Variant report

Variant	rs4980525
Chromosome Location	chr11:63948354-63948355
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:8)
CpG islands
(count:0)
Chromatin interactive
region (count:10)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

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

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr11:63947964-63948430	K562	blood:	n/a	n/a
2	POLR2A	chr11:63947977-63949668	MCF10A-Er-Src	breast:	n/a	n/a
3	MXI1	chr11:63948182-63949841	SK-N-SH	brain:	n/a	n/a
4	ZBTB7A	chr11:63948220-63948384	K562	blood:	n/a	n/a
5	POLR2A	chr11:63948000-63948677	Hela-S3	cervix:	n/a	n/a
6	POLR2A	chr11:63948218-63948391	HepG2	liver:	n/a	n/a
7	POLR2A	chr11:63947988-63948542	SK-N-MC	brain:	n/a	n/a
8	POLR2A	chr11:63946527-63949471	MCF10A-Er-Src	breast:	n/a	n/a

No data

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

No.	Distal block	Cell Line	Cell type
1	chr11:63929801..63939249-chr11:63945151..63958671,77	MCF-7	breast:
2	chr11:63927314..63929406-chr11:63948232..63951130,3	K562	blood:
3	chr11:63948212..63950691-chr11:64013231..64015499,3	MCF-7	breast:
4	chr11:63929784..63936274-chr11:63944807..63955078,25	K562	blood:
5	chr11:63929784..63936174-chr11:63947045..63954638,30	K562	blood:
6	chr11:63941163..63943232-chr11:63946290..63948899,3	K562	blood:
7	chr11:63779445..63782328-chr11:63947827..63950114,2	K562	blood:
8	chr11:63931311..63936745-chr11:63945647..63958123,49	MCF-7	breast:
9	chr11:63947888..63950001-chr11:63962324..63964689,2	K562	blood:
10	chr11:63943658..63945912-chr11:63947047..63949667,3	K562	blood:

No data

Variant related genes	Relation type
STIP1	TF binding region
ENSG00000168439	Chromatin interaction
ENSG00000256940	Chromatin interaction
ENSG00000133315	Chromatin interaction
ENSG00000173457	Chromatin interaction

Extended variants
information (count: 36 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:18)

rs_ID	r²[population]
rs10897474	0.82[AMR][1000 genomes];0.82[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs11231704	0.85[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs11231741	0.84[JPT][hapmap]
rs1123251	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[AMR][1000 genomes];0.82[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs12787945	0.85[CEU][hapmap]
rs1317494	1.00[JPT][hapmap]
rs2186643	0.85[CEU][hapmap];1.00[CHB][hapmap];0.91[JPT][hapmap]
rs2236647	0.89[CEU][hapmap]
rs2236648	0.85[CEU][hapmap]
rs2325786	0.89[AMR][1000 genomes];0.82[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2875748	0.81[CEU][hapmap]
rs3815362	0.84[JPT][hapmap]
rs4930152	0.84[CHB][hapmap];0.84[JPT][hapmap]
rs4980524	0.82[CEU][hapmap]
rs55970722	0.84[AFR][1000 genomes];0.88[AMR][1000 genomes];0.86[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs627055	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[AFR][1000 genomes];0.83[EUR][1000 genomes]
rs7944314	1.00[YRI][hapmap]
rs882147	0.82[CEU][hapmap]

Variant overlapped rSNPs/rCNVs (count:18 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	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
2	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
3	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
4	nsv1035875	chr11:63800238-64132030	Weak transcription Enhancers Flanking Active TSS Transcr. at gene 5' and 3' Genic enhancers Active TSS Bivalent Enhancer Strong transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	234 gene(s)	inside rSNPs	diseases
5	nsv832185	chr11:63819946-63963532	Flanking Active TSS Enhancers Active TSS Weak transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers Strong transcription Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	89 gene(s)	inside rSNPs	diseases
6	nsv469961	chr11:63822940-64085967	Weak transcription Bivalent/Poised TSS Transcr. at gene 5' and 3' Enhancers Active TSS Flanking Active TSS Genic enhancers Flanking Bivalent TSS/Enh Strong transcription ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	224 gene(s)	inside rSNPs	diseases
7	nsv897660	chr11:63860826-64125142	Weak transcription Active TSS Enhancers Flanking Active TSS Transcr. at gene 5' and 3' Genic enhancers Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	231 gene(s)	inside rSNPs	diseases
8	nsv897661	chr11:63863405-64129722	Flanking Active TSS Enhancers Weak transcription Active TSS Bivalent/Poised TSS Strong transcription Transcr. at gene 5' and 3' Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	233 gene(s)	inside rSNPs	diseases
9	nsv897662	chr11:63889749-64150370	Flanking Active TSS Enhancers Weak transcription Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh Active TSS Strong transcription Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	237 gene(s)	inside rSNPs	diseases
10	nsv897663	chr11:63910153-63962152	Weak transcription Flanking Active TSS Enhancers Transcr. at gene 5' and 3' Strong transcription Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	86 gene(s)	inside rSNPs	n/a
11	nsv897664	chr11:63919742-64150370	Weak transcription Strong transcription Flanking Active TSS Enhancers Genic enhancers Active TSS 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 miRNA target site	237 gene(s)	inside rSNPs	diseases
12	nsv468592	chr11:63924446-64042997	Enhancers Flanking Active TSS Strong transcription Active TSS Weak transcription ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	166 gene(s)	inside rSNPs	diseases
13	nsv555184	chr11:63924446-64042997	Genic enhancers Enhancers Flanking Active TSS Active TSS Strong transcription Weak transcription Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	166 gene(s)	inside rSNPs	diseases
14	nsv897665	chr11:63927695-64026144	Enhancers Weak transcription Flanking Active TSS Strong transcription Active TSS Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	155 gene(s)	inside rSNPs	diseases
15	nsv897666	chr11:63929493-64026144	Enhancers Active TSS Flanking Active TSS Weak transcription Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS Strong transcription Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	155 gene(s)	inside rSNPs	diseases
16	nsv869944	chr11:63932152-64123062	Weak transcription Enhancers Strong transcription Flanking Active TSS Genic enhancers Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	227 gene(s)	inside rSNPs	diseases
17	nsv468593	chr11:63941734-64089874	Flanking Bivalent TSS/Enh Flanking Active TSS Active TSS Enhancers Genic enhancers Strong transcription Weak transcription Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	212 gene(s)	inside rSNPs	diseases
18	nsv555185	chr11:63941734-64089874	Weak transcription Enhancers Active TSS Flanking Active TSS Genic enhancers Bivalent Enhancer Strong transcription 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	212 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs4980525	TRPT1	cis	Muscle Skeletal	GTEx

Chromatin state (count:98 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:63934200-63948800	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
2	chr11:63934200-63950800	Weak transcription	Gastric	stomach
3	chr11:63941600-63949000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
4	chr11:63943200-63949000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
5	chr11:63943600-63951000	Weak transcription	Breast Myoepithelial Primary Cells	Breast
6	chr11:63944600-63949000	Weak transcription	iPS-18 Cell Line	embryonic stem cell
7	chr11:63944800-63948400	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
8	chr11:63944800-63948400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
9	chr11:63944800-63948800	Weak transcription	Primary T helper naive cells from peripheral blood	blood
10	chr11:63944800-63948800	Weak transcription	Primary T helper cells PMA-I stimulated	--
11	chr11:63944800-63948800	Weak transcription	Primary T killer memory cells from peripheral blood	blood
12	chr11:63944800-63950600	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
13	chr11:63945000-63948400	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
14	chr11:63945000-63948600	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
15	chr11:63945000-63948600	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
16	chr11:63945000-63948800	Weak transcription	Primary T helper cells fromperipheralblood	blood
17	chr11:63945000-63949000	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
18	chr11:63945000-63949000	Weak transcription	Dnd41	blood
19	chr11:63945000-63952000	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
20	chr11:63945400-63948400	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
21	chr11:63945400-63948400	Weak transcription	Fetal Kidney	kidney
22	chr11:63945600-63949000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
23	chr11:63945800-63948400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
24	chr11:63945800-63948400	Weak transcription	NH-A	brain
25	chr11:63946200-63948600	Weak transcription	iPS-15b Cell Line	embryonic stem cell
26	chr11:63946200-63948600	Weak transcription	Primary monocytes fromperipheralblood	blood
27	chr11:63946400-63948800	Weak transcription	Primary B cells from peripheral blood	blood
28	chr11:63946600-63948400	Weak transcription	Brain Cingulate Gyrus	brain
29	chr11:63947200-63948400	Enhancers	Fetal Heart	heart
30	chr11:63947400-63948400	Weak transcription	Hela-S3	cervix
31	chr11:63947400-63948800	Weak transcription	HUES64 Cell Line	embryonic stem cell
32	chr11:63947400-63948800	Weak transcription	iPS-20b Cell Line	embryonic stem cell
33	chr11:63947400-63949000	Weak transcription	Primary B cells from cord blood	blood
34	chr11:63947400-63950000	Enhancers	Psoas Muscle	Psoas
35	chr11:63947600-63948800	Weak transcription	HUES48 Cell Line	embryonic stem cell
36	chr11:63947600-63948800	Weak transcription	HUES6 Cell Line	embryonic stem cell
37	chr11:63947600-63949000	Weak transcription	H1 Cell Line	embryonic stem cell
38	chr11:63947600-63949000	Weak transcription	H9 Cell Line	embryonic stem cell
39	chr11:63947600-63952200	Weak transcription	Primary T cells from cord blood	blood
40	chr11:63947800-63949400	Enhancers	Brain Germinal Matrix	brain
41	chr11:63948000-63948400	Enhancers	Brain Anterior Caudate	brain
42	chr11:63948000-63948400	Enhancers	Brain Hippocampus Middle	brain
43	chr11:63948000-63948400	Enhancers	Brain Dorsolateral Prefrontal Cortex	brain
44	chr11:63948000-63948400	Enhancers	Colon Smooth Muscle	Colon
45	chr11:63948000-63948400	Enhancers	Fetal Muscle Leg	muscle
46	chr11:63948000-63948600	Flanking Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
47	chr11:63948000-63948600	Enhancers	HSMM	muscle
48	chr11:63948000-63948800	Enhancers	Duodenum Smooth Muscle	Duodenum
49	chr11:63948000-63948800	Enhancers	Rectal Smooth Muscle	rectum
50	chr11:63948000-63948800	Enhancers	Right Ventricle	heart

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