Variant report

Variant	rs7300650
Chromosome Location	chr12:10328635-10328636
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	CTCF	chr12:10328620-10328770	HEEpiC	esophagus:	n/a	n/a
2	CTCF	chr12:10328580-10328730	HMEC	breast:	n/a	chr12:10328587-10328608 chr12:10328593-10328609 chr12:10328594-10328607
3	CTCF	chr12:10328500-10328650	GM12873	blood:	n/a	chr12:10328587-10328608 chr12:10328593-10328609 chr12:10328594-10328607
4	CTCF	chr12:10328536-10328663	LNCaP	prostate:	n/a	chr12:10328587-10328608 chr12:10328593-10328609 chr12:10328594-10328607
5	CTCF	chr12:10328560-10328710	HEEpiC	esophagus:	n/a	chr12:10328587-10328608 chr12:10328593-10328609 chr12:10328594-10328607
6	CTCF	chr12:10328500-10328650	WERI-Rb-1	eye:	n/a	chr12:10328587-10328608 chr12:10328593-10328609 chr12:10328594-10328607
7	CTCF	chr12:10328540-10328690	HMEC	breast:	n/a	chr12:10328587-10328608 chr12:10328593-10328609 chr12:10328594-10328607
8	CTCF	chr12:10328497-10328700	Hela-S3	cervix:	n/a	chr12:10328587-10328608 chr12:10328593-10328609 chr12:10328594-10328607
9	RAD21	chr12:10328444-10328756	Hela-S3	cervix:	n/a	chr12:10328590-10328609
10	CTCF	chr12:10328504-10328706	MCF-7	breast:	n/a	chr12:10328587-10328608 chr12:10328593-10328609 chr12:10328594-10328607
11	RAD21	chr12:10328479-10328799	MCF-7	breast:	n/a	chr12:10328590-10328609
12	CTCF	chr12:10328540-10328690	Caco-2	colon:	n/a	chr12:10328587-10328608 chr12:10328593-10328609 chr12:10328594-10328607
13	CTCF	chr12:10328520-10328670	Caco-2	colon:	n/a	chr12:10328587-10328608 chr12:10328593-10328609 chr12:10328594-10328607
14	CTCF	chr12:10328520-10328670	A549	lung:	n/a	chr12:10328587-10328608 chr12:10328593-10328609 chr12:10328594-10328607
15	CTCF	chr12:10328501-10328754	GM12878	blood:	n/a	chr12:10328587-10328608 chr12:10328593-10328609 chr12:10328594-10328607
16	CTCF	chr12:10328520-10328670	HRPEpiC	eye:	n/a	chr12:10328587-10328608 chr12:10328593-10328609 chr12:10328594-10328607
17	SMC3	chr12:10328445-10328776	Hela-S3	cervix:	n/a	chr12:10328594-10328608
18	CTCF	chr12:10328508-10328676	Pancreas_OC	pancreas:	n/a	chr12:10328587-10328608 chr12:10328593-10328609 chr12:10328594-10328607
19	CTCF	chr12:10328513-10328698	MCF-7	breast:	n/a	chr12:10328587-10328608 chr12:10328593-10328609 chr12:10328594-10328607
20	CTCF	chr12:10328520-10328670	GM12865	blood:	n/a	chr12:10328587-10328608 chr12:10328593-10328609 chr12:10328594-10328607
21	FOXA1	chr12:10328460-10328678	T-47D	breast:	n/a	n/a
22	CTCF	chr12:10328560-10328710	MCF-7	breast:	n/a	chr12:10328587-10328608 chr12:10328593-10328609 chr12:10328594-10328607
23	FOXA1	chr12:10328380-10328707	T-47D	breast:	n/a	n/a
24	CTCF	chr12:10328548-10328696	GM12878	blood:	n/a	chr12:10328587-10328608 chr12:10328593-10328609 chr12:10328594-10328607
25	CTCF	chr12:10328598-10328730	LNCaP	prostate:	n/a	n/a
26	CTCF	chr12:10328540-10328690	SAEC	small airway:	n/a	chr12:10328587-10328608 chr12:10328593-10328609 chr12:10328594-10328607
27	CTCF	chr12:10328364-10328752	MCF-7	breast:	n/a	chr12:10328587-10328608 chr12:10328593-10328609 chr12:10328594-10328607
28	CTCF	chr12:10328580-10328730	GM12872	blood:	n/a	chr12:10328587-10328608 chr12:10328593-10328609 chr12:10328594-10328607
29	CTCF	chr12:10328500-10328650	NHEK	skin:	n/a	chr12:10328587-10328608 chr12:10328593-10328609 chr12:10328594-10328607
30	CTCF	chr12:10328520-10328670	GM06990	blood:	n/a	chr12:10328587-10328608 chr12:10328593-10328609 chr12:10328594-10328607

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr12:10305977..10306953-chr12:10328333..10329049,2	MCF-7	breast:

Variant related genes	Relation type
TMEM52B	TF binding region
OLR1	TF binding region

Extended variants
information (count: 24 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:23)

rs_ID	r²[population]
rs1050283	0.84[CEU][hapmap];0.93[JPT][hapmap]
rs1050286	0.85[JPT][hapmap]
rs10505755	0.93[JPT][hapmap]
rs11053647	0.90[JPT][hapmap]
rs11053648	0.93[JPT][hapmap]
rs11053649	0.92[JPT][hapmap]
rs11053654	0.81[CEU][hapmap];0.85[JPT][hapmap];0.82[EUR][1000 genomes]
rs12311169	0.81[AMR][1000 genomes]
rs12822177	0.92[JPT][hapmap]
rs2537777	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];1.00[TSI][hapmap];0.85[YRI][hapmap];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2537778	0.88[ASW][hapmap];1.00[CEU][hapmap];0.92[CHB][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];1.00[TSI][hapmap];0.88[YRI][hapmap];0.88[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2537779	1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[YRI][hapmap];0.95[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2634164	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs3736232	0.93[JPT][hapmap]
rs3736233	0.93[JPT][hapmap]
rs3736234	0.93[JPT][hapmap]
rs3736235	0.93[JPT][hapmap]
rs3816844	0.93[JPT][hapmap]
rs4764299	0.81[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.81[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6488265	0.96[CEU][hapmap];0.88[GIH][hapmap];0.93[JPT][hapmap];0.95[TSI][hapmap];0.92[EUR][1000 genomes]
rs7296800	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[YRI][hapmap];0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7315498	0.86[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[TSI][hapmap];0.88[YRI][hapmap];0.97[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7958778	0.87[ASW][hapmap];0.96[CEU][hapmap];0.81[TSI][hapmap];0.91[YRI][hapmap];0.90[AMR][1000 genomes];0.90[EUR][1000 genomes]

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

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv898757	chr12:10229281-10614641	Enhancers Weak transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Flanking Active TSS Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Strong transcription Genic enhancers Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	48 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs7300650	OLR1	cis	multi-tissue	Pritchard

Chromatin state (count:18 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:10321800-10331200	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
2	chr12:10325400-10330600	Weak transcription	Primary monocytes fromperipheralblood	blood
3	chr12:10325400-10330600	Weak transcription	Monocytes-CD14+_RO01746	blood
4	chr12:10325400-10335000	Weak transcription	A549	lung
5	chr12:10326200-10334800	Weak transcription	Primary neutrophils fromperipheralblood	blood
6	chr12:10327200-10329000	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
7	chr12:10327600-10329000	Enhancers	Hela-S3	cervix
8	chr12:10327600-10329600	Enhancers	Fetal Intestine Large	intestine
9	chr12:10327600-10330200	Enhancers	Fetal Intestine Small	intestine
10	chr12:10327800-10330200	Enhancers	Breast Myoepithelial Primary Cells	Breast
11	chr12:10328000-10328800	Flanking Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
12	chr12:10328000-10329200	Enhancers	Colonic Mucosa	Colon
13	chr12:10328400-10328800	Enhancers	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
14	chr12:10328400-10329000	Flanking Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
15	chr12:10328400-10329200	Enhancers	Small Intestine	intestine
16	chr12:10328400-10329200	Flanking Active TSS	NHEK	skin
17	chr12:10328600-10329000	Flanking Active TSS	HMEC	breast
18	chr12:10328600-10330600	Weak transcription	Placenta	Placenta

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