Variant report

Variant	rs3317
Chromosome Location	chr5:112212151-112212152
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr5:112199637..112202533-chr5:112210303..112212318,2	MCF-7	breast:
2	chr5:112206451..112208757-chr5:112210968..112212741,2	MCF-7	breast:
3	chr5:112211665..112213695-chr5:112223485..112225532,2	K562	blood:
4	chr5:112197996..112200677-chr5:112212037..112214219,2	K562	blood:
5	chr5:112210185..112212366-chr5:112214528..112217503,2	K562	blood:
6	chr5:112200124..112202418-chr5:112211371..112213575,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000272869	Chromatin interaction
ENSG00000153037	Chromatin interaction

Extended variants
information (count: 99 )
Associated
traits (count: 8 )

rSNPs within LD-proxies of this variant (count:90)

rs_ID	r²[population]
rs10075281	0.92[ASW][hapmap];0.82[GIH][hapmap];0.83[TSI][hapmap]
rs1093611	1.00[CHB][hapmap];0.98[CHD][hapmap];0.94[JPT][hapmap];0.82[MEX][hapmap];0.93[ASN][1000 genomes]
rs11241182	0.92[ASW][hapmap];0.81[CHD][hapmap];0.80[GIH][hapmap]
rs11241185	0.92[ASW][hapmap];0.81[CEU][hapmap];0.83[CHD][hapmap];0.87[GIH][hapmap];0.81[TSI][hapmap]
rs12518091	0.85[CEU][hapmap]
rs149130	0.83[ASW][hapmap];0.85[CEU][hapmap];0.91[MEX][hapmap];0.87[TSI][hapmap]
rs149190	0.85[CEU][hapmap];0.87[MEX][hapmap];0.85[TSI][hapmap]
rs149191	0.80[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs149192	0.81[CEU][hapmap];0.82[TSI][hapmap]
rs149193	0.89[AMR][1000 genomes];0.90[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs153544	1.00[CEU][hapmap];1.00[CHB][hapmap];0.91[AMR][1000 genomes];0.92[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs153546	1.00[CHB][hapmap];0.98[CHD][hapmap];0.94[JPT][hapmap];0.91[ASN][1000 genomes]
rs153548	1.00[CHB][hapmap];0.97[CHD][hapmap];0.94[JPT][hapmap];0.91[ASN][1000 genomes]
rs153549	1.00[CHB][hapmap];0.94[JPT][hapmap];0.92[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs153550	0.91[ASN][1000 genomes]
rs153551	0.96[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs153552	0.89[AMR][1000 genomes];0.92[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs153556	0.86[EUR][1000 genomes]
rs153557	0.84[EUR][1000 genomes]
rs153560	0.87[MEX][hapmap]
rs153561	0.83[EUR][1000 genomes]
rs153563	0.83[EUR][1000 genomes]
rs154344	0.91[AMR][1000 genomes];0.92[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs17135222	0.84[TSI][hapmap]
rs1866924	0.83[ASW][hapmap];0.81[TSI][hapmap]
rs1914	0.81[CEU][hapmap]
rs1974786	0.83[CEU][hapmap]
rs2019720	0.81[CEU][hapmap]
rs2229992	0.95[CHD][hapmap]
rs2289484	0.92[ASW][hapmap];0.88[CHD][hapmap];0.84[GIH][hapmap]
rs2431241	0.83[ASW][hapmap];0.81[CEU][hapmap];0.83[TSI][hapmap]
rs2431512	0.92[ASW][hapmap];0.85[CEU][hapmap];0.88[CHD][hapmap];0.87[GIH][hapmap];0.81[TSI][hapmap]
rs2464803	0.83[ASW][hapmap];0.90[CHD][hapmap];0.84[GIH][hapmap];0.83[TSI][hapmap]
rs2545155	0.87[ASN][1000 genomes]
rs2545156	0.92[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];0.85[LWK][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2545170	0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2546106	0.90[CHD][hapmap];0.84[GIH][hapmap];0.81[TSI][hapmap]
rs2546108	0.83[ASW][hapmap];0.81[CEU][hapmap];0.85[CHB][hapmap];0.93[CHD][hapmap];0.87[GIH][hapmap];0.81[TSI][hapmap]
rs2546110	0.92[ASW][hapmap];0.93[CHD][hapmap]
rs2546112	0.84[CHB][hapmap];0.81[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2546115	0.95[CHB][hapmap];0.88[CHD][hapmap];0.89[ASN][1000 genomes]
rs2707765	0.81[CEU][hapmap]
rs351767	0.95[ASN][1000 genomes]
rs351768	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];0.98[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs351770	1.00[CHB][hapmap];0.88[JPT][hapmap];0.94[ASN][1000 genomes]
rs368575	0.83[ASW][hapmap];1.00[CEU][hapmap];0.91[GIH][hapmap];0.85[LWK][hapmap];0.90[MKK][hapmap];0.96[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs373059	0.82[AMR][1000 genomes];0.90[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs374613	0.92[ASW][hapmap];1.00[CEU][hapmap];0.90[CHB][hapmap];0.95[CHD][hapmap];0.93[GIH][hapmap];0.81[LWK][hapmap];0.98[TSI][hapmap];0.84[AMR][1000 genomes];0.89[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs382427	1.00[CEU][hapmap];0.89[CHB][hapmap];1.00[YRI][hapmap];0.86[AFR][1000 genomes];0.83[AMR][1000 genomes];0.89[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs395858	1.00[CEU][hapmap];0.88[CHB][hapmap];0.83[AMR][1000 genomes];0.90[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs396321	0.92[ASW][hapmap];0.93[CHD][hapmap];0.80[GIH][hapmap]
rs410701	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs41116	0.82[ASN][1000 genomes]
rs414098	0.84[CEU][hapmap]
rs419155	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.88[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs448162	0.83[ASW][hapmap];0.90[CHB][hapmap];0.95[CHD][hapmap];0.84[ASN][1000 genomes]
rs448475	0.82[ASN][1000 genomes]
rs448613	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs454968	0.83[ASN][1000 genomes]
rs456531	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs459102	0.93[ASN][1000 genomes]
rs460137	0.92[ASW][hapmap];1.00[CEU][hapmap];0.95[CHB][hapmap];0.86[CHD][hapmap];0.95[GIH][hapmap];0.85[LWK][hapmap];0.81[MKK][hapmap];1.00[TSI][hapmap];0.87[AMR][1000 genomes];0.94[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs467033	0.92[ASW][hapmap];0.85[CEU][hapmap];0.90[CHD][hapmap];0.86[GIH][hapmap]
rs468610	0.83[ASN][1000 genomes]
rs468751	0.89[AMR][1000 genomes];0.91[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs468854	0.88[ASN][1000 genomes]
rs469827	1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[ASN][1000 genomes]
rs469886	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[AMR][1000 genomes];0.91[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs4705486	0.92[ASW][hapmap];0.81[CEU][hapmap];0.81[CHD][hapmap];0.87[GIH][hapmap];0.85[TSI][hapmap]
rs4705559	0.92[ASW][hapmap];0.85[CEU][hapmap];0.81[CHD][hapmap];0.82[GIH][hapmap];0.81[TSI][hapmap]
rs4705608	0.85[CEU][hapmap]
rs4705610	0.92[ASW][hapmap];0.85[CEU][hapmap];0.84[GIH][hapmap];0.83[TSI][hapmap]
rs495794	1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[ASN][1000 genomes]
rs505382	0.94[AFR][1000 genomes];0.87[AMR][1000 genomes];0.91[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs514763	1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[ASN][1000 genomes]
rs566419	0.96[CEU][hapmap];0.89[CHB][hapmap];0.83[AMR][1000 genomes];0.83[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs6594646	0.92[ASW][hapmap];0.85[CEU][hapmap];0.83[CHD][hapmap];0.87[GIH][hapmap]
rs67293732	0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6862050	0.81[CEU][hapmap]
rs712663	0.92[ASN][1000 genomes]
rs712670	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7213	1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[ASN][1000 genomes]
rs7704618	0.85[CEU][hapmap]
rs818426	0.96[EUR][1000 genomes]
rs818428	1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs818429	0.93[ASN][1000 genomes]
rs818430	0.94[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs818782	0.82[EUR][1000 genomes]
rs818797	1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9326863	0.92[ASW][hapmap];0.83[CHD][hapmap];0.80[GIH][hapmap]

Variant overlapped rSNPs/rCNVs (count:9 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv33290	chr5:112110808-112238295	Weak transcription Strong transcription Flanking Active TSS Enhancers Genic enhancers Transcr. at gene 5' and 3' Active TSS ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	19 gene(s)	inside rSNPs	diseases
2	nsv1029271	chr5:112113308-112325943	Strong transcription Bivalent Enhancer Weak transcription Enhancers Flanking Active TSS Genic enhancers Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	30 gene(s)	inside rSNPs	diseases
3	nsv529536	chr5:112174106-112269758	Genic enhancers Strong transcription Weak transcription Flanking Active TSS Enhancers Flanking Bivalent TSS/Enh Active TSS Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	19 gene(s)	inside rSNPs	diseases
4	nsv599394	chr5:112185491-112446323	Weak transcription Active TSS Strong transcription Genic enhancers Enhancers Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	31 gene(s)	inside rSNPs	diseases
5	nsv870231	chr5:112192379-112247084	Strong transcription Weak transcription Genic enhancers Flanking Active TSS Enhancers Transcr. at gene 5' and 3' Active TSS Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	14 gene(s)	inside rSNPs	diseases
6	nsv1029595	chr5:112197662-112242375	Strong transcription Weak transcription Flanking Active TSS Active TSS Transcr. at gene 5' and 3' Genic enhancers Enhancers Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	10 gene(s)	inside rSNPs	diseases
7	nsv1030103	chr5:112197662-112255712	Weak transcription Genic enhancers Enhancers Strong transcription Flanking Active TSS Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	10 gene(s)	inside rSNPs	diseases
8	nsv537863	chr5:112197662-112255712	Weak transcription Strong transcription Genic enhancers Active TSS Enhancers Flanking Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	10 gene(s)	inside rSNPs	diseases
9	nsv4960	chr5:112200199-112218299	Weak transcription Strong transcription Flanking Active TSS Genic enhancers Enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region miRNA target site	6 gene(s)	inside rSNPs	diseases

mRNA abundance (count:8)

SNP	Gene	Cis/trans	Tissue	Source
rs3317	NCRNA00219	cis	parietal	SCAN
rs3317	REEP5	cis	cerebellum	SCAN
rs3317	REEP5	cis	uninvolved skin	skin_eQTL
rs3317	REEP5	cis	parietal	SCAN
rs3317	REEP5	cis	lymphoblastoid	seeQTL
rs3317	REEP5	Cis_1M	lymphoblastoid	RTeQTL
rs3317	REEP5	cis	Esophagus Muscularis	GTEx
rs3317	MCC	cis	cerebellum	SCAN

Chromatin state (count:126 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:112198400-112220600	Weak transcription	Placenta Amnion	Placenta Amnion
2	chr5:112199000-112226000	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
3	chr5:112199200-112213200	Weak transcription	Fetal Heart	heart
4	chr5:112199200-112213400	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
5	chr5:112199400-112215000	Weak transcription	Small Intestine	intestine
6	chr5:112199600-112214400	Strong transcription	Primary hematopoietic stem cells short term culture	blood
7	chr5:112199800-112212200	Weak transcription	Pancreatic Islets	Pancreatic Islet
8	chr5:112200600-112213800	Weak transcription	Primary T killer memory cells from peripheral blood	blood
9	chr5:112200600-112242000	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
10	chr5:112202800-112217800	Weak transcription	Brain Substantia Nigra	brain
11	chr5:112203400-112213000	Weak transcription	Fetal Lung	lung
12	chr5:112203400-112218200	Weak transcription	Colonic Mucosa	Colon
13	chr5:112203600-112214400	Weak transcription	Stomach Mucosa	stomach
14	chr5:112204000-112213800	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
15	chr5:112205000-112214600	Weak transcription	Fetal Kidney	kidney
16	chr5:112205200-112212800	Weak transcription	Primary T helper naive cells from peripheral blood	blood
17	chr5:112205400-112213600	Weak transcription	Primary T helper cells fromperipheralblood	blood
18	chr5:112205600-112212800	Weak transcription	Brain Cingulate Gyrus	brain
19	chr5:112206200-112218400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
20	chr5:112206400-112212200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
21	chr5:112206400-112213800	Weak transcription	HUVEC	blood vessel
22	chr5:112206400-112242800	Weak transcription	Fetal Brain Male	brain
23	chr5:112206600-112213000	Weak transcription	iPS-18 Cell Line	embryonic stem cell
24	chr5:112206600-112213200	Weak transcription	Brain Germinal Matrix	brain
25	chr5:112206600-112213200	Weak transcription	Fetal Brain Female	brain
26	chr5:112206600-112213400	Weak transcription	Rectal Smooth Muscle	rectum
27	chr5:112206600-112214000	Weak transcription	Primary hematopoietic stem cells	blood
28	chr5:112206600-112214200	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
29	chr5:112206600-112214400	Weak transcription	Hela-S3	cervix
30	chr5:112206600-112215400	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
31	chr5:112206600-112215800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
32	chr5:112206600-112216400	Weak transcription	Aorta	Aorta
33	chr5:112206600-112217200	Weak transcription	Right Ventricle	heart
34	chr5:112206600-112219400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
35	chr5:112206600-112219800	Weak transcription	Skeletal Muscle Male	skeletal muscle
36	chr5:112206800-112212800	Weak transcription	NHLF	lung
37	chr5:112206800-112213000	Weak transcription	Stomach Smooth Muscle	stomach
38	chr5:112206800-112213000	Weak transcription	NHEK	skin
39	chr5:112206800-112213200	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
40	chr5:112206800-112213200	Weak transcription	Adipose Nuclei	Adipose
41	chr5:112206800-112213200	Weak transcription	Brain Anterior Caudate	brain
42	chr5:112206800-112214000	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
43	chr5:112206800-112215400	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
44	chr5:112206800-112215800	Weak transcription	Pancreas	Pancrea
45	chr5:112206800-112215800	Weak transcription	Spleen	Spleen
46	chr5:112206800-112217000	Weak transcription	Brain Angular Gyrus	brain
47	chr5:112206800-112217200	Weak transcription	H9 Cell Line	embryonic stem cell
48	chr5:112206800-112217200	Weak transcription	Gastric	stomach
49	chr5:112206800-112220800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
50	chr5:112206800-112220800	Weak transcription	Ovary	ovary

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