Variant report

Variant	rs480617
Chromosome Location	chr11:64478320-64478321
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr11:64478005..64481824-chr11:64534394..64538447,4	K562	blood:
2	chr11:64478255..64481463-chr11:64489766..64492365,3	K562	blood:
3	chr11:64476395..64479259-chr11:64497435..64499658,2	K562	blood:
4	chr11:64472309..64475005-chr11:64477653..64479345,2	MCF-7	breast:
5	chr11:64471601..64473400-chr11:64476354..64479027,3	MCF-7	breast:
6	chr11:64477247..64478814-chr11:64479470..64481853,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000110076	Chromatin interaction
ENSG00000168066	Chromatin interaction

Extended variants
information (count: 24 )
Associated
traits (count: 8 )

rSNPs within LD-proxies of this variant (count:3)

rs_ID	r²[population]
rs2518907	0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs475688	0.89[CEU][hapmap];0.82[CHD][hapmap];0.81[GIH][hapmap];0.86[MEX][hapmap]
rs487662	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][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	esv2422214	chr11:64312491-64483418	Weak transcription Enhancers Bivalent/Poised TSS Strong transcription Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Active TSS Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	21 gene(s)	inside rSNPs	diseases
2	nsv832188	chr11:64315368-64485209	Flanking Active TSS Enhancers Active TSS Bivalent Enhancer Weak transcription Flanking Bivalent TSS/Enh Genic enhancers Strong transcription ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	21 gene(s)	inside rSNPs	diseases
3	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
4	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
5	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
6	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
7	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
8	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
9	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
10	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
11	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
12	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
13	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
14	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
15	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
16	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
17	nsv359	chr11:64477008-64502873	Bivalent/Poised TSS Flanking Active TSS Genic enhancers Enhancers Weak transcription Flanking Bivalent TSS/Enh Active TSS Bivalent Enhancer Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	12 gene(s)	inside rSNPs	diseases
18	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
19	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
20	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
21	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

mRNA abundance (count:8)

SNP	Gene	Cis/trans	Tissue	Source
rs480617	MALAT1	cis	parietal	SCAN
rs480617	TMEM138	cis	cerebellum	SCAN
rs480617	SSSCA1	cis	parietal	SCAN
rs480617	MIR192	cis	lymphoblastoid	seeQTL
rs480617	CDC42BPG	cis	parietal	SCAN
rs480617	SF1	cis	lymphoblastoid	seeQTL
rs480617	POLA2	cis	cerebellum	SCAN
rs480617	EHD1	cis	cerebellum	SCAN

Chromatin state (count:61 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:64473400-64478400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
2	chr11:64477000-64478400	Enhancers	Fetal Brain Male	brain
3	chr11:64477600-64478600	Bivalent Enhancer	HUES48 Cell Line	embryonic stem cell
4	chr11:64477600-64478800	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
5	chr11:64477800-64478400	Enhancers	H1 Cell Line	embryonic stem cell
6	chr11:64477800-64478400	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
7	chr11:64477800-64478400	Enhancers	HSMM	muscle
8	chr11:64477800-64478600	Enhancers	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
9	chr11:64477800-64478600	Enhancers	H9 Cell Line	embryonic stem cell
10	chr11:64477800-64478600	Bivalent Enhancer	HUES6 Cell Line	embryonic stem cell
11	chr11:64477800-64478600	Bivalent Enhancer	iPS-20b Cell Line	embryonic stem cell
12	chr11:64477800-64478600	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
13	chr11:64477800-64478600	Bivalent Enhancer	Primary hematopoietic stem cells	blood
14	chr11:64477800-64478600	Enhancers	Brain Angular Gyrus	brain
15	chr11:64477800-64478600	Enhancers	A549	lung
16	chr11:64477800-64478600	Bivalent Enhancer	Osteobl	bone
17	chr11:64477800-64478800	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
18	chr11:64477800-64478800	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
19	chr11:64477800-64478800	Enhancers	Hela-S3	cervix
20	chr11:64477800-64479400	Enhancers	Brain Inferior Temporal Lobe	brain
21	chr11:64477800-64479600	Enhancers	K562	blood
22	chr11:64477800-64479800	Enhancers	Brain Substantia Nigra	brain
23	chr11:64477800-64479800	Flanking Active TSS	Fetal Brain Female	brain
24	chr11:64477800-64481600	Bivalent Enhancer	Foreskin Fibroblast Primary Cells skin02	Skin
25	chr11:64478000-64478400	Flanking Bivalent TSS/Enh	iPS-15b Cell Line	embryonic stem cell
26	chr11:64478000-64478400	Flanking Bivalent TSS/Enh	iPS-18 Cell Line	embryonic stem cell
27	chr11:64478000-64478400	Bivalent Enhancer	Primary T killer memory cells from peripheral blood	blood
28	chr11:64478000-64478600	Enhancers	iPS DF 6.9 Cell Line	embryonic stem cell
29	chr11:64478000-64478600	Enhancers	Brain Cingulate Gyrus	brain
30	chr11:64478000-64478600	Bivalent Enhancer	Stomach Mucosa	stomach
31	chr11:64478000-64478800	Bivalent Enhancer	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
32	chr11:64478000-64478800	Bivalent Enhancer	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
33	chr11:64478000-64478800	Bivalent Enhancer	NH-A	brain
34	chr11:64478000-64479000	Bivalent Enhancer	ES-WA7 Cell Line	embryonic stem cell
35	chr11:64478000-64479200	Enhancers	Brain Hippocampus Middle	brain
36	chr11:64478000-64479200	Bivalent Enhancer	Fetal Kidney	kidney
37	chr11:64478000-64479200	Bivalent Enhancer	Fetal Lung	lung
38	chr11:64478000-64479400	Flanking Active TSS	Brain Germinal Matrix	brain
39	chr11:64478000-64480000	Enhancers	Brain Anterior Caudate	brain
40	chr11:64478000-64480200	Bivalent Enhancer	Fetal Muscle Leg	muscle
41	chr11:64478000-64480800	Bivalent Enhancer	Foreskin Keratinocyte Primary Cells skin03	Skin
42	chr11:64478000-64480800	Weak transcription	Right Atrium	heart
43	chr11:64478000-64481000	Bivalent Enhancer	Foreskin Melanocyte Primary Cells skin01	Skin
44	chr11:64478200-64478400	Flanking Active TSS	ES-I3 Cell Line	embryonic stem cell
45	chr11:64478200-64478400	Flanking Bivalent TSS/Enh	HUES64 Cell Line	embryonic stem cell
46	chr11:64478200-64478400	Bivalent Enhancer	IMR90 fetal lung fibroblasts Cell Line	lung
47	chr11:64478200-64478400	Bivalent Enhancer	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
48	chr11:64478200-64478400	Bivalent Enhancer	Muscle Satellite Cultured Cells	--
49	chr11:64478200-64478400	Flanking Bivalent TSS/Enh	Foreskin Fibroblast Primary Cells skin01	Skin
50	chr11:64478200-64478600	Bivalent Enhancer	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived

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