Variant report

Variant	rs351223
Chromosome Location	chr15:74499407-74499408
allele	C/T
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	TCF12	chr15:74498916-74499807	ECC-1	luminal epithelium:	n/a	n/a
2	EP300	chr15:74498962-74499879	ECC-1	luminal epithelium:	n/a	n/a
3	USF1	chr15:74498993-74499646	ECC-1	luminal epithelium:	n/a	n/a
4	TCF7L2	chr15:74499363-74499649	Hela-S3	cervix:	n/a	n/a
5	RAD21	chr15:74499192-74499730	ECC-1	luminal epithelium:	n/a	n/a
6	TCF12	chr15:74499078-74499848	ECC-1	luminal epithelium:	n/a	n/a
7	MXI1	chr15:74499385-74499635	Hela-S3	cervix:	n/a	n/a
8	USF1	chr15:74498922-74499662	ECC-1	luminal epithelium:	n/a	n/a
9	TEAD4	chr15:74499200-74499760	ECC-1	luminal epithelium:	n/a	n/a
10	EP300	chr15:74499101-74499732	ECC-1	luminal epithelium:	n/a	n/a
11	NFIC	chr15:74498896-74500428	ECC-1	luminal epithelium:	n/a	chr15:74499534-74499550
12	MAX	chr15:74499010-74499664	Hela-S3	cervix:	n/a	chr15:74499088-74499107 chr15:74499488-74499497 chr15:74499190-74499200 chr15:74499028-74499038 chr15:74499491-74499498 chr15:74499489-74499499 chr15:74499191-74499201
13	NFIC	chr15:74498963-74499869	ECC-1	luminal epithelium:	n/a	chr15:74499534-74499550
14	MAX	chr15:74499345-74499673	Hela-S3	cervix:	n/a	chr15:74499488-74499497 chr15:74499491-74499498 chr15:74499489-74499499
15	TEAD4	chr15:74499036-74499803	ECC-1	luminal epithelium:	n/a	n/a
16	MAX	chr15:74498998-74499726	ECC-1	luminal epithelium:	n/a	chr15:74499088-74499107 chr15:74499488-74499497 chr15:74499190-74499200 chr15:74499028-74499038 chr15:74499491-74499498 chr15:74499489-74499499 chr15:74499191-74499201
17	MAX	chr15:74498903-74499789	ECC-1	luminal epithelium:	n/a	chr15:74499088-74499107 chr15:74499488-74499497 chr15:74499190-74499200 chr15:74499028-74499038 chr15:74499491-74499498 chr15:74499489-74499499 chr15:74499191-74499201

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr15:74497610..74499444-chr15:74504967..74507735,2	K562	blood:
2	chr15:74497783..74499933-chr15:74500852..74503314,2	K562	blood:

Variant related genes	Relation type
STRA6	TF binding region
ENSG00000137868	Chromatin interaction

Extended variants
information (count: 17 )
Associated
traits (count: 0)

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

rs_ID	r²[population]
rs10851870	0.89[AFR][1000 genomes];0.99[ASN][1000 genomes]
rs12911385	0.82[ASN][1000 genomes]
rs17386715	0.81[CEU][hapmap];0.90[AMR][1000 genomes];0.85[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs2629727	0.88[CEU][hapmap];0.83[JPT][hapmap];0.85[YRI][hapmap];0.92[AMR][1000 genomes];0.90[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs351156	0.85[AFR][1000 genomes];0.86[ASN][1000 genomes]
rs351219	0.95[CHB][hapmap];0.95[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.91[ASN][1000 genomes]
rs351220	0.90[ASN][1000 genomes]
rs351222	1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs351224	1.00[ASW][hapmap];0.92[CEU][hapmap];0.95[CHB][hapmap];0.95[CHD][hapmap];0.95[JPT][hapmap];0.93[LWK][hapmap];0.90[MEX][hapmap];0.80[MKK][hapmap];0.95[TSI][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs531491	0.94[ASW][hapmap];0.95[GIH][hapmap];0.85[MEX][hapmap];0.89[TSI][hapmap];0.89[YRI][hapmap];0.85[AMR][1000 genomes];0.88[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:7 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv833053	chr15:74360156-74555140	Flanking Bivalent TSS/Enh Bivalent Enhancer Weak transcription Enhancers Flanking Active TSS Genic enhancers Bivalent/Poised TSS Active TSS Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	17 gene(s)	inside rSNPs	diseases
2	nsv833054	chr15:74457643-74625283	Enhancers Weak transcription Flanking Active TSS Bivalent Enhancer Strong transcription Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Active TSS ZNF genes & repeats Genic enhancers Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases
3	nsv904345	chr15:74458181-74526596	Active TSS Bivalent Enhancer Weak transcription Flanking Active TSS Enhancers Flanking Bivalent TSS/Enh Strong transcription Bivalent/Poised TSS Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
4	nsv904346	chr15:74458181-74548773	Flanking Active TSS Enhancers Transcr. at gene 5' and 3' Weak transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Active TSS Genic enhancers Bivalent/Poised TSS Strong transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
5	nsv904347	chr15:74462629-74537101	Flanking Active TSS Weak transcription Bivalent Enhancer Genic enhancers Enhancers Flanking Bivalent TSS/Enh Strong transcription Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
6	nsv904348	chr15:74462629-74542686	Genic enhancers Enhancers Active TSS Bivalent Enhancer Bivalent/Poised TSS Flanking Active TSS Weak transcription Strong transcription Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
7	nsv471253	chr15:74489207-74545148	Weak transcription Enhancers Bivalent/Poised TSS Bivalent Enhancer Flanking Active TSS Flanking Bivalent TSS/Enh Genic enhancers Strong transcription Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:45 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:74489200-74509600	Weak transcription	Gastric	stomach
2	chr15:74491000-74503200	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
3	chr15:74492600-74503200	Enhancers	Fetal Muscle Leg	muscle
4	chr15:74494000-74500200	Enhancers	Cortex derived primary cultured neurospheres	brain
5	chr15:74494200-74501000	Weak transcription	HSMM	muscle
6	chr15:74494400-74500200	Enhancers	Fetal Brain Male	brain
7	chr15:74495800-74499600	Enhancers	Brain Germinal Matrix	brain
8	chr15:74495800-74500200	Enhancers	Fetal Thymus	thymus
9	chr15:74496400-74500200	Enhancers	Fetal Brain Female	brain
10	chr15:74496800-74500600	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
11	chr15:74496800-74501200	Enhancers	Spleen	Spleen
12	chr15:74496800-74501600	Weak transcription	A549	lung
13	chr15:74497000-74499800	Weak transcription	iPS-18 Cell Line	embryonic stem cell
14	chr15:74497000-74500000	Weak transcription	Brain Inferior Temporal Lobe	brain
15	chr15:74497000-74500000	Enhancers	Fetal Muscle Trunk	muscle
16	chr15:74497000-74501200	Weak transcription	Placenta Amnion	Placenta Amnion
17	chr15:74497000-74505800	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
18	chr15:74497400-74501000	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
19	chr15:74497600-74500200	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
20	chr15:74497600-74501400	Weak transcription	Osteobl	bone
21	chr15:74497600-74502000	Enhancers	Primary hematopoietic stem cells short term culture	blood
22	chr15:74497800-74499800	Weak transcription	GM12878-XiMat	blood
23	chr15:74498000-74500000	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
24	chr15:74498000-74502600	Enhancers	Fetal Intestine Small	intestine
25	chr15:74498200-74500200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
26	chr15:74498200-74500600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
27	chr15:74498200-74501000	Weak transcription	Right Atrium	heart
28	chr15:74498200-74501600	Weak transcription	H9 Cell Line	embryonic stem cell
29	chr15:74498400-74500600	Enhancers	Hela-S3	cervix
30	chr15:74498400-74500800	Weak transcription	Primary hematopoietic stem cells	blood
31	chr15:74498400-74506000	Weak transcription	Left Ventricle	heart
32	chr15:74498800-74499600	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
33	chr15:74498800-74503200	Enhancers	Fetal Stomach	stomach
34	chr15:74499000-74499600	Enhancers	Fetal Intestine Large	intestine
35	chr15:74499000-74500400	Enhancers	Fetal Lung	lung
36	chr15:74499000-74500600	Enhancers	Breast Myoepithelial Primary Cells	Breast
37	chr15:74499000-74501400	Enhancers	Fetal Kidney	kidney
38	chr15:74499000-74503400	Enhancers	NH-A	brain
39	chr15:74499200-74499600	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
40	chr15:74499200-74501000	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
41	chr15:74499200-74502400	Enhancers	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
42	chr15:74499200-74503600	Enhancers	Fetal Heart	heart
43	chr15:74499400-74499800	Enhancers	HUES6 Cell Line	embryonic stem cell
44	chr15:74499400-74501400	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
45	chr15:74499400-74502200	Bivalent Enhancer	Fetal Adrenal Gland	Adrenal Gland

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