Variant report

Variant	rs4616261
Chromosome Location	chr15:75965169-75965170
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	POLR2A	chr15:75964945-75965459	HCT-116	colon:	n/a	n/a
2	RAD21	chr15:75964990-75966135	IMR90	lung:	n/a	chr15:75965695-75965708 chr15:75965433-75965446 chr15:75965449-75965459
3	ARID3A	chr15:75965051-75965181	HepG2	liver:	n/a	n/a
4	POLR2A	chr15:75964833-75966169	PANC-1	pancreas:	n/a	n/a
5	MYC	chr15:75965153-75965227	MCF10A-Er-Src	breast:	n/a	n/a
6	MXI1	chr15:75965024-75965201	HepG2	liver:	n/a	n/a
7	POLR2A	chr15:75963778-75966547	Hela-S3	cervix:	n/a	n/a
8	POLR2A	chr15:75964969-75965479	MCF10A-Er-Src	breast:	n/a	n/a
9	MAZ	chr15:75963794-75966405	IMR90	lung:	n/a	chr15:75966377-75966387 chr15:75966378-75966387 chr15:75966378-75966387 chr15:75965682-75965692 chr15:75966379-75966386
10	POLR2A	chr15:75963541-75966466	U87	brain:	n/a	n/a
11	POLR2A	chr15:75964417-75965734	Hela-S3	cervix:	n/a	n/a
12	POLR2A	chr15:75964032-75966447	U87	brain:	n/a	n/a
13	POLR2A	chr15:75964798-75966630	IMR90	lung:	n/a	n/a
14	TCF7L2	chr15:75965157-75965355	Hela-S3	cervix:	n/a	n/a
15	POLR2A	chr15:75964885-75966337	PANC-1	pancreas:	n/a	n/a
16	NFIC	chr15:75965108-75965709	ECC-1	luminal epithelium:	n/a	n/a
17	POLR2A	chr15:75961392-75968208	U87	brain:	n/a	n/a
18	TFAP2C	chr15:75965108-75965802	Hela-S3	cervix:	n/a	n/a
19	POLR2A	chr15:75964551-75966130	PFSK-1	brain:	n/a	n/a
20	MAFK	chr15:75964381-75965339	IMR90	lung:	n/a	chr15:75964900-75964911 chr15:75964865-75964882
21	GATA3	chr15:75965001-75965347	T-47D	breast:	n/a	n/a
22	SPI1	chr15:75965070-75965261	K562	blood:	n/a	n/a
23	POLR2A	chr15:75963030-75967116	U87	brain:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr15:75659530..75662177-chr15:75962521..75965318,2	K562	blood:
2	chr15:75743241..75745218-chr15:75963628..75965414,2	MCF-7	breast:
3	chr15:75956801..75958310-chr15:75964736..75966304,2	K562	blood:
4	chr15:75927186..75935349-chr15:75957229..75967736,17	MCF-7	breast:
5	chr15:75660561..75662117-chr15:75964805..75967036,2	MCF-7	breast:
6	chr15:75937430..75939214-chr15:75963572..75966390,2	MCF-7	breast:
7	chr15:75951981..75955869-chr15:75961912..75967583,8	MCF-7	breast:
8	chr15:75744190..75746911-chr15:75963679..75965801,2	MCF-7	breast:
9	chr15:75659386..75661885-chr15:75964274..75966249,2	K562	blood:
10	chr15:75961153..75963477-chr15:75964870..75966671,2	K562	blood:
11	chr15:75953678..75955508-chr15:75964203..75966702,2	K562	blood:

Variant related genes	Relation type
ENSG00000260892	TF binding region
ENSG00000169375	Chromatin interaction
ENSG00000260206	Chromatin interaction
ENSG00000177971	Chromatin interaction
ENSG00000260274	Chromatin interaction
ENSG00000140400	Chromatin interaction

Extended variants
information (count: 38 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:22)

rs_ID	r²[population]
rs11072556	0.87[ASN][1000 genomes]
rs1127646	0.96[ASN][1000 genomes]
rs1127649	0.93[AFR][1000 genomes];0.99[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11634290	0.80[CHB][hapmap];0.97[CHD][hapmap];1.00[JPT][hapmap];0.90[ASN][1000 genomes]
rs11636280	0.91[JPT][hapmap];0.90[ASN][1000 genomes]
rs12905062	0.92[JPT][hapmap];0.85[YRI][hapmap]
rs12913388	0.82[AMR][1000 genomes];0.84[ASN][1000 genomes]
rs1964473	0.92[JPT][hapmap]
rs2017312	0.92[JPT][hapmap];0.85[YRI][hapmap]
rs2290484	0.85[YRI][hapmap]
rs34175377	0.85[AFR][1000 genomes];0.94[AMR][1000 genomes];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs34611707	0.83[CHD][hapmap];0.92[JPT][hapmap]
rs3751536	0.92[JPT][hapmap];0.85[YRI][hapmap]
rs4503758	0.83[CHD][hapmap];0.92[JPT][hapmap]
rs7181595	0.81[JPT][hapmap]
rs7182902	0.96[ASN][1000 genomes]
rs7182906	0.86[EUR][1000 genomes]
rs8023621	1.00[CEU][hapmap];0.86[CHD][hapmap];0.90[GIH][hapmap];0.86[LWK][hapmap];1.00[TSI][hapmap];0.81[AFR][1000 genomes];0.82[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs8026234	0.90[JPT][hapmap];0.82[YRI][hapmap]
rs8027311	0.90[JPT][hapmap]
rs8028002	0.83[CHD][hapmap];0.92[JPT][hapmap]
rs8030131	0.91[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:16 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv531901	chr15:75600108-76019966	Genic enhancers Flanking Active TSS Enhancers Weak transcription Strong transcription Transcr. at gene 5' and 3' Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	166 gene(s)	inside rSNPs	diseases
2	esv3445070	chr15:75623136-76045948	Enhancers Active TSS Weak transcription Genic enhancers Flanking Active TSS Bivalent/Poised TSS Strong transcription ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	165 gene(s)	inside rSNPs	diseases
3	nsv1048028	chr15:75637515-76019967	Strong transcription Genic enhancers Weak transcription Enhancers ZNF genes & repeats Bivalent/Poised TSS Flanking Active TSS Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	161 gene(s)	inside rSNPs	diseases
4	nsv542436	chr15:75637515-76019967	Strong transcription Weak transcription Flanking Active TSS Genic enhancers Enhancers Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	161 gene(s)	inside rSNPs	diseases
5	esv1800424	chr15:75692303-75991451	Flanking Active TSS Strong transcription Weak transcription Genic enhancers Enhancers Transcr. at gene 5' and 3' Active TSS ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	124 gene(s)	inside rSNPs	diseases
6	nsv531903	chr15:75889302-76342128	Weak transcription Enhancers Strong transcription Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Active TSS Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	97 gene(s)	inside rSNPs	diseases
7	esv1813854	chr15:75898640-76002392	Enhancers Flanking Active TSS Weak transcription Bivalent Enhancer Strong transcription Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	66 gene(s)	inside rSNPs	diseases
8	nsv527186	chr15:75924443-76107730	Active TSS Enhancers Weak transcription Flanking Active TSS Transcr. at gene 5' and 3' Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Strong transcription Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA	69 gene(s)	inside rSNPs	diseases
9	nsv904391	chr15:75930757-76001654	Weak transcription Strong transcription Flanking Active TSS Enhancers Flanking Bivalent TSS/Enh Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	52 gene(s)	inside rSNPs	diseases
10	nsv904392	chr15:75930757-76039262	Enhancers Flanking Active TSS Active TSS Weak transcription Strong transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	58 gene(s)	inside rSNPs	diseases
11	nsv904393	chr15:75932177-76001654	Flanking Active TSS Strong transcription Enhancers Transcr. at gene 5' and 3' Weak transcription Bivalent Enhancer Active TSS Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	51 gene(s)	inside rSNPs	diseases
12	nsv984485	chr15:75932760-75965433	Weak transcription Active TSS Enhancers Flanking Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Genic enhancers Strong transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	41 gene(s)	inside rSNPs	diseases
13	nsv904394	chr15:75948671-76039262	Active TSS Weak transcription Enhancers Bivalent Enhancer Flanking Active TSS Transcr. at gene 5' and 3' Genic enhancers Flanking Bivalent TSS/Enh Strong transcription Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	21 gene(s)	inside rSNPs	diseases
14	nsv904395	chr15:75957928-75984095	Weak transcription Flanking Active TSS Enhancers Genic enhancers Strong transcription Bivalent Enhancer Transcr. at gene 5' and 3' Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region	13 gene(s)	inside rSNPs	diseases
15	nsv904396	chr15:75961518-76071105	Enhancers Bivalent Enhancer Flanking Active TSS Weak transcription Active TSS Flanking Bivalent TSS/Enh Genic enhancers Strong transcription Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA	26 gene(s)	inside rSNPs	diseases
16	nsv569997	chr15:75965169-75991451	Weak transcription Genic enhancers Enhancers Strong transcription Active TSS Flanking Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region	14 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs4616261	ETFA	cis	cerebellum	SCAN
rs4616261	FBXO22	cis	parietal	SCAN
rs4616261	SCAMP5	cis	parietal	SCAN

Chromatin state (count:90 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:75953000-75969600	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
2	chr15:75955600-75965400	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
3	chr15:75956200-75966400	Enhancers	HMEC	breast
4	chr15:75956600-75967000	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
5	chr15:75957800-75967200	Enhancers	Placenta Amnion	Placenta Amnion
6	chr15:75958200-75967200	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
7	chr15:75958400-75967000	Enhancers	Fetal Muscle Leg	muscle
8	chr15:75959400-75967600	Weak transcription	Liver	Liver
9	chr15:75960000-75965600	Weak transcription	Aorta	Aorta
10	chr15:75960200-75965200	Weak transcription	Psoas Muscle	Psoas
11	chr15:75960200-75966200	Weak transcription	Rectal Mucosa Donor 29	rectum
12	chr15:75961000-75968200	Enhancers	NHDF-Ad	bronchial
13	chr15:75961200-75966600	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
14	chr15:75962000-75965400	Enhancers	Skeletal Muscle Male	skeletal muscle
15	chr15:75962400-75968600	Enhancers	Adipose Nuclei	Adipose
16	chr15:75962400-75968800	Enhancers	Right Ventricle	heart
17	chr15:75962400-75969000	Enhancers	Skeletal Muscle Female	skeletal muscle
18	chr15:75962800-75966000	Enhancers	Lung	lung
19	chr15:75962800-75966200	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
20	chr15:75963000-75965400	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
21	chr15:75963200-75965400	Enhancers	Fetal Muscle Trunk	muscle
22	chr15:75963200-75968400	Enhancers	Placenta	Placenta
23	chr15:75963400-75965200	Genic enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
24	chr15:75963400-75965200	Enhancers	NH-A	brain
25	chr15:75963400-75965400	Enhancers	NHLF	lung
26	chr15:75963400-75968000	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
27	chr15:75963600-75965200	Enhancers	Osteobl	bone
28	chr15:75963600-75965400	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
29	chr15:75963600-75966000	Enhancers	Gastric	stomach
30	chr15:75963800-75967000	Enhancers	Esophagus	oesophagus
31	chr15:75963800-75968200	Enhancers	Left Ventricle	heart
32	chr15:75964000-75965200	Enhancers	Foreskin Melanocyte Primary Cells skin01	Skin
33	chr15:75964000-75965200	Enhancers	Hela-S3	cervix
34	chr15:75964000-75965600	Transcr. at gene 5' and 3'	Foreskin Fibroblast Primary Cells skin02	Skin
35	chr15:75964000-75965800	Enhancers	Spleen	Spleen
36	chr15:75964000-75966000	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
37	chr15:75964000-75966200	Enhancers	Pancreas	Pancrea
38	chr15:75964000-75966600	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
39	chr15:75964000-75967000	Enhancers	Breast Myoepithelial Primary Cells	Breast
40	chr15:75964000-75967400	Enhancers	Fetal Heart	heart
41	chr15:75964200-75965200	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
42	chr15:75964200-75966200	Enhancers	NHEK	skin
43	chr15:75964200-75966400	Enhancers	ES-I3 Cell Line	embryonic stem cell
44	chr15:75964200-75967000	Enhancers	Fetal Stomach	stomach
45	chr15:75964200-75968600	Enhancers	Ovary	ovary
46	chr15:75964200-75969200	Enhancers	Right Atrium	heart
47	chr15:75964400-75965600	Enhancers	iPS-18 Cell Line	embryonic stem cell
48	chr15:75964400-75966000	Enhancers	iPS-20b Cell Line	embryonic stem cell
49	chr15:75964400-75966200	Enhancers	Fetal Intestine Small	intestine
50	chr15:75964400-75966400	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived

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