Variant report

Variant	rs1863052
Chromosome Location	chr2:86559358-86559359
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr2:86557932..86559986-chr2:86586521..86589056,2	MCF-7	breast:
2	chr2:86552980..86555003-chr2:86557144..86560058,2	K562	blood:
3	chr2:86558503..86561277-chr2:86568134..86571104,2	MCF-7	breast:

Extended variants
information (count: 81 )
Associated
traits (count: 7 )

rSNPs within LD-proxies of this variant (count:80)

rs_ID	r²[population]
rs10186289	0.84[CEU][hapmap];0.83[CHB][hapmap]
rs10189492	0.96[CEU][hapmap];0.82[CHB][hapmap];1.00[JPT][hapmap];0.83[ASN][1000 genomes]
rs10200186	0.84[AFR][1000 genomes];0.97[ASN][1000 genomes]
rs10200526	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[YRI][hapmap];0.84[AFR][1000 genomes];0.97[ASN][1000 genomes]
rs10200619	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10201457	0.81[CHB][hapmap];1.00[JPT][hapmap]
rs10204589	0.82[MEX][hapmap]
rs10520415	1.00[ASW][hapmap];0.92[CEU][hapmap];1.00[CHB][hapmap];0.89[CHD][hapmap];0.85[GIH][hapmap];1.00[JPT][hapmap];0.82[MEX][hapmap];0.81[TSI][hapmap];0.85[YRI][hapmap];0.83[AFR][1000 genomes];0.94[ASN][1000 genomes]
rs11127026	1.00[ASW][hapmap];0.92[CEU][hapmap];1.00[CHB][hapmap];0.85[CHD][hapmap];0.87[GIH][hapmap];1.00[JPT][hapmap];0.87[LWK][hapmap];0.82[MEX][hapmap];0.81[TSI][hapmap];0.92[YRI][hapmap];0.84[AFR][1000 genomes];0.97[ASN][1000 genomes]
rs11127028	0.82[AFR][1000 genomes];0.98[ASN][1000 genomes]
rs11127029	0.92[CEU][hapmap];0.91[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs11675942	0.85[CEU][hapmap];0.82[JPT][hapmap];0.86[MEX][hapmap];0.85[TSI][hapmap]
rs11681689	0.81[CEU][hapmap];0.82[JPT][hapmap]
rs11685863	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11691122	0.87[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs11691726	0.85[CEU][hapmap];0.93[CHB][hapmap];0.82[JPT][hapmap]
rs11691807	0.81[CEU][hapmap];0.82[JPT][hapmap];0.83[TSI][hapmap]
rs12052607	0.85[CEU][hapmap];0.82[JPT][hapmap];0.81[AMR][1000 genomes]
rs12466728	0.81[CEU][hapmap];0.82[JPT][hapmap]
rs12472390	0.92[CEU][hapmap];0.81[CHB][hapmap];1.00[JPT][hapmap];0.83[ASN][1000 genomes]
rs12472676	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[ASN][1000 genomes]
rs12476706	0.85[CEU][hapmap]
rs12476826	0.85[CEU][hapmap];0.82[JPT][hapmap]
rs12478575	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[YRI][hapmap];0.84[AFR][1000 genomes];0.97[ASN][1000 genomes]
rs12478653	1.00[ASW][hapmap];0.88[CEU][hapmap];1.00[CHB][hapmap];0.89[CHD][hapmap];1.00[JPT][hapmap];0.87[LWK][hapmap];0.82[MEX][hapmap];0.92[YRI][hapmap];0.84[AFR][1000 genomes];0.97[ASN][1000 genomes]
rs12620833	0.92[CEU][hapmap];0.81[ASN][1000 genomes]
rs12622200	1.00[ASW][hapmap];0.92[CEU][hapmap];1.00[CHB][hapmap];0.89[CHD][hapmap];0.85[GIH][hapmap];1.00[JPT][hapmap];0.81[LWK][hapmap];0.82[MEX][hapmap];0.81[TSI][hapmap];0.85[YRI][hapmap];0.83[AFR][1000 genomes];0.94[ASN][1000 genomes]
rs12714179	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[YRI][hapmap];0.97[ASN][1000 genomes]
rs12714180	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[YRI][hapmap];0.84[AFR][1000 genomes];0.97[ASN][1000 genomes]
rs12988844	0.81[CEU][hapmap];0.82[JPT][hapmap];0.83[TSI][hapmap]
rs12999029	0.92[CEU][hapmap];1.00[CHB][hapmap];0.89[CHD][hapmap];0.85[GIH][hapmap];0.93[JPT][hapmap];0.82[MEX][hapmap];0.81[TSI][hapmap];0.94[ASN][1000 genomes]
rs13015186	0.85[CEU][hapmap]
rs13017143	0.81[CEU][hapmap]
rs13017338	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[YRI][hapmap];0.83[AFR][1000 genomes];0.92[ASN][1000 genomes]
rs13020869	0.97[ASN][1000 genomes]
rs13023154	0.85[CEU][hapmap];0.83[GIH][hapmap]
rs13024964	0.88[CEU][hapmap]
rs13421310	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[YRI][hapmap];0.94[ASN][1000 genomes]
rs17438687	0.81[CEU][hapmap];0.82[JPT][hapmap];0.83[TSI][hapmap]
rs17737955	0.85[CEU][hapmap]
rs17738096	0.92[CEU][hapmap];1.00[CHB][hapmap];0.89[CHD][hapmap];0.85[GIH][hapmap];1.00[JPT][hapmap];0.81[LWK][hapmap];0.82[MEX][hapmap];0.81[TSI][hapmap];0.97[ASN][1000 genomes]
rs1863051	1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1863058	0.82[MEX][hapmap]
rs1863059	0.85[CEU][hapmap];0.82[JPT][hapmap];0.86[MEX][hapmap];0.85[TSI][hapmap];0.82[AMR][1000 genomes]
rs1863063	0.84[CEU][hapmap];0.83[CHB][hapmap]
rs2278105	0.88[CEU][hapmap];0.82[CHB][hapmap];0.81[GIH][hapmap];1.00[JPT][hapmap];0.82[MEX][hapmap];0.81[TSI][hapmap]
rs2367233	0.92[CEU][hapmap];0.87[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs34048420	0.84[AFR][1000 genomes];0.97[ASN][1000 genomes]
rs34069316	0.84[AFR][1000 genomes];0.97[ASN][1000 genomes]
rs35281683	0.84[AFR][1000 genomes];0.97[ASN][1000 genomes]
rs35370705	0.83[ASN][1000 genomes]
rs35762338	0.97[ASN][1000 genomes]
rs4392258	0.97[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4832031	0.81[CEU][hapmap];0.82[JPT][hapmap];0.83[TSI][hapmap]
rs4832033	0.81[CEU][hapmap];0.82[JPT][hapmap];0.80[AMR][1000 genomes]
rs4832261	0.81[CEU][hapmap];0.82[JPT][hapmap];0.82[MEX][hapmap];0.83[TSI][hapmap]
rs4832262	0.81[CEU][hapmap];0.82[JPT][hapmap];0.82[MEX][hapmap];0.83[TSI][hapmap]
rs4832263	0.82[MEX][hapmap]
rs4832269	0.85[CEU][hapmap];0.82[CHB][hapmap];0.81[JPT][hapmap]
rs4832270	0.85[CEU][hapmap];0.82[JPT][hapmap];0.82[MEX][hapmap];0.83[TSI][hapmap]
rs4832271	0.86[MEX][hapmap]
rs4832276	0.83[MEX][hapmap]
rs6547668	0.85[CEU][hapmap];0.82[JPT][hapmap]
rs6547673	0.84[CEU][hapmap];0.83[CHB][hapmap]
rs6547674	0.92[CEU][hapmap];0.98[GIH][hapmap];0.89[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs6713456	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[ASN][1000 genomes]
rs6714362	0.92[CEU][hapmap];0.82[CHB][hapmap];0.85[GIH][hapmap];1.00[JPT][hapmap];0.81[LWK][hapmap];0.82[MEX][hapmap];0.81[TSI][hapmap];0.83[ASN][1000 genomes]
rs6725234	0.84[CEU][hapmap];0.88[CHB][hapmap];0.81[JPT][hapmap];0.80[AMR][1000 genomes]
rs6728029	0.82[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs6738585	0.80[AMR][1000 genomes]
rs67407963	0.83[AFR][1000 genomes];0.96[ASN][1000 genomes]
rs6745235	0.85[CEU][hapmap];0.82[JPT][hapmap]
rs6746198	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs67903513	0.97[ASN][1000 genomes]
rs7560886	0.81[JPT][hapmap]
rs7563887	0.84[CEU][hapmap];0.83[CHB][hapmap]
rs7571424	0.92[CEU][hapmap];1.00[CHB][hapmap];0.89[CHD][hapmap];1.00[JPT][hapmap];0.82[MEX][hapmap];0.80[TSI][hapmap];0.98[ASN][1000 genomes]
rs7593440	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9309635	0.83[MEX][hapmap]
rs9677502	0.81[CEU][hapmap];0.82[JPT][hapmap];0.83[TSI][hapmap]

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	esv3412938	chr2:86370969-86867936	Strong transcription Enhancers Genic enhancers Weak transcription Flanking Bivalent TSS/Enh Active TSS Flanking Active TSS ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	77 gene(s)	inside rSNPs	diseases

mRNA abundance (count:7)

SNP	Gene	Cis/trans	Tissue	Source
rs1863052	MRPL35	cis	parietal	SCAN
rs1863052	VAMP5	cis	parietal	SCAN
rs1863052	IMMT	cis	cerebellum	SCAN
rs1863052	REEP1	cis	lymphoblastoid	seeQTL
rs1863052	IMMT	cis	Whole Blood	GTEx
rs1863052	REEP1	cis	multi-tissue	Pritchard
rs1863052	MRPL35	cis	cerebellum	SCAN

Chromatin state (count:22 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:86533200-86563000	Weak transcription	Brain Germinal Matrix	brain
2	chr2:86536200-86559800	Weak transcription	HSMMtube	muscle
3	chr2:86537600-86563000	Weak transcription	Brain Anterior Caudate	brain
4	chr2:86542200-86559400	Weak transcription	Stomach Smooth Muscle	stomach
5	chr2:86549200-86563000	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
6	chr2:86552200-86563800	Weak transcription	Aorta	Aorta
7	chr2:86555400-86559600	Weak transcription	Colon Smooth Muscle	Colon
8	chr2:86555400-86563200	Weak transcription	Spleen	Spleen
9	chr2:86556800-86561200	Enhancers	Skeletal Muscle Female	skeletal muscle
10	chr2:86557400-86559800	Weak transcription	Right Atrium	heart
11	chr2:86557600-86561000	Weak transcription	Left Ventricle	heart
12	chr2:86557800-86559800	Enhancers	Fetal Intestine Large	intestine
13	chr2:86557800-86560200	Enhancers	Psoas Muscle	Psoas
14	chr2:86558200-86559800	Enhancers	Fetal Intestine Small	intestine
15	chr2:86558400-86560200	Enhancers	Right Ventricle	heart
16	chr2:86558400-86560800	Enhancers	Fetal Heart	heart
17	chr2:86558600-86559600	Weak transcription	Fetal Brain Female	brain
18	chr2:86558600-86562200	Enhancers	Skeletal Muscle Male	skeletal muscle
19	chr2:86558600-86563000	Weak transcription	Pancreas	Pancrea
20	chr2:86559000-86561000	Enhancers	Fetal Stomach	stomach
21	chr2:86559000-86561000	Enhancers	Rectal Smooth Muscle	rectum
22	chr2:86559200-86563000	Enhancers	Fetal Brain Male	brain

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