Variant report

Variant	rs35517826
Chromosome Location	chr4:16207102-16207103
allele	C/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	MAFK	chr4:16206971-16207518	K562	blood:	n/a	n/a
2	RUNX3	chr4:16206981-16207499	GM12878	blood:	n/a	n/a
3	RAD21	chr4:16207061-16207744	SK-N-SH	brain:	n/a	n/a
4	EP300	chr4:16207027-16207228	GM12878	blood:	n/a	n/a
5	CTCF	chr4:16207091-16207390	GM19238	blood:	n/a	n/a
6	RAD21	chr4:16207096-16207530	H1-hESC	embryonic stem cell:	n/a	n/a
7	CTCF	chr4:16207020-16207170	A549	lung:	n/a	n/a
8	CTCF	chr4:16207097-16207692	HCT-116	colon:	n/a	n/a
9	BHLHE40	chr4:16206930-16207535	GM12878	blood:	n/a	n/a
10	KAP1	chr4:16207042-16207621	HEK293	kidney:	n/a	n/a
11	EBF1	chr4:16206874-16207284	GM12878	blood:	n/a	chr4:16207107-16207118 chr4:16207109-16207118
12	RUNX3	chr4:16206772-16207489	GM12878	blood:	n/a	n/a
13	CTCF	chr4:16207080-16207230	HFF	foreskin:	n/a	n/a
14	CTCF	chr4:16207053-16207896	A549	lung:	n/a	n/a
15	IKZF1	chr4:16206855-16207116	GM12878	blood:	n/a	n/a
16	CTCF	chr4:16207040-16207190	HepG2	liver:	n/a	n/a
17	MAX	chr4:16206905-16207543	NB4	blood:	n/a	chr4:16207433-16207441
18	WRNIP1	chr4:16207069-16207360	GM12878	blood:	n/a	n/a
19	STAT3	chr4:16207054-16207538	GM12878	blood:	n/a	n/a
20	RCOR1	chr4:16206914-16207497	GM12878	blood:	n/a	n/a
21	PAX5	chr4:16207004-16207195	GM12892	blood:	n/a	n/a
22	CUX1	chr4:16207057-16207135	GM12878	blood:	n/a	n/a
23	CTCF	chr4:16207080-16207230	WI-38	lung:	n/a	n/a
24	EBF1	chr4:16206872-16207330	GM12878	blood:	n/a	chr4:16207107-16207118 chr4:16207109-16207118
25	POLR2A	chr4:16207054-16207215	Hela-S3	cervix:	n/a	n/a
26	EBF1	chr4:16206887-16207554	GM12878	blood:	n/a	chr4:16207107-16207118 chr4:16207109-16207118
27	CTCF	chr4:16207077-16207161	Gliobla	brain:	n/a	n/a
28	CTCF	chr4:16206998-16207576	IMR90	lung:	n/a	n/a
29	CTCF	chr4:16206596-16207770	SK-N-SH	brain:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr4:16206884..16207732-chr4:16266166..16267115,3	MCF-7	breast:
2	chr4:15807303..15808035-chr4:16206943..16207548,2	MCF-7	breast:
3	chr4:16205687..16210095-chr4:16211514..16215415,4	K562	blood:
4	chr4:16206563..16211517-chr4:16224602..16229225,6	K562	blood:
5	chr4:16202184..16204166-chr4:16205762..16207815,2	K562	blood:
6	chr4:16204628..16208605-chr4:16216498..16220405,4	K562	blood:

Variant related genes	Relation type
TAPT1	TF binding region
ENSG00000263327	Chromatin interaction
ENSG00000169762	Chromatin interaction

Extended variants
information (count: 37 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:33)

rs_ID	r²[population]
rs10017532	0.83[ASN][1000 genomes]
rs10516297	0.93[ASN][1000 genomes]
rs11730922	0.95[ASN][1000 genomes]
rs13120908	1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs13132678	1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs13136055	0.84[AMR][1000 genomes];0.88[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs13136172	1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2028631	0.84[ASN][1000 genomes]
rs28654954	0.83[ASN][1000 genomes]
rs2872216	0.89[ASN][1000 genomes]
rs33980476	0.83[ASN][1000 genomes]
rs34129131	0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs34496855	1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs34592687	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs34663238	0.82[AFR][1000 genomes];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs34837883	0.89[EUR][1000 genomes]
rs35475888	1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs35804424	0.95[AFR][1000 genomes];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs35806798	0.99[ASN][1000 genomes]
rs35899968	0.86[AFR][1000 genomes];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs35931597	0.86[ASN][1000 genomes]
rs3749544	0.91[ASN][1000 genomes]
rs4235382	0.85[ASN][1000 genomes]
rs4481232	0.83[ASN][1000 genomes]
rs4571326	0.83[ASN][1000 genomes]
rs4698138	0.81[ASN][1000 genomes]
rs4698457	0.81[ASN][1000 genomes]
rs56353092	1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6810390	0.89[AMR][1000 genomes];0.90[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6823229	0.89[ASN][1000 genomes]
rs6823230	0.89[ASN][1000 genomes]
rs6852432	0.89[AMR][1000 genomes];0.90[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9995025	0.83[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv998299	chr4:16031459-16226466	Bivalent/Poised TSS Weak transcription Enhancers Strong transcription Bivalent Enhancer Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	4 gene(s)	inside rSNPs	diseases
2	nsv1004821	chr4:16055996-16830629	Enhancers Flanking Active TSS Weak transcription Strong transcription Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Active TSS Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	22 gene(s)	inside rSNPs	diseases
3	nsv537046	chr4:16055996-16830629	Enhancers Flanking Active TSS ZNF genes & repeats Strong transcription Weak transcription Genic enhancers Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	22 gene(s)	inside rSNPs	diseases
4	nsv537047	chr4:16182060-16375787	Strong transcription Weak transcription Active TSS Enhancers Flanking Active TSS Genic enhancers 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 lncRNA	17 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs35517826	TAPT1	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:109 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:16168000-16208000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
2	chr4:16168000-16213800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
3	chr4:16170800-16208000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
4	chr4:16171400-16207200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
5	chr4:16181200-16223800	Weak transcription	Fetal Brain Male	brain
6	chr4:16193000-16207600	Weak transcription	Brain Germinal Matrix	brain
7	chr4:16193000-16208200	Weak transcription	Esophagus	oesophagus
8	chr4:16193000-16216000	Weak transcription	Spleen	Spleen
9	chr4:16193000-16225800	Weak transcription	Colonic Mucosa	Colon
10	chr4:16193200-16208000	Weak transcription	H9 Cell Line	embryonic stem cell
11	chr4:16193200-16208000	Weak transcription	Lung	lung
12	chr4:16193200-16225800	Weak transcription	Fetal Brain Female	brain
13	chr4:16193400-16211200	Weak transcription	Placenta	Placenta
14	chr4:16193600-16208600	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
15	chr4:16196200-16207600	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
16	chr4:16198600-16207200	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
17	chr4:16198600-16211200	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
18	chr4:16198600-16216400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
19	chr4:16198600-16221200	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
20	chr4:16198600-16222400	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
21	chr4:16198800-16211400	Weak transcription	Aorta	Aorta
22	chr4:16198800-16218800	Weak transcription	HSMM	muscle
23	chr4:16198800-16225600	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
24	chr4:16198800-16226000	Weak transcription	NHEK	skin
25	chr4:16198800-16226400	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
26	chr4:16199800-16208000	Weak transcription	Small Intestine	intestine
27	chr4:16199800-16209800	Weak transcription	NHLF	lung
28	chr4:16199800-16215800	Weak transcription	Sigmoid Colon	Sigmoid Colon
29	chr4:16200000-16208600	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
30	chr4:16200000-16214200	Weak transcription	Fetal Heart	heart
31	chr4:16200200-16209000	Weak transcription	NHDF-Ad	bronchial
32	chr4:16200600-16207600	Weak transcription	HUES48 Cell Line	embryonic stem cell
33	chr4:16200800-16213600	Weak transcription	HUVEC	blood vessel
34	chr4:16200800-16214800	Weak transcription	Stomach Mucosa	stomach
35	chr4:16200800-16218000	Weak transcription	Cortex derived primary cultured neurospheres	brain
36	chr4:16201600-16207200	Strong transcription	Primary T cells from cord blood	blood
37	chr4:16202200-16208000	Weak transcription	Fetal Stomach	stomach
38	chr4:16202400-16207200	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
39	chr4:16202600-16208200	Strong transcription	Dnd41	blood
40	chr4:16202800-16220800	Weak transcription	Rectal Mucosa Donor 31	rectum
41	chr4:16203600-16208000	Weak transcription	Duodenum Mucosa	Duodenum
42	chr4:16203600-16209600	Enhancers	Brain Anterior Caudate	brain
43	chr4:16203800-16208000	Weak transcription	Monocytes-CD14+_RO01746	blood
44	chr4:16203800-16211200	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
45	chr4:16204200-16213800	Weak transcription	Ovary	ovary
46	chr4:16204400-16209800	Enhancers	Brain Substantia Nigra	brain
47	chr4:16204600-16209600	Enhancers	Brain Inferior Temporal Lobe	brain
48	chr4:16204600-16210400	Enhancers	Brain Angular Gyrus	brain
49	chr4:16204800-16210800	Enhancers	Brain Hippocampus Middle	brain
50	chr4:16204800-16226600	Weak transcription	NH-A	brain

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