880	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.87[GIH][hapmap];1.00[JPT][hapmap];0.96[MEX][hapmap];0.98[TSI][hapmap];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs505141	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.96[MEX][hapmap];1.00[TSI][hapmap];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs517241	0.95[AMR][1000 genomes];0.92[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs519472	0.99[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs520964	0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs522029	0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs522280	0.99[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs524150	0.84[AMR][1000 genomes];1.00[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs579398	0.95[ASN][1000 genomes]
rs583515	0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs585703	0.98[ASN][1000 genomes]
rs586096	0.87[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs586223	0.96[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.84[MEX][hapmap];1.00[TSI][hapmap];0.83[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs597441	0.96[CEU][hapmap];0.89[GIH][hapmap];0.81[TSI][hapmap];0.85[EUR][1000 genomes]
rs628462	0.86[CHB][hapmap];0.83[JPT][hapmap]
rs632690	0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs634358	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.91[GIH][hapmap];1.00[JPT][hapmap];0.97[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs643400	0.89[EUR][1000 genomes]
rs649101	0.96[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.96[MEX][hapmap];1.00[TSI][hapmap];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs649639	0.86[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs655271	0.80[EUR][1000 genomes]
rs666583	0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs667366	0.93[AMR][1000 genomes];0.90[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs670666	0.96[CEU][hapmap];0.91[CHB][hapmap];0.85[CHD][hapmap];0.86[JPT][hapmap];0.87[MEX][hapmap];0.84[TSI][hapmap]
rs672606	0.86[EUR][1000 genomes]
rs673254	0.96[CEU][hapmap]
rs678850	0.98[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs681448	0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs681495	0.93[AMR][1000 genomes];0.91[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs684016	0.92[CEU][hapmap];0.80[GIH][hapmap]
rs7548453	0.81[CEU][hapmap]

Variant overlapped rSNPs/rCNVs (count:7 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv2757722	chr1:10238070-10582554	Weak transcription Enhancers Genic enhancers Active TSS Strong transcription Flanking Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	39 gene(s)	inside rSNPs	diseases
2	esv2758920	chr1:10238070-10582554	Strong transcription Weak transcription Flanking Active TSS Enhancers ZNF genes & repeats Active TSS Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	39 gene(s)	inside rSNPs	diseases
3	nsv817370	chr1:10305470-10697150	Weak transcription Flanking Active TSS Enhancers Strong transcription Transcr. at gene 5' and 3' Active TSS Genic enhancers ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	33 gene(s)	inside rSNPs	diseases
4	nsv1008021	chr1:10363794-10802633	Strong transcription Enhancers Weak transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Flanking Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Active TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	36 gene(s)	inside rSNPs	diseases
5	esv2764192	chr1:10383734-10594186	Strong transcription Weak transcription Enhancers Bivalent Enhancer Flanking Active TSS Active TSS Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	26 gene(s)	inside rSNPs	diseases
6	nsv1003498	chr1:10445928-10607351	Weak transcription Enhancers Flanking Active TSS Genic enhancers Strong transcription Active TSS Bivalent Enhancer ZNF genes & repeats 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	26 gene(s)	inside rSNPs	diseases
7	nsv998731	chr1:10464176-10607351	Weak transcription Active TSS Strong transcription Enhancers Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	21 gene(s)	inside rSNPs	diseases

mRNA abundance (count:6)

SNP	Gene	Cis/trans	Tissue	Source
rs528713	PEX14	cis	multi-tissue	Pritchard
rs528713	APITD1	cis	cerebellum	SCAN
rs528713	KIAA2013	cis	parietal	SCAN
rs528713	NPPA	cis	cerebellum	SCAN
rs528713	PLEKHG5	cis	parietal	SCAN
rs528713	KIF1B	cis	multi-tissue	Pritchard

Chromatin state (count:125 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:10460000-10490200	Weak transcription	Psoas Muscle	Psoas
2	chr1:10461200-10490000	Weak transcription	Right Atrium	heart
3	chr1:10468800-10489800	Weak transcription	Primary T killer memory cells from peripheral blood	blood
4	chr1:10472000-10490000	Weak transcription	Stomach Mucosa	stomach
5	chr1:10475600-10489600	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
6	chr1:10475800-10490000	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
7	chr1:10477800-10490000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
8	chr1:10477800-10490000	Weak transcription	Fetal Heart	heart
9	chr1:10478200-10490000	Weak transcription	Fetal Brain Male	brain
10	chr1:10479800-10490200	Weak transcription	Placenta Amnion	Placenta Amnion
11	chr1:10480200-10490000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
12	chr1:10480200-10490000	Weak transcription	Pancreas	Pancrea
13	chr1:10480200-10490400	Weak transcription	Aorta	Aorta
14	chr1:10480400-10489600	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
15	chr1:10480400-10489800	Weak transcription	iPS-15b Cell Line	embryonic stem cell
16	chr1:10480400-10490000	Weak transcription	Colonic Mucosa	Colon
17	chr1:10480400-10490000	Weak transcription	Small Intestine	intestine
18	chr1:10480400-10490000	Weak transcription	NH-A	brain
19	chr1:10480600-10489600	Weak transcription	Primary T helper naive cells from peripheral blood	blood
20	chr1:10480600-10489800	Weak transcription	Hela-S3	cervix
21	chr1:10480800-10489200	Weak transcription	Stomach Smooth Muscle	stomach
22	chr1:10480800-10489600	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
23	chr1:10480800-10489600	Weak transcription	HUVEC	blood vessel
24	chr1:10480800-10490000	Weak transcription	Placenta	Placenta
25	chr1:10480800-10490200	Weak transcription	Left Ventricle	heart
26	chr1:10481000-10489600	Weak transcription	Primary T helper cells PMA-I stimulated	--
27	chr1:10481000-10489600	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
28	chr1:10481000-10489800	Weak transcription	Brain Inferior Temporal Lobe	brain
29	chr1:10481000-10490000	Weak transcription	Right Ventricle	heart
30	chr1:10481200-10489600	Weak transcription	Primary T helper cells fromperipheralblood	blood
31	chr1:10481200-10489800	Weak transcription	Osteobl	bone
32	chr1:10481200-10490000	Weak transcription	H1 Cell Line	embryonic stem cell
33	chr1:10481400-10490200	Weak transcription	Ovary	ovary
34	chr1:10481600-10489800	Weak transcription	Rectal Mucosa Donor 29	rectum
35	chr1:10481600-10489800	Weak transcription	HMEC	breast
36	chr1:10481600-10490000	Weak transcription	Gastric	stomach
37	chr1:10481600-10490000	Weak transcription	HSMM	muscle
38	chr1:10481800-10489600	Weak transcription	Primary T cells from cord blood	blood
39	chr1:10481800-10489800	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
40	chr1:10481800-10489800	Weak transcription	Rectal Mucosa Donor 31	rectum
41	chr1:10481800-10490000	Weak transcription	HUES6 Cell Line	embryonic stem cell
42	chr1:10481800-10490000	Weak transcription	iPS-20b Cell Line	embryonic stem cell
43	chr1:10481800-10490000	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
44	chr1:10481800-10490000	Weak transcription	HSMMtube	muscle
45	chr1:10482000-10489800	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
46	chr1:10482000-10490000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
47	chr1:10482000-10490000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
48	chr1:10482000-10490000	Weak transcription	H9 Cell Line	embryonic stem cell
49	chr1:10482000-10490000	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
50	chr1:10482000-10490000	Weak transcription	HUES64 Cell Line	embryonic stem cell

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