Variant report

Variant	rs4075475
Chromosome Location	chr15:77309419-77309420
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	EBF1	chr15:77309348-77309970	GM12878	blood:	n/a	chr15:77309746-77309757 chr15:77309747-77309756
2	MYC	chr15:77309398-77309475	H1-hESC	embryonic stem cell:	n/a	n/a

Variant related genes	Relation type
PSTPIP1	TF binding region

Extended variants
information (count: 28 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:10)

rs_ID	r²[population]
rs11072639	1.00[JPT][hapmap];0.83[ASN][1000 genomes]
rs11854745	0.88[JPT][hapmap]
rs11858973	0.88[JPT][hapmap]
rs16968616	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.94[LWK][hapmap];1.00[MKK][hapmap];1.00[YRI][hapmap];0.85[AFR][1000 genomes];0.93[EUR][1000 genomes]
rs2469228	1.00[CEU][hapmap];1.00[CHB][hapmap]
rs2469235	1.00[CEU][hapmap];1.00[CHB][hapmap];0.88[JPT][hapmap];0.89[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs3812912	1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.87[LWK][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs57036819	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs62007170	0.82[ASN][1000 genomes]
rs74024533	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]

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	esv3440794	chr15:76764595-77571114	Weak transcription Enhancers Strong transcription Active TSS Flanking Active TSS Genic enhancers ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	25 gene(s)	inside rSNPs	diseases
2	esv3367577	chr15:77015618-77442634	Genic enhancers Weak transcription Strong transcription Enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Flanking Active TSS Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	20 gene(s)	inside rSNPs	diseases
3	nsv1040852	chr15:77160237-78137541	Enhancers Flanking Active TSS Active TSS Strong transcription Weak transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	42 gene(s)	inside rSNPs	diseases
4	esv2758388	chr15:77170550-77373448	Weak transcription Enhancers Flanking Active TSS Genic enhancers Strong transcription Bivalent Enhancer Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	18 gene(s)	inside rSNPs	diseases
5	esv2760041	chr15:77170550-77373448	Enhancers Genic enhancers Weak transcription Flanking Active TSS Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Strong transcription Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	18 gene(s)	inside rSNPs	diseases
6	nsv833058	chr15:77235895-77393640	Enhancers Strong transcription Active TSS Weak transcription Flanking Active TSS Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases
7	nsv517068	chr15:77254544-77381222	Enhancers Weak transcription Genic enhancers Active TSS Flanking Active TSS Strong transcription Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases
8	esv1808532	chr15:77257714-77332539	Weak transcription Strong transcription Flanking Active TSS Enhancers Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
9	nsv1043017	chr15:77266776-77309938	Weak transcription Enhancers Flanking Active TSS Genic enhancers Bivalent Enhancer ZNF genes & repeats Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Strong transcription Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
10	nsv1035874	chr15:77266776-77328742	Enhancers Weak transcription Bivalent Enhancer Active TSS Flanking Active TSS Genic enhancers Strong transcription Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
11	esv1822592	chr15:77283956-77332539	Flanking Active TSS Weak transcription Genic enhancers Enhancers ZNF genes & repeats Active TSS Strong transcription Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region	3 gene(s)	inside rSNPs	diseases
12	nsv570111	chr15:77286693-77332606	Genic enhancers Flanking Active TSS Weak transcription Enhancers Strong transcription Active TSS ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region	3 gene(s)	inside rSNPs	diseases
13	nsv1048833	chr15:77294593-77339260	Strong transcription Enhancers Weak transcription Genic enhancers Flanking Active TSS Bivalent Enhancer ZNF genes & repeats Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
14	esv1848501	chr15:77301357-77327571	Bivalent Enhancer Enhancers Weak transcription Transcr. at gene 5' and 3' Genic enhancers Flanking Active TSS Strong transcription Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region	2 gene(s)	inside rSNPs	diseases
15	esv1804890	chr15:77302969-77332482	Strong transcription Enhancers Weak transcription Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Active TSS ZNF genes & repeats Flanking Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	3 gene(s)	inside rSNPs	diseases
16	esv1836749	chr15:77302969-77332606	Genic enhancers Enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Strong transcription Weak transcription Flanking Active TSS Active TSS Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	3 gene(s)	inside rSNPs	diseases
17	nsv904414	chr15:77304310-77400388	Weak transcription Enhancers Strong transcription Flanking Active TSS Genic enhancers Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
18	esv1842687	chr15:77307260-77332606	Weak transcription Bivalent Enhancer Flanking Active TSS Active TSS Genic enhancers Enhancers Flanking Bivalent TSS/Enh Strong transcription Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	3 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs4075475	KCNQ1OT1	trans	lymphoblastoid	seeQTL

Chromatin state (count:47 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:77289200-77311200	Weak transcription	Aorta	Aorta
2	chr15:77289400-77310000	Weak transcription	Colon Smooth Muscle	Colon
3	chr15:77303000-77319600	Weak transcription	Pancreas	Pancrea
4	chr15:77304600-77310600	Enhancers	Primary B cells from cord blood	blood
5	chr15:77304800-77312600	Enhancers	Fetal Thymus	thymus
6	chr15:77305000-77310200	Enhancers	Primary hematopoietic stem cells short term culture	blood
7	chr15:77306000-77311400	Enhancers	Primary T killer naive cells fromperipheralblood	blood
8	chr15:77306200-77309600	Enhancers	Primary T helper naive cells fromperipheralblood	blood
9	chr15:77306200-77310200	Enhancers	Primary T helper naive cells from peripheral blood	blood
10	chr15:77306600-77310200	Enhancers	Primary T cells effector/memory enriched fromperipheralblood	blood
11	chr15:77306600-77314000	Weak transcription	NHEK	skin
12	chr15:77306600-77316800	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
13	chr15:77306800-77311200	Enhancers	Primary T killer memory cells from peripheral blood	blood
14	chr15:77307200-77310000	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
15	chr15:77307200-77310400	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
16	chr15:77307200-77310400	Enhancers	Primary T helper cells PMA-I stimulated	--
17	chr15:77307400-77309800	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
18	chr15:77307400-77322400	Weak transcription	Sigmoid Colon	Sigmoid Colon
19	chr15:77307600-77310800	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
20	chr15:77307800-77310400	Weak transcription	Thymus	Thymus
21	chr15:77307800-77320800	Weak transcription	Rectal Mucosa Donor 29	rectum
22	chr15:77308000-77310000	Bivalent Enhancer	Fetal Adrenal Gland	Adrenal Gland
23	chr15:77308000-77311000	Enhancers	Duodenum Mucosa	Duodenum
24	chr15:77308400-77309600	Weak transcription	Colonic Mucosa	Colon
25	chr15:77308400-77310000	Enhancers	HSMMtube	muscle
26	chr15:77308400-77313200	Weak transcription	Skeletal Muscle Female	skeletal muscle
27	chr15:77308600-77310000	Genic enhancers	Primary T regulatory cells fromperipheralblood	blood
28	chr15:77308600-77311800	Weak transcription	Placenta	Placenta
29	chr15:77308600-77314200	Weak transcription	Placenta Amnion	Placenta Amnion
30	chr15:77308600-77317400	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
31	chr15:77308800-77311800	Weak transcription	Left Ventricle	heart
32	chr15:77308800-77314200	Weak transcription	Right Atrium	heart
33	chr15:77308800-77327600	Weak transcription	Esophagus	oesophagus
34	chr15:77309000-77309600	Enhancers	Primary T helper cells fromperipheralblood	blood
35	chr15:77309000-77309800	Weak transcription	Primary B cells from peripheral blood	blood
36	chr15:77309000-77310600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
37	chr15:77309000-77311200	Weak transcription	Fetal Muscle Leg	muscle
38	chr15:77309000-77311400	Weak transcription	GM12878-XiMat	blood
39	chr15:77309000-77312000	Weak transcription	Primary hematopoietic stem cells	blood
40	chr15:77309000-77313400	Genic enhancers	Primary monocytes fromperipheralblood	blood
41	chr15:77309200-77313000	Genic enhancers	Monocytes-CD14+_RO01746	blood
42	chr15:77309200-77315400	Genic enhancers	Primary mononuclear cells fromperipheralblood	Blood
43	chr15:77309400-77310000	Enhancers	Primary neutrophils fromperipheralblood	blood
44	chr15:77309400-77310600	Genic enhancers	Primary T cells from cord blood	blood
45	chr15:77309400-77313000	Genic enhancers	Primary T helper 17 cells PMA-I stimulated	--
46	chr15:77309400-77316000	Genic enhancers	Spleen	Spleen
47	chr15:77309400-77320000	Genic enhancers	Primary T cells fromperipheralblood	blood

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