Variant report

Variant	rs10897466
Chromosome Location	chr11:63723238-63723239
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr11:63531921..63533948-chr11:63721164..63724023,2	K562	blood:
2	chr11:63716457..63721344-chr11:63722093..63724085,4	MCF-7	breast:
3	chr11:63710236..63713268-chr11:63721628..63723810,3	K562	blood:
4	chr11:63717794..63720318-chr11:63722548..63724637,2	K562	blood:
5	chr11:63710236..63713090-chr11:63721173..63723810,3	K562	blood:
6	chr11:63721106..63724001-chr11:63724769..63727723,3	MCF-7	breast:
7	chr11:63721885..63726224-chr11:63740500..63742483,3	K562	blood:

Variant related genes	Relation type
ENSG00000176340	Chromatin interaction
ENSG00000188070	Chromatin interaction
ENSG00000256100	Chromatin interaction
ENSG00000110583	Chromatin interaction

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

rSNPs within LD-proxies of this variant (count:69)

rs_ID	r²[population]
rs10751004	0.83[AMR][1000 genomes];0.94[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs10792424	0.94[EUR][1000 genomes]
rs10897464	1.00[CEU][hapmap];0.97[EUR][1000 genomes]
rs10897467	0.81[EUR][1000 genomes]
rs10897468	0.91[EUR][1000 genomes]
rs11231646	0.85[CEU][hapmap];0.80[TSI][hapmap];0.85[EUR][1000 genomes]
rs11231653	0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11231655	0.80[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs11231657	0.90[LWK][hapmap];0.92[YRI][hapmap];0.82[AFR][1000 genomes]
rs11231659	0.81[AFR][1000 genomes]
rs11231662	0.85[TSI][hapmap]
rs11231671	0.82[JPT][hapmap];0.85[TSI][hapmap]
rs11601228	0.96[AFR][1000 genomes];0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs11605797	0.85[TSI][hapmap]
rs11607028	0.97[EUR][1000 genomes]
rs12417507	0.82[EUR][1000 genomes]
rs12421757	0.82[EUR][1000 genomes]
rs12786124	0.81[TSI][hapmap]
rs12790749	0.86[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs12797540	0.82[EUR][1000 genomes]
rs12798491	0.94[ASW][hapmap];1.00[CEU][hapmap];0.84[CHB][hapmap];1.00[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];0.84[LWK][hapmap];1.00[MEX][hapmap];0.96[MKK][hapmap];0.98[TSI][hapmap];0.92[YRI][hapmap];0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs12800703	0.80[CEU][hapmap]
rs12808604	0.85[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs1386346	1.00[CEU][hapmap];0.98[GIH][hapmap];1.00[MEX][hapmap];0.98[TSI][hapmap];0.98[EUR][1000 genomes]
rs1684950	0.94[EUR][1000 genomes]
rs1783964	0.95[EUR][1000 genomes]
rs2318110	0.84[EUR][1000 genomes]
rs2508584	0.89[EUR][1000 genomes]
rs3019782	0.95[EUR][1000 genomes]
rs320121	0.87[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs320156	1.00[CEU][hapmap];0.86[GIH][hapmap];0.93[MEX][hapmap];0.98[TSI][hapmap];0.94[EUR][1000 genomes]
rs35492216	0.90[EUR][1000 genomes]
rs3740636	1.00[CEU][hapmap];0.82[GIH][hapmap];1.00[MEX][hapmap];0.95[TSI][hapmap];0.97[EUR][1000 genomes]
rs3740637	0.84[MEX][hapmap];0.82[TSI][hapmap];0.82[EUR][1000 genomes]
rs4426138	0.92[EUR][1000 genomes]
rs481835	0.94[ASW][hapmap];1.00[CEU][hapmap];0.84[CHB][hapmap];1.00[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.89[AMR][1000 genomes];0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs483340	1.00[CEU][hapmap];0.93[GIH][hapmap];0.93[MEX][hapmap];0.98[TSI][hapmap];0.94[EUR][1000 genomes]
rs487540	0.94[EUR][1000 genomes]
rs488082	1.00[CEU][hapmap];0.94[EUR][1000 genomes]
rs4980499	0.84[MEX][hapmap];0.83[TSI][hapmap];0.82[EUR][1000 genomes]
rs4980500	0.84[MEX][hapmap];0.83[TSI][hapmap];0.82[EUR][1000 genomes]
rs4980509	0.83[EUR][1000 genomes]
rs4980512	1.00[CEU][hapmap];0.95[GIH][hapmap];1.00[MEX][hapmap];0.95[TSI][hapmap];0.81[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs4980516	0.94[EUR][1000 genomes]
rs499118	0.94[EUR][1000 genomes]
rs500493	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]
rs502858	0.94[EUR][1000 genomes]
rs504314	0.83[EUR][1000 genomes]
rs509701	0.82[TSI][hapmap]
rs528927	0.84[CEU][hapmap];0.89[EUR][1000 genomes]
rs529915	0.95[EUR][1000 genomes]
rs539432	1.00[CEU][hapmap];1.00[JPT][hapmap];0.90[EUR][1000 genomes]
rs553724	1.00[CEU][hapmap];0.93[EUR][1000 genomes]
rs562865	1.00[CEU][hapmap];0.92[EUR][1000 genomes]
rs567386	1.00[CEU][hapmap];0.93[MEX][hapmap];0.98[TSI][hapmap];0.93[EUR][1000 genomes]
rs578295	0.94[EUR][1000 genomes]
rs58341870	0.87[AFR][1000 genomes]
rs6591830	0.92[EUR][1000 genomes]
rs709594	0.93[EUR][1000 genomes]
rs7111130	0.85[EUR][1000 genomes]
rs7112348	0.81[EUR][1000 genomes]
rs728919	1.00[CEU][hapmap];0.95[GIH][hapmap];1.00[MEX][hapmap];0.95[TSI][hapmap];0.97[EUR][1000 genomes]
rs7926608	0.81[EUR][1000 genomes]
rs7928990	0.89[AMR][1000 genomes];0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7936614	0.81[EUR][1000 genomes]
rs7938498	1.00[CEU][hapmap];0.95[GIH][hapmap];1.00[MEX][hapmap];0.98[TSI][hapmap];0.95[EUR][1000 genomes]
rs7942318	0.94[EUR][1000 genomes]
rs7951529	0.97[EUR][1000 genomes]
rs9943682	0.88[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:8 , 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

mRNA abundance (count:10)

SNP	Gene	Cis/trans	Tissue	Source
rs10897466	FTH1	cis	parietal	SCAN
rs10897466	GPR137	cis	parietal	SCAN
rs10897466	SLC22A12	cis	parietal	SCAN
rs10897466	EHD1	cis	parietal	SCAN
rs10897466	B3GNT1	cis	parietal	SCAN
rs10897466	SLC22A24	cis	parietal	SCAN
rs10897466	PLCB3	cis	cerebellum	SCAN
rs10897466	HNRNPUL2	cis	parietal	SCAN
rs10897466	RBM4B	cis	cerebellum	SCAN
rs10897466	MS4A6E	cis	cerebellum	SCAN

Chromatin state (count:124 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:63707200-63724200	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
2	chr11:63708200-63723400	Weak transcription	NH-A	brain
3	chr11:63713200-63725400	Weak transcription	Psoas Muscle	Psoas
4	chr11:63713200-63725800	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
5	chr11:63713400-63724200	Strong transcription	K562	blood
6	chr11:63713400-63725200	Strong transcription	Fetal Intestine Small	intestine
7	chr11:63713400-63725400	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
8	chr11:63713400-63725800	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
9	chr11:63713400-63726200	Strong transcription	Fetal Stomach	stomach
10	chr11:63713400-63726800	Weak transcription	Fetal Brain Male	brain
11	chr11:63713400-63733800	Weak transcription	Right Atrium	heart
12	chr11:63713600-63724200	Strong transcription	iPS-20b Cell Line	embryonic stem cell
13	chr11:63713600-63724200	Strong transcription	Cortex derived primary cultured neurospheres	brain
14	chr11:63713600-63724400	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
15	chr11:63713600-63725200	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
16	chr11:63713600-63726000	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
17	chr11:63713800-63724400	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
18	chr11:63713800-63726000	Strong transcription	Fetal Muscle Leg	muscle
19	chr11:63714000-63726200	Strong transcription	Fetal Muscle Trunk	muscle
20	chr11:63716400-63724000	Strong transcription	Sigmoid Colon	Sigmoid Colon
21	chr11:63717600-63726200	Strong transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
22	chr11:63717600-63726200	Strong transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
23	chr11:63717800-63724000	Strong transcription	HSMMtube	muscle
24	chr11:63717800-63726000	Strong transcription	Brain Germinal Matrix	brain
25	chr11:63717800-63726000	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
26	chr11:63718200-63724000	Strong transcription	Monocytes-CD14+_RO01746	blood
27	chr11:63718200-63725800	Strong transcription	Foreskin Fibroblast Primary Cells skin01	Skin
28	chr11:63718800-63726000	Strong transcription	Fetal Brain Female	brain
29	chr11:63719000-63724000	Strong transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
30	chr11:63719000-63724000	Strong transcription	Hela-S3	cervix
31	chr11:63719000-63724200	Strong transcription	Fetal Lung	lung
32	chr11:63719200-63725800	Strong transcription	HUES6 Cell Line	embryonic stem cell
33	chr11:63719400-63723800	Strong transcription	HepG2	liver
34	chr11:63719400-63724200	Strong transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
35	chr11:63719400-63724200	Strong transcription	Skeletal Muscle Male	skeletal muscle
36	chr11:63719400-63724200	Strong transcription	Spleen	Spleen
37	chr11:63719400-63726000	Strong transcription	iPS-15b Cell Line	embryonic stem cell
38	chr11:63719600-63724000	Strong transcription	Primary monocytes fromperipheralblood	blood
39	chr11:63719600-63724000	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
40	chr11:63719600-63724000	Strong transcription	Brain Cingulate Gyrus	brain
41	chr11:63719600-63724200	Strong transcription	H9 Cell Line	embryonic stem cell
42	chr11:63719600-63724200	Strong transcription	HUES48 Cell Line	embryonic stem cell
43	chr11:63719600-63724200	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
44	chr11:63719600-63724200	Strong transcription	Brain Angular Gyrus	brain
45	chr11:63719600-63724200	Strong transcription	Lung	lung
46	chr11:63719600-63724200	Strong transcription	Right Ventricle	heart
47	chr11:63719600-63724400	Strong transcription	Gastric	stomach
48	chr11:63719600-63725200	Strong transcription	iPS-18 Cell Line	embryonic stem cell
49	chr11:63719600-63725200	Strong transcription	Pancreas	Pancrea
50	chr11:63719600-63725800	Strong transcription	H1 Cell Line	embryonic stem cell

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