Variant report

Variant	rs4980499
Chromosome Location	chr11:63707203-63707204
allele	A/G
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:10)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:10 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr11:63682242..63690244-chr11:63703955..63713214,18	K562	blood:
2	chr11:63531277..63535286-chr11:63705300..63707994,3	MCF-7	breast:
3	chr11:63655390..63658583-chr11:63705235..63708313,3	K562	blood:
4	chr11:63683456..63690158-chr11:63704393..63714412,17	K562	blood:
5	chr11:63601389..63603149-chr11:63706339..63708895,2	K562	blood:
6	chr11:63703471..63707661-chr11:63741980..63743610,3	K562	blood:
7	chr11:63704888..63707484-chr11:63951709..63953319,2	MCF-7	breast:
8	chr11:63705424..63708366-chr11:63719461..63721078,2	MCF-7	breast:
9	chr11:63683018..63687693-chr11:63704987..63708969,9	MCF-7	breast:
10	chr11:63683295..63687930-chr11:63703819..63708534,6	MCF-7	breast:

No data

Variant related genes	Relation type
ENSG00000188070	Chromatin interaction
ENSG00000176340	Chromatin interaction
ENSG00000256280	Chromatin interaction
ENSG00000110583	Chromatin interaction
ENSG00000167771	Chromatin interaction
ENSG00000168439	Chromatin interaction
ENSG00000256100	Chromatin interaction
ENSG00000072518	Chromatin interaction

Extended variants
information (count: 85 )
Associated
traits (count: 13 )

rSNPs within LD-proxies of this variant (count:75)

rs_ID	r²[population]
rs10897459	0.92[CEU][hapmap];0.81[GIH][hapmap];0.87[MEX][hapmap];0.91[TSI][hapmap];0.82[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs10897464	0.83[EUR][1000 genomes]
rs10897465	1.00[ASW][hapmap];0.88[CEU][hapmap];1.00[CHB][hapmap];0.85[CHD][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.80[MKK][hapmap];0.88[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.84[AMR][1000 genomes];0.92[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10897466	0.84[MEX][hapmap];0.83[TSI][hapmap];0.82[EUR][1000 genomes]
rs10897467	0.83[AFR][1000 genomes];0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs10897469	0.86[AMR][1000 genomes];0.92[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs10897470	0.88[AMR][1000 genomes];0.93[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs11231603	1.00[YRI][hapmap]
rs11231628	0.92[CEU][hapmap];0.87[MEX][hapmap];0.86[TSI][hapmap];0.80[EUR][1000 genomes]
rs11231643	0.90[AFR][1000 genomes];0.95[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs11231646	0.85[CEU][hapmap];0.86[GIH][hapmap];0.80[MEX][hapmap];0.98[TSI][hapmap];0.90[EUR][1000 genomes]
rs11231653	0.84[EUR][1000 genomes]
rs11231655	1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11231662	0.82[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.93[MEX][hapmap];0.86[MKK][hapmap];0.98[TSI][hapmap];1.00[YRI][hapmap];0.93[AMR][1000 genomes];0.93[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs11231663	0.90[AMR][1000 genomes];0.93[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs11231664	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.93[AMR][1000 genomes];0.93[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs11231670	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.90[AMR][1000 genomes];0.93[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs11231671	1.00[CEU][hapmap];0.89[CHB][hapmap];0.97[GIH][hapmap];0.85[MEX][hapmap];0.95[TSI][hapmap];0.85[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs11600062	0.90[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs11601228	0.81[EUR][1000 genomes]
rs11605797	0.82[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.93[MEX][hapmap];0.86[MKK][hapmap];0.98[TSI][hapmap];1.00[YRI][hapmap];0.86[AMR][1000 genomes];0.89[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs11607028	0.83[EUR][1000 genomes]
rs12417157	0.85[AMR][1000 genomes];0.91[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs12417507	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12418000	1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs12421757	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12786124	0.92[CEU][hapmap];0.90[GIH][hapmap];0.82[MEX][hapmap];0.93[TSI][hapmap];1.00[YRI][hapmap];0.88[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs12793201	0.90[AFR][1000 genomes];0.96[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs12794404	0.95[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs12797540	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12798491	0.87[MEX][hapmap];0.85[TSI][hapmap];0.84[EUR][1000 genomes]
rs12800703	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.93[AMR][1000 genomes];0.93[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs1386346	0.81[TSI][hapmap];0.81[EUR][1000 genomes]
rs2129467	0.93[AMR][1000 genomes];0.93[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2186572	1.00[YRI][hapmap]
rs224170	1.00[LWK][hapmap]
rs224173	0.91[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs2318110	0.87[EUR][1000 genomes]
rs2318126	0.92[CEU][hapmap];0.81[GIH][hapmap];0.86[TSI][hapmap]
rs3019785	0.91[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs320156	0.82[MEX][hapmap];0.81[TSI][hapmap]
rs34134698	0.83[AFR][1000 genomes];0.89[AMR][1000 genomes];0.92[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs34595065	0.85[AMR][1000 genomes];0.89[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs3740636	0.87[MEX][hapmap];0.83[TSI][hapmap];0.83[EUR][1000 genomes]
rs3740637	1.00[ASW][hapmap];0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs449047	0.92[CEU][hapmap];0.86[GIH][hapmap];1.00[LWK][hapmap];0.88[TSI][hapmap];1.00[YRI][hapmap]
rs454474	0.92[CEU][hapmap];0.88[GIH][hapmap];1.00[LWK][hapmap];0.88[TSI][hapmap];1.00[YRI][hapmap]
rs479975	0.90[AMR][1000 genomes];0.92[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs481835	0.87[MEX][hapmap];0.83[TSI][hapmap]
rs483340	0.82[MEX][hapmap];0.81[TSI][hapmap]
rs492357	0.96[CEU][hapmap];0.88[CHB][hapmap];1.00[YRI][hapmap];0.90[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs4980500	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];1.00[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]
rs4980501	0.93[AMR][1000 genomes];0.91[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs4980509	0.88[EUR][1000 genomes]
rs4980512	0.87[MEX][hapmap];0.83[TSI][hapmap];0.83[EUR][1000 genomes]
rs4980517	0.93[AMR][1000 genomes];0.92[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs4980530	0.92[CEU][hapmap];0.81[GIH][hapmap];0.87[MEX][hapmap];0.91[TSI][hapmap];0.82[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs501278	0.88[AMR][1000 genomes];0.88[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs504060	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.90[AMR][1000 genomes];0.92[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs509701	1.00[ASW][hapmap];0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.95[GIH][hapmap];1.00[LWK][hapmap];0.93[MEX][hapmap];1.00[MKK][hapmap];0.95[TSI][hapmap];1.00[YRI][hapmap];0.90[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs567386	0.82[MEX][hapmap];0.81[TSI][hapmap]
rs579669	0.82[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs581355	0.88[AMR][1000 genomes];0.86[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs646384	1.00[YRI][hapmap]
rs660070	1.00[YRI][hapmap]
rs67136175	0.85[EUR][1000 genomes]
rs7112348	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs728919	0.87[MEX][hapmap];0.83[TSI][hapmap];0.83[EUR][1000 genomes]
rs7926608	0.83[AFR][1000 genomes];0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7936614	0.83[AFR][1000 genomes];0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7938498	0.87[MEX][hapmap];0.81[TSI][hapmap]
rs7950543	0.90[AFR][1000 genomes]
rs7951529	0.83[EUR][1000 genomes]
rs928948	0.92[CEU][hapmap];0.87[MEX][hapmap];0.86[TSI][hapmap]
rs947939	1.00[YRI][hapmap]

Variant overlapped rSNPs/rCNVs (count:10 , 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	nsv468589	chr11:63515752-63713239	Weak transcription Strong transcription Transcr. at gene 5' and 3' Genic enhancers Active TSS Enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	39 gene(s)	inside rSNPs	diseases
3	nsv555180	chr11:63515752-63713239	Weak transcription Strong transcription Flanking Active TSS Enhancers Genic enhancers Bivalent Enhancer Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	39 gene(s)	inside rSNPs	diseases
4	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
5	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
6	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
7	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
8	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
9	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
10	esv3321721	chr11:63705201-63707749	Flanking Active TSS Enhancers Active TSS Weak transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	n/a

mRNA abundance (count:13)

SNP	Gene	Cis/trans	Tissue	Source
rs4980499	GANAB	cis	parietal	SCAN
rs4980499	FTH1	cis	parietal	SCAN
rs4980499	MS4A6E	cis	cerebellum	SCAN
rs4980499	MS4A12	cis	parietal	SCAN
rs4980499	HNRNPUL2	cis	parietal	SCAN
rs4980499	HRASLS3	cis	multi-tissue	Pritchard
rs4980499	SCYL1	cis	cerebellum	SCAN
rs4980499	C11orf95	cis	cerebellum	SCAN
rs4980499	RBM4B	cis	cerebellum	SCAN
rs4980499	MS4A8B	cis	parietal	SCAN
rs4980499	SLC22A24	cis	parietal	SCAN
rs4980499	B3GNT1	cis	parietal	SCAN
rs4980499	SLC22A12	cis	parietal	SCAN

Chromatin state (count:127 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:63705000-63707400	Active TSS	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
2	chr11:63705200-63707600	Active TSS	ES-I3 Cell Line	embryonic stem cell
3	chr11:63705200-63707600	Active TSS	H9 Cell Line	embryonic stem cell
4	chr11:63705200-63707600	Active TSS	HUES6 Cell Line	embryonic stem cell
5	chr11:63705200-63707600	Active TSS	iPS-15b Cell Line	embryonic stem cell
6	chr11:63705200-63708400	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
7	chr11:63705400-63707600	Active TSS	HUES48 Cell Line	embryonic stem cell
8	chr11:63705400-63707600	Active TSS	HUES64 Cell Line	embryonic stem cell
9	chr11:63705400-63707600	Active TSS	Fetal Intestine Large	intestine
10	chr11:63705400-63707800	Active TSS	Pancreatic Islets	Pancreatic Islet
11	chr11:63705400-63708000	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
12	chr11:63705400-63708200	Active TSS	iPS-20b Cell Line	embryonic stem cell
13	chr11:63705600-63707400	Active TSS	iPS DF 6.9 Cell Line	embryonic stem cell
14	chr11:63705600-63707400	Active TSS	Psoas Muscle	Psoas
15	chr11:63705600-63707600	Active TSS	iPS-18 Cell Line	embryonic stem cell
16	chr11:63705600-63707600	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
17	chr11:63705600-63707600	Active TSS	Fetal Kidney	kidney
18	chr11:63705800-63707400	Active TSS	Aorta	Aorta
19	chr11:63705800-63707400	Active TSS	Colon Smooth Muscle	Colon
20	chr11:63705800-63707400	Active TSS	Lung	lung
21	chr11:63705800-63707400	Active TSS	NHDF-Ad	bronchial
22	chr11:63705800-63707600	Active TSS	A549	lung
23	chr11:63706000-63707400	Active TSS	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
24	chr11:63706000-63707400	Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
25	chr11:63706000-63707800	Active TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
26	chr11:63706000-63707800	Active TSS	GM12878-XiMat	blood
27	chr11:63706200-63707400	Active TSS	HepG2	liver
28	chr11:63706200-63707600	Active TSS	HSMMtube	muscle
29	chr11:63706400-63708800	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
30	chr11:63706600-63707400	Flanking Active TSS	Primary T cells fromperipheralblood	blood
31	chr11:63706600-63707400	Flanking Active TSS	Primary T helper cells fromperipheralblood	blood
32	chr11:63706600-63707400	Flanking Active TSS	Adipose Nuclei	Adipose
33	chr11:63706600-63707400	Flanking Active TSS	Liver	Liver
34	chr11:63706600-63707600	Flanking Active TSS	Primary B cells from cord blood	blood
35	chr11:63706600-63707600	Flanking Active TSS	Primary hematopoietic stem cells	blood
36	chr11:63706600-63707600	Flanking Active TSS	Primary T regulatory cells fromperipheralblood	blood
37	chr11:63706600-63707600	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
38	chr11:63706600-63707800	Flanking Active TSS	Cortex derived primary cultured neurospheres	brain
39	chr11:63706600-63708800	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
40	chr11:63706800-63707400	Flanking Active TSS	iPS DF 19.11 Cell Line	embryonic stem cell
41	chr11:63706800-63707400	Flanking Active TSS	Primary monocytes fromperipheralblood	blood
42	chr11:63706800-63707400	Flanking Active TSS	Primary B cells from peripheral blood	blood
43	chr11:63706800-63707400	Flanking Active TSS	Primary T helper naive cells from peripheral blood	blood
44	chr11:63706800-63707400	Flanking Active TSS	Primary T helper memory cells from peripheral blood 1	blood
45	chr11:63706800-63707400	Flanking Active TSS	Primary T helper cells PMA-I stimulated	--
46	chr11:63706800-63707400	Flanking Active TSS	Primary T helper 17 cells PMA-I stimulated	--
47	chr11:63706800-63707400	Flanking Active TSS	Primary Natural Killer cells fromperipheralblood	blood
48	chr11:63706800-63707400	Flanking Active TSS	Primary T killer memory cells from peripheral blood	blood
49	chr11:63706800-63707400	Flanking Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
50	chr11:63706800-63707400	Flanking Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin

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