Variant report

Variant	rs477549
Chromosome Location	chr11:64527080-64527081
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr11:64507790..64516181-chr11:64524582..64537783,30	K562	blood:

Variant related genes	Relation type
ENSG00000068831	Chromatin interaction

Extended variants
information (count: 84 )
Associated
traits (count: 14 )

rSNPs within LD-proxies of this variant (count:63)

rs_ID	r²[population]
rs10400348	0.82[EUR][1000 genomes]
rs10792444	0.84[EUR][1000 genomes]
rs10897524	0.88[TSI][hapmap];0.97[EUR][1000 genomes]
rs10897525	0.89[MEX][hapmap]
rs11231853	0.86[CEU][hapmap];0.84[EUR][1000 genomes]
rs11231859	1.00[CEU][hapmap];0.83[MEX][hapmap];0.82[TSI][hapmap];0.95[EUR][1000 genomes]
rs11231869	0.88[CHD][hapmap];0.90[GIH][hapmap];0.85[JPT][hapmap];0.89[MEX][hapmap];0.81[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs1143937	1.00[CEU][hapmap];0.86[GIH][hapmap];0.89[MEX][hapmap]
rs1207181	0.86[EUR][1000 genomes]
rs12223914	0.83[EUR][1000 genomes]
rs12417551	0.85[EUR][1000 genomes]
rs12575704	0.84[EUR][1000 genomes]
rs1633462	1.00[CEU][hapmap];0.95[CHB][hapmap];0.90[JPT][hapmap];0.96[AMR][1000 genomes];0.93[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs17146121	0.89[CEU][hapmap];0.89[MEX][hapmap];0.81[EUR][1000 genomes]
rs2003293	0.95[EUR][1000 genomes]
rs2073797	0.86[EUR][1000 genomes]
rs2073798	0.86[CHB][hapmap];0.81[CHD][hapmap];0.86[GIH][hapmap];0.89[MEX][hapmap];0.82[TSI][hapmap];0.86[EUR][1000 genomes]
rs2230414	0.95[EUR][1000 genomes]
rs2267918	1.00[CEU][hapmap];0.94[MEX][hapmap];0.88[TSI][hapmap];0.97[EUR][1000 genomes]
rs2284301	1.00[CEU][hapmap];0.81[CHB][hapmap];0.83[MEX][hapmap];0.88[TSI][hapmap];0.97[EUR][1000 genomes]
rs2375335	0.93[EUR][1000 genomes]
rs2959652	1.00[CEU][hapmap];0.86[CHB][hapmap];0.81[CHD][hapmap];0.86[GIH][hapmap];0.89[MEX][hapmap];0.94[TSI][hapmap];0.97[EUR][1000 genomes]
rs3741398	1.00[CEU][hapmap];0.86[CHB][hapmap];0.91[CHD][hapmap];1.00[GIH][hapmap];0.85[JPT][hapmap];0.94[MEX][hapmap];0.88[TSI][hapmap];0.88[AMR][1000 genomes];0.87[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs3809076	0.89[CEU][hapmap];0.89[MEX][hapmap];0.82[TSI][hapmap];0.90[EUR][1000 genomes]
rs474707	0.81[CEU][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];1.00[GIH][hapmap];0.95[JPT][hapmap];0.80[LWK][hapmap];1.00[MEX][hapmap];0.83[MKK][hapmap];0.94[TSI][hapmap];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs476037	0.89[CEU][hapmap];0.89[MEX][hapmap];0.81[EUR][1000 genomes]
rs483962	1.00[CEU][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];1.00[GIH][hapmap];0.95[JPT][hapmap];1.00[MEX][hapmap];0.94[TSI][hapmap];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs487105	1.00[CEU][hapmap];0.95[CHB][hapmap];0.91[CHD][hapmap];1.00[GIH][hapmap];0.90[JPT][hapmap];0.94[MEX][hapmap];0.88[TSI][hapmap];0.96[AMR][1000 genomes];0.93[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs489192	1.00[CEU][hapmap];0.86[CHB][hapmap];0.86[GIH][hapmap];0.80[JPT][hapmap];0.82[TSI][hapmap];0.85[EUR][1000 genomes]
rs490980	0.89[CEU][hapmap];0.90[EUR][1000 genomes]
rs494128	0.92[EUR][1000 genomes]
rs496914	1.00[CEU][hapmap];0.89[MEX][hapmap];0.88[TSI][hapmap];0.97[EUR][1000 genomes]
rs523200	1.00[CEU][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];1.00[GIH][hapmap];0.95[JPT][hapmap];0.94[MEX][hapmap];0.88[TSI][hapmap];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs523752	0.83[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs532747	0.89[MEX][hapmap];0.83[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs547066	0.85[GIH][hapmap];0.88[MEX][hapmap];0.83[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs555974	0.86[EUR][1000 genomes]
rs569602	0.86[CHB][hapmap];0.81[CHD][hapmap];0.89[MEX][hapmap];0.85[EUR][1000 genomes]
rs580374	0.97[EUR][1000 genomes]
rs58483071	0.95[EUR][1000 genomes]
rs589691	1.00[CEU][hapmap];0.85[CHB][hapmap];0.86[GIH][hapmap];0.89[MEX][hapmap];0.88[TSI][hapmap];0.95[EUR][1000 genomes]
rs593394	0.96[AMR][1000 genomes];0.93[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs606458	1.00[CEU][hapmap];0.95[CHB][hapmap];0.90[CHD][hapmap];1.00[GIH][hapmap];0.90[JPT][hapmap];0.94[MEX][hapmap];0.88[TSI][hapmap];0.89[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs607389	1.00[CEU][hapmap];0.81[CHB][hapmap];0.85[JPT][hapmap];0.90[AMR][1000 genomes];0.87[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs620006	0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs624975	0.90[CEU][hapmap];0.82[GIH][hapmap];0.89[MEX][hapmap]
rs625172	0.86[CHB][hapmap];0.81[CHD][hapmap];0.86[GIH][hapmap];0.89[MEX][hapmap];0.82[TSI][hapmap];0.86[EUR][1000 genomes]
rs630966	0.86[EUR][1000 genomes]
rs633923	0.98[AMR][1000 genomes];0.95[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs637332	1.00[CEU][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];1.00[GIH][hapmap];0.95[JPT][hapmap];0.80[LWK][hapmap];1.00[MEX][hapmap];0.94[MKK][hapmap];0.94[TSI][hapmap];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs667237	0.95[EUR][1000 genomes]
rs669976	0.90[CEU][hapmap];0.86[GIH][hapmap];0.89[MEX][hapmap]
rs674297	0.94[AMR][1000 genomes];0.92[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs677298	1.00[CEU][hapmap];0.83[MEX][hapmap];0.81[AMR][1000 genomes]
rs680273	1.00[CEU][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];0.90[GIH][hapmap];0.95[JPT][hapmap];0.94[MEX][hapmap];0.88[TSI][hapmap];0.92[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs683841	0.87[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs684720	0.94[AMR][1000 genomes];0.84[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs686171	0.83[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs693235	0.90[CEU][hapmap];0.89[MEX][hapmap];0.88[TSI][hapmap]
rs72643567	0.89[EUR][1000 genomes]
rs72643568	0.89[EUR][1000 genomes]
rs7938455	0.81[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs7939965	0.89[CEU][hapmap];0.89[MEX][hapmap];0.84[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:21 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv468596	chr11:64334114-64527080	Flanking Bivalent TSS/Enh Weak transcription Genic enhancers Active TSS Enhancers Bivalent Enhancer Flanking Active TSS Bivalent/Poised TSS Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	28 gene(s)	inside rSNPs	diseases
2	nsv555195	chr11:64334114-64527080	Bivalent Enhancer Weak transcription Strong transcription Flanking Bivalent TSS/Enh Enhancers Genic enhancers Flanking Active TSS Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	28 gene(s)	inside rSNPs	diseases
3	nsv897694	chr11:64334114-64584959	Weak transcription Bivalent/Poised TSS Bivalent Enhancer Enhancers Flanking Bivalent TSS/Enh Active TSS Strong transcription Genic enhancers ZNF genes & repeats Flanking Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	83 gene(s)	inside rSNPs	diseases
4	nsv818842	chr11:64345448-64546391	Bivalent Enhancer Enhancers Weak transcription Strong transcription Active TSS Genic enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	75 gene(s)	inside rSNPs	diseases
5	nsv528506	chr11:64345448-64701030	Strong transcription Weak transcription Enhancers Flanking Bivalent TSS/Enh Active TSS Genic enhancers Flanking Active TSS Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	1075 gene(s)	inside rSNPs	diseases
6	nsv555196	chr11:64357072-64559898	Enhancers Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Weak transcription Bivalent/Poised TSS Active TSS Strong transcription Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	77 gene(s)	inside rSNPs	diseases
7	nsv897695	chr11:64357072-64701030	Weak transcription Genic enhancers Enhancers Active TSS Transcr. at gene 5' and 3' Strong transcription Flanking Active TSS Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	1075 gene(s)	inside rSNPs	diseases
8	nsv1051350	chr11:64372906-64533632	Weak transcription Active TSS Enhancers Flanking Active TSS Bivalent/Poised TSS Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Strong transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	33 gene(s)	inside rSNPs	diseases
9	nsv555198	chr11:64373899-64573589	Weak transcription Transcr. at gene 5' and 3' Genic enhancers Enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Flanking Active TSS Active TSS Strong transcription Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	80 gene(s)	inside rSNPs	diseases
10	esv1804443	chr11:64386453-64534785	Weak transcription Bivalent Enhancer Enhancers Flanking Active TSS Bivalent/Poised TSS Active TSS Flanking Bivalent TSS/Enh Strong transcription Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	33 gene(s)	inside rSNPs	diseases
11	nsv897697	chr11:64447420-64584959	Flanking Bivalent TSS/Enh Weak transcription Enhancers Flanking Active TSS Genic enhancers Bivalent Enhancer Active TSS Bivalent/Poised TSS Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	79 gene(s)	inside rSNPs	diseases
12	nsv897698	chr11:64447420-64621573	Active TSS Bivalent Enhancer Genic enhancers Enhancers Weak transcription Flanking Active TSS Strong transcription 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	82 gene(s)	inside rSNPs	diseases
13	nsv897699	chr11:64447420-64638041	Flanking Active TSS Active TSS Transcr. at gene 5' and 3' Strong transcription Enhancers Weak transcription Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	83 gene(s)	inside rSNPs	diseases
14	nsv897700	chr11:64447420-64701030	Flanking Active TSS Enhancers Active TSS Strong transcription Genic enhancers Transcr. at gene 5' and 3' Weak transcription Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	1071 gene(s)	inside rSNPs	diseases
15	nsv555202	chr11:64477050-64573589	Strong transcription Bivalent/Poised TSS Enhancers Active TSS Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Weak transcription Flanking Bivalent TSS/Enh Flanking Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	73 gene(s)	inside rSNPs	diseases
16	nsv468597	chr11:64477050-64584959	Enhancers Strong transcription Flanking Active TSS Flanking Bivalent TSS/Enh Genic enhancers Active TSS Weak transcription Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	77 gene(s)	inside rSNPs	diseases
17	nsv468598	chr11:64477050-64584959	Weak transcription Flanking Active TSS Strong transcription Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS Active TSS Enhancers Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	77 gene(s)	inside rSNPs	diseases
18	nsv555203	chr11:64477050-64584959	Strong transcription Genic enhancers Bivalent Enhancer Active TSS Enhancers Flanking Bivalent TSS/Enh Weak transcription Flanking 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	77 gene(s)	inside rSNPs	diseases
19	nsv1049744	chr11:64486615-64630149	Flanking Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Active TSS Weak transcription Enhancers Genic enhancers Strong transcription Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	79 gene(s)	inside rSNPs	diseases
20	nsv832189	chr11:64487183-64620199	Weak transcription Transcr. at gene 5' and 3' Active TSS Enhancers Strong transcription Flanking Active TSS Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	79 gene(s)	inside rSNPs	diseases
21	nsv469962	chr11:64527080-64621573	Flanking Active TSS Enhancers Weak transcription Genic enhancers Active TSS Strong transcription Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	72 gene(s)	inside rSNPs	diseases

mRNA abundance (count:14)

SNP	Gene	Cis/trans	Tissue	Source
rs477549	LRRN4CL	cis	cerebellum	SCAN
rs477549	B3GNT1	cis	cerebellum	SCAN
rs477549	PYGM	cis	cerebellum	SCAN
rs477549	ANKRD13D	cis	parietal	SCAN
rs477549	SF1	cis	lymphoblastoid	seeQTL
rs477549	PYGM	cis	parietal	SCAN
rs477549	POLA2	cis	cerebellum	SCAN
rs477549	TMEM138	cis	cerebellum	SCAN
rs477549	SF1	cis	multi-tissue	Pritchard
rs477549	EHD1	cis	cerebellum	SCAN
rs477549	TMEM138	cis	parietal	SCAN
rs477549	CABP2	cis	parietal	SCAN
rs477549	SF1	Cis_1M	lymphoblastoid	RTeQTL
rs477549	MALAT1	cis	parietal	SCAN

Chromatin state (count:109 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:64513400-64529800	Weak transcription	Liver	Liver
2	chr11:64513400-64530000	Weak transcription	Aorta	Aorta
3	chr11:64514000-64529800	Weak transcription	Primary monocytes fromperipheralblood	blood
4	chr11:64514600-64529800	Weak transcription	Dnd41	blood
5	chr11:64515200-64527600	Weak transcription	Primary hematopoietic stem cells	blood
6	chr11:64516000-64527400	Weak transcription	Fetal Intestine Small	intestine
7	chr11:64516000-64529800	Weak transcription	Fetal Brain Female	brain
8	chr11:64518400-64527600	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
9	chr11:64518800-64527400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
10	chr11:64520600-64529600	Weak transcription	NHEK	skin
11	chr11:64521000-64527400	Weak transcription	Primary neutrophils fromperipheralblood	blood
12	chr11:64521400-64527200	Transcr. at gene 5' and 3'	Skeletal Muscle Female	skeletal muscle
13	chr11:64521400-64527400	Transcr. at gene 5' and 3'	Skeletal Muscle Male	skeletal muscle
14	chr11:64521800-64527400	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
15	chr11:64523600-64527400	Weak transcription	Gastric	stomach
16	chr11:64524400-64527200	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
17	chr11:64524600-64529600	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
18	chr11:64524800-64530000	Strong transcription	Thymus	Thymus
19	chr11:64525000-64529800	Enhancers	Primary T helper naive cells fromperipheralblood	blood
20	chr11:64525000-64530000	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
21	chr11:64525000-64530400	Enhancers	Primary T killer naive cells fromperipheralblood	blood
22	chr11:64525200-64527600	Genic enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
23	chr11:64525200-64530000	Enhancers	Primary T helper cells fromperipheralblood	blood
24	chr11:64525400-64533400	Genic enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
25	chr11:64525800-64528400	Enhancers	Placenta	Placenta
26	chr11:64525800-64528800	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
27	chr11:64525800-64528800	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
28	chr11:64526000-64527400	Enhancers	Primary B cells from peripheral blood	blood
29	chr11:64526000-64528000	Enhancers	Primary T killer memory cells from peripheral blood	blood
30	chr11:64526000-64528200	Flanking Active TSS	Stomach Smooth Muscle	stomach
31	chr11:64526000-64528200	Genic enhancers	Spleen	Spleen
32	chr11:64526000-64528400	Enhancers	Primary T cells fromperipheralblood	blood
33	chr11:64526000-64530400	Enhancers	H1 Cell Line	embryonic stem cell
34	chr11:64526000-64530600	Enhancers	Primary T helper naive cells from peripheral blood	blood
35	chr11:64526200-64527200	Enhancers	HUES64 Cell Line	embryonic stem cell
36	chr11:64526200-64527200	Enhancers	Brain Inferior Temporal Lobe	brain
37	chr11:64526200-64527400	Weak transcription	Breast Myoepithelial Primary Cells	Breast
38	chr11:64526200-64527800	Flanking Active TSS	Fetal Muscle Trunk	muscle
39	chr11:64526200-64528000	Flanking Active TSS	Fetal Muscle Leg	muscle
40	chr11:64526200-64528600	Enhancers	Rectal Mucosa Donor 29	rectum
41	chr11:64526200-64528600	Enhancers	Hela-S3	cervix
42	chr11:64526200-64531200	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
43	chr11:64526400-64527200	Enhancers	HUES6 Cell Line	embryonic stem cell
44	chr11:64526400-64527200	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
45	chr11:64526400-64527400	Active TSS	Brain Substantia Nigra	brain
46	chr11:64526400-64527400	Active TSS	Right Atrium	heart
47	chr11:64526400-64528400	Enhancers	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
48	chr11:64526400-64528600	Enhancers	iPS DF 6.9 Cell Line	embryonic stem cell
49	chr11:64526400-64528600	Enhancers	Primary hematopoietic stem cells short term culture	blood
50	chr11:64526400-64528800	Enhancers	Ovary	ovary

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