Variant report

Variant	rs500493
Chromosome Location	chr11:63782228-63782229
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:0)
CpG islands
(count:0)
Chromatin interactive
region (count:8)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:8 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr11:63779234..63782933-chr11:63784307..63787917,5	MCF-7	breast:
2	chr11:63779445..63782328-chr11:63947827..63950114,2	K562	blood:
3	chr11:63781876..63786325-chr11:63787038..63791246,5	K562	blood:
4	chr11:63781000..63782965-chr11:63900428..63903008,2	MCF-7	breast:
5	chr11:63779470..63782792-chr11:63782839..63786863,3	K562	blood:
6	chr11:63770454..63773392-chr11:63780828..63782649,3	K562	blood:
7	chr11:63779610..63782296-chr11:63923822..63926567,2	MCF-7	breast:
8	chr11:63770570..63773392-chr11:63780661..63782649,3	K562	blood:

No data

Extended variants
information (count: 77 )
Associated
traits (count: 10 )

rSNPs within LD-proxies of this variant (count:52)

rs_ID	r²[population]
rs10751004	0.84[AMR][1000 genomes];0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs10792424	0.91[AFR][1000 genomes];0.95[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs10897464	0.85[CEU][hapmap];0.95[YRI][hapmap];0.84[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs10897466	0.85[CEU][hapmap];0.84[CHB][hapmap];1.00[CHD][hapmap];0.84[GIH][hapmap];1.00[JPT][hapmap];0.86[MEX][hapmap];0.95[TSI][hapmap];0.89[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs10897468	0.92[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs11231646	0.93[ASW][hapmap];0.88[LWK][hapmap];0.83[MKK][hapmap];0.81[TSI][hapmap];0.95[YRI][hapmap];0.80[AMR][1000 genomes]
rs11231653	0.88[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs11231662	0.81[TSI][hapmap]
rs11231671	0.82[JPT][hapmap];0.81[TSI][hapmap]
rs11601228	0.91[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs11605797	0.81[TSI][hapmap]
rs11607028	0.84[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs12790749	0.93[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs12798491	0.85[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.87[GIH][hapmap];1.00[JPT][hapmap];0.81[MEX][hapmap];0.93[TSI][hapmap];0.88[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs12808604	0.94[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs1386346	1.00[ASW][hapmap];0.85[CEU][hapmap];0.82[GIH][hapmap];0.87[LWK][hapmap];0.86[MEX][hapmap];0.83[MKK][hapmap];0.98[TSI][hapmap];0.90[YRI][hapmap];0.82[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs1684950	0.92[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs1783964	0.91[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs2508584	0.82[AFR][1000 genomes];0.92[AMR][1000 genomes];0.90[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs3019782	0.91[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs320121	0.92[EUR][1000 genomes]
rs320156	0.93[ASW][hapmap];0.85[CEU][hapmap];0.93[GIH][hapmap];0.88[MEX][hapmap];0.98[TSI][hapmap];0.95[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs35492216	0.88[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs3740636	1.00[ASW][hapmap];0.85[CEU][hapmap];0.85[LWK][hapmap];0.81[MEX][hapmap];0.83[MKK][hapmap];0.95[TSI][hapmap];0.95[YRI][hapmap];0.84[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs4426138	0.92[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs481835	0.85[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.87[GIH][hapmap];1.00[JPT][hapmap];0.81[MEX][hapmap];0.95[TSI][hapmap];0.92[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs483340	1.00[ASW][hapmap];0.85[CEU][hapmap];0.87[GIH][hapmap];0.90[LWK][hapmap];0.88[MEX][hapmap];0.86[MKK][hapmap];0.98[TSI][hapmap];1.00[YRI][hapmap];0.91[AFR][1000 genomes];0.92[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs487540	0.91[AFR][1000 genomes];0.95[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs488082	0.85[CEU][hapmap];0.95[YRI][hapmap];0.91[AFR][1000 genomes];0.95[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs4980512	0.87[ASW][hapmap];0.85[CEU][hapmap];0.84[GIH][hapmap];0.81[MEX][hapmap];0.95[TSI][hapmap];0.84[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs4980516	0.88[AFR][1000 genomes];0.92[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs499118	0.90[AFR][1000 genomes];0.92[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs501278	0.82[EUR][1000 genomes]
rs502858	0.82[AFR][1000 genomes];0.92[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs504314	0.96[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs528927	1.00[CEU][hapmap];0.90[YRI][hapmap];0.95[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs529915	0.91[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs539432	0.85[CEU][hapmap];0.92[CHB][hapmap];1.00[JPT][hapmap];0.82[AMR][1000 genomes];0.92[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs553724	0.83[CEU][hapmap];1.00[YRI][hapmap];0.92[AFR][1000 genomes];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs562865	0.85[CEU][hapmap];1.00[YRI][hapmap];0.91[AFR][1000 genomes];0.96[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs567386	1.00[ASW][hapmap];0.85[CEU][hapmap];0.89[GIH][hapmap];0.90[LWK][hapmap];0.88[MEX][hapmap];0.96[MKK][hapmap];0.98[TSI][hapmap];0.95[YRI][hapmap];0.91[AFR][1000 genomes];0.95[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs578295	0.80[AFR][1000 genomes];0.92[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs579669	0.82[EUR][1000 genomes]
rs581355	0.80[EUR][1000 genomes]
rs6591830	0.92[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs709594	0.88[AFR][1000 genomes];0.95[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs728919	1.00[ASW][hapmap];0.85[CEU][hapmap];0.84[GIH][hapmap];0.88[LWK][hapmap];0.81[MEX][hapmap];0.83[MKK][hapmap];0.95[TSI][hapmap];0.95[YRI][hapmap];0.84[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs7928990	0.90[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7938498	0.93[ASW][hapmap];0.85[CEU][hapmap];0.84[GIH][hapmap];0.81[MEX][hapmap];0.98[TSI][hapmap];0.89[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs7942318	0.91[AFR][1000 genomes];0.95[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs7951529	0.84[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs9943682	0.85[AMR][1000 genomes];0.90[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:25 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1051171	chr11:62987064-63835715	Genic enhancers Enhancers Weak transcription Flanking Active TSS Active TSS Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	100 gene(s)	inside rSNPs	diseases
2	nsv468590	chr11:63639881-63783352	Flanking Active TSS Bivalent Enhancer Active TSS Strong transcription Weak transcription Genic enhancers Flanking Bivalent TSS/Enh Enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	41 gene(s)	inside rSNPs	diseases
3	nsv555181	chr11:63639881-63783352	Weak transcription Enhancers Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Strong transcription Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	41 gene(s)	inside rSNPs	diseases
4	nsv897629	chr11:63664882-63866959	Flanking Bivalent TSS/Enh Enhancers Flanking Active TSS Bivalent Enhancer Weak transcription Bivalent/Poised TSS Strong transcription Genic enhancers Active TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	43 gene(s)	inside rSNPs	diseases
5	nsv897630	chr11:63664882-63924446	Weak transcription Enhancers Flanking Active TSS Strong transcription Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	46 gene(s)	inside rSNPs	diseases
6	nsv897631	chr11:63664882-64129722	Flanking Active TSS Strong transcription Enhancers Weak transcription Active TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	254 gene(s)	inside rSNPs	diseases
7	nsv897639	chr11:63691049-63844683	Bivalent Enhancer Active TSS Enhancers Genic enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Strong transcription Weak transcription Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	38 gene(s)	inside rSNPs	diseases
8	esv1849906	chr11:63719273-63880383	Enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Weak transcription Bivalent Enhancer Strong transcription Active TSS Flanking Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	35 gene(s)	inside rSNPs	diseases
9	nsv1042075	chr11:63732454-63813164	Enhancers Strong transcription Genic enhancers Weak transcription Flanking Active TSS Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	31 gene(s)	inside rSNPs	diseases
10	esv29993	chr11:63738642-63864211	Flanking Active TSS Genic enhancers Enhancers Weak transcription Active TSS Bivalent Enhancer Strong transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	32 gene(s)	inside rSNPs	diseases
11	nsv897640	chr11:63744152-63835611	Enhancers Weak transcription Active TSS Transcr. at gene 5' and 3' Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer Strong transcription Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	22 gene(s)	inside rSNPs	diseases
12	nsv897641	chr11:63744152-63844683	Bivalent Enhancer Enhancers Flanking Active TSS Transcr. at gene 5' and 3' Weak transcription Active TSS Strong transcription Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	23 gene(s)	inside rSNPs	diseases
13	nsv897642	chr11:63744152-63866959	Weak transcription Enhancers Active TSS Strong transcription Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	24 gene(s)	inside rSNPs	diseases
14	esv1802079	chr11:63746066-64151373	Bivalent Enhancer Flanking Active TSS Weak transcription Enhancers Genic enhancers Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS Strong transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	247 gene(s)	inside rSNPs	diseases
15	nsv897643	chr11:63754986-63844683	Flanking Active TSS Enhancers Weak transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Active TSS Bivalent/Poised TSS Strong transcription Genic enhancers 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
16	nsv897644	chr11:63754986-63849330	Bivalent Enhancer Genic enhancers Active TSS Weak transcription Enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Strong transcription Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	19 gene(s)	inside rSNPs	diseases
17	nsv897645	chr11:63754986-63859751	Enhancers Weak transcription Bivalent Enhancer Flanking Active TSS Bivalent/Poised TSS Active TSS Genic enhancers Strong transcription Flanking Bivalent TSS/Enh 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
18	nsv897646	chr11:63754986-64150370	Strong transcription Weak transcription Bivalent Enhancer Flanking Active TSS Enhancers Transcr. at gene 5' and 3' Active TSS Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	245 gene(s)	inside rSNPs	diseases
19	nsv897647	chr11:63755961-63835611	Strong transcription Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Enhancers Flanking Active TSS Weak transcription Active TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	14 gene(s)	inside rSNPs	diseases
20	nsv897649	chr11:63761169-63844683	Active TSS Enhancers Weak transcription Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Flanking Active TSS ZNF genes & repeats Strong transcription Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	11 gene(s)	inside rSNPs	diseases
21	nsv897650	chr11:63761169-63849330	Bivalent Enhancer Genic enhancers Enhancers Flanking Bivalent TSS/Enh Active TSS Weak transcription Bivalent/Poised TSS Strong transcription Transcr. at gene 5' and 3' Flanking Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	11 gene(s)	inside rSNPs	diseases
22	nsv897651	chr11:63761169-63863405	Bivalent Enhancer Flanking Active TSS Active TSS Enhancers Flanking Bivalent TSS/Enh Weak transcription Genic enhancers Strong transcription Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	13 gene(s)	inside rSNPs	diseases
23	nsv897652	chr11:63761169-63866959	Flanking Bivalent TSS/Enh Flanking Active TSS Enhancers Bivalent Enhancer Strong transcription Weak transcription Bivalent/Poised TSS Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	13 gene(s)	inside rSNPs	diseases
24	nsv897653	chr11:63761169-63875456	Strong transcription Bivalent Enhancer Flanking Active TSS Enhancers Active TSS Weak transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	13 gene(s)	inside rSNPs	diseases
25	nsv897654	chr11:63772000-63875456	Bivalent/Poised TSS Enhancers Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Weak transcription Flanking Active TSS Strong transcription ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases

mRNA abundance (count:10)

SNP	Gene	Cis/trans	Tissue	Source
rs500493	MS4A6E	cis	cerebellum	SCAN
rs500493	SLC22A12	cis	parietal	SCAN
rs500493	PLCB3	cis	cerebellum	SCAN
rs500493	HNRNPUL2	cis	parietal	SCAN
rs500493	FTH1	cis	parietal	SCAN
rs500493	SLC22A24	cis	parietal	SCAN
rs500493	GANAB	cis	parietal	SCAN
rs500493	EHD1	cis	parietal	SCAN
rs500493	SNORA57	cis	cerebellum	SCAN
rs500493	GPR137	cis	parietal	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:63775800-63783400	Weak transcription	Brain Inferior Temporal Lobe	brain
2	chr11:63776000-63785000	Weak transcription	Lung	lung
3	chr11:63776200-63785000	Weak transcription	Right Ventricle	heart
4	chr11:63778600-63785400	Weak transcription	Esophagus	oesophagus
5	chr11:63778800-63786000	Weak transcription	Hela-S3	cervix
6	chr11:63779000-63789000	Weak transcription	Fetal Intestine Small	intestine
7	chr11:63779400-63783200	Weak transcription	Spleen	Spleen
8	chr11:63779600-63784800	Weak transcription	Pancreas	Pancrea
9	chr11:63780800-63783400	Enhancers	Brain Germinal Matrix	brain
10	chr11:63781200-63785400	Weak transcription	A549	lung
11	chr11:63781600-63782400	Enhancers	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
12	chr11:63781600-63782400	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
13	chr11:63781600-63782800	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
14	chr11:63781800-63783600	Weak transcription	Fetal Muscle Leg	muscle
15	chr11:63781800-63784400	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
16	chr11:63782000-63782400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
17	chr11:63782000-63782800	Bivalent Enhancer	Fetal Muscle Trunk	muscle
18	chr11:63782000-63785600	Enhancers	Fetal Brain Female	brain
19	chr11:63782200-63782600	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
20	chr11:63782200-63782800	Strong transcription	Skeletal Muscle Male	skeletal muscle
21	chr11:63782200-63784400	Bivalent Enhancer	iPS DF 19.11 Cell Line	embryonic stem cell
22	chr11:63782200-63786400	Enhancers	Fetal Brain Male	brain

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