Variant report

Variant	rs28707336
Chromosome Location	chr5:177027110-177027111
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	BCLAF1	chr5:177026839-177027305	K562	blood:	n/a	chr5:177027266-177027275 chr5:177027042-177027055
2	MAZ	chr5:177026680-177027681	K562	blood:	n/a	chr5:177027452-177027462
3	MAZ	chr5:177026773-177027491	Hela-S3	cervix:	n/a	chr5:177027452-177027462
4	POLR2A	chr5:177026680-177027447	SK-N-SH	brain:	n/a	n/a
5	TAF1	chr5:177026768-177027336	GM12878	blood:	n/a	n/a
6	POLR2A	chr5:177026543-177028107	HUVEC	blood vessel:	n/a	n/a
7	ZNF143	chr5:177026615-177027496	H1-hESC	embryonic stem cell:	n/a	chr5:177027296-177027306
8	TCF7L2	chr5:177026840-177027184	PANC-1	pancreas:	n/a	n/a
9	FOXP2	chr5:177026873-177027361	PFSK-1	brain:	n/a	n/a
10	SP1	chr5:177026842-177027206	GM12878	blood:	n/a	n/a
11	YY1	chr5:177026891-177027325	GM12891	blood:	n/a	chr5:177027272-177027286 chr5:177027266-177027277 chr5:177027042-177027056
12	POLR2A	chr5:177026591-177027587	HepG2	liver:	n/a	n/a
13	TAF1	chr5:177026829-177027265	Hela-S3	cervix:	n/a	n/a
14	BCLAF1	chr5:177026702-177027478	GM12878	blood:	n/a	chr5:177027266-177027275 chr5:177027450-177027459 chr5:177027042-177027055
15	POLR2A	chr5:177026575-177027512	A549	lung:	n/a	n/a
16	IRF1	chr5:177026825-177027488	K562	blood:	n/a	chr5:177027447-177027461
17	JUND	chr5:177026825-177027386	H1-hESC	embryonic stem cell:	n/a	n/a
18	MYC	chr5:177026927-177027209	GM12878	blood:	n/a	n/a
19	HA-E2F1	chr5:177026632-177027443	MCF-7	breast:	n/a	chr5:177026787-177026797
20	NR2F2	chr5:177027090-177027730	K562	blood:	n/a	n/a
21	POLR2A	chr5:177026872-177027462	A549	lung:	n/a	n/a
22	REST	chr5:177026934-177027112	H1-hESC	embryonic stem cell:	n/a	n/a
23	STAT5A	chr5:177026612-177027612	GM12878	blood:	n/a	chr5:177027442-177027454 chr5:177027454-177027466
24	SP2	chr5:177026961-177027135	K562	blood:	n/a	n/a
25	EP300	chr5:177026836-177027236	T-47D	breast:	n/a	n/a
26	BRCA1	chr5:177026899-177027424	Hela-S3	cervix:	n/a	n/a
27	CREB1	chr5:177026617-177027545	HepG2	liver:	n/a	n/a
28	GABPA	chr5:177026909-177027284	GM12878	blood:	n/a	n/a
29	POLR2A	chr5:177026719-177028275	Raji	blood:	n/a	n/a
30	POLR2A	chr5:177026607-177027888	GM12892	blood:	n/a	n/a
31	MYC	chr5:177026843-177027948	NB4	blood:	n/a	chr5:177027452-177027462
32	MAZ	chr5:177026731-177027640	GM12878	blood:	n/a	chr5:177027452-177027462
33	POLR2A	chr5:177026654-177027555	MCF-7	breast:	n/a	n/a
34	USF1	chr5:177026956-177027151	HepG2	liver:	n/a	n/a
35	USF2	chr5:177026750-177027215	GM12878	blood:	n/a	n/a
36	PML	chr5:177026764-177027545	MCF-7	breast:	n/a	n/a
37	ETS1	chr5:177026706-177027307	GM12878	blood:	n/a	chr5:177027266-177027277
38	GTF2F1	chr5:177026882-177027410	K562	blood:	n/a	n/a
39	TAF1	chr5:177026635-177027597	ECC-1	luminal epithelium:	n/a	n/a
40	RAD21	chr5:177026902-177027190	K562	blood:	n/a	n/a
41	TCF12	chr5:177026548-177027539	A549	lung:	n/a	n/a
42	ARID3A	chr5:177026806-177027407	K562	blood:	n/a	n/a
43	MEF2C	chr5:177026835-177027289	GM12878	blood:	n/a	n/a
44	MYBL2	chr5:177026744-177027302	HepG2	liver:	n/a	n/a
45	ZBTB33	chr5:177026922-177027126	HCT-116	colon:	n/a	n/a
46	ELF1	chr5:177026858-177027551	K562	blood:	n/a	n/a
47	HMGN3	chr5:177026659-177027764	K562	blood:	n/a	n/a
48	POLR2A	chr5:177024652-177028404	MCF10A-Er-Src	breast:	n/a	n/a
49	EP300	chr5:177026836-177027144	T-47D	breast:	n/a	n/a
50	GABPA	chr5:177026821-177027764	HL-60	blood:	n/a	chr5:177027451-177027460

No.	Distal block	Cell Line	Cell type
1	chr5:176920960..176923857-chr5:177025688..177028389,2	K562	blood:
2	chr5:176918624..176922037-chr5:177026653..177029036,4	MCF-7	breast:
3	chr5:176920960..176922896-chr5:177025688..177028644,2	K562	blood:
4	chr5:176942605..176945227-chr5:177026714..177029241,3	K562	blood:
5	chr5:176923252..176925841-chr5:177025670..177028479,3	K562	blood:
6	chr5:177025539..177028252-chr5:177630597..177632555,2	K562	blood:
7	chr5:176980839..176983786-chr5:177025411..177027346,2	MCF-7	breast:
8	chr12:120729256..120731052-chr5:177027034..177028925,2	MCF-7	breast:
9	chr5:177026767..177027493-chr6:99963070..99963586,2	Hela-S3	cervix:
10	chr5:176923028..176926285-chr5:177025596..177029619,3	MCF-7	breast:
11	chr5:177025398..177027289-chr5:177540105..177542434,2	MCF-7	breast:
12	chr5:176979154..176982725-chr5:177026070..177029438,5	MCF-7	breast:
13	chr5:176922985..176925564-chr5:177025681..177028407,2	MCF-7	breast:
14	chr5:176942355..176946513-chr5:177025554..177029046,7	MCF-7	breast:

Variant related genes	Relation type
B4GALT7	TF binding region
ENSG00000146067	Chromatin interaction
ENSG00000196923	Chromatin interaction
ENSG00000202538	Chromatin interaction
ENSG00000183258	Chromatin interaction
ENSG00000248996	Chromatin interaction
ENSG00000145911	Chromatin interaction
ENSG00000272459	Chromatin interaction
ENSG00000200795	Chromatin interaction
ENSG00000123552	Chromatin interaction
ENSG00000197451	Chromatin interaction

Extended variants
information (count: 23 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:15)

rs_ID	r²[population]
rs10036396	0.83[EUR][1000 genomes]
rs10040391	0.82[EUR][1000 genomes]
rs1047577	0.83[EUR][1000 genomes]
rs11490750	0.80[AMR][1000 genomes];0.83[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs13164561	0.83[EUR][1000 genomes]
rs1872623	0.83[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs1872624	0.88[AMR][1000 genomes];0.86[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs28375402	0.90[ASN][1000 genomes]
rs28579790	0.88[ASN][1000 genomes]
rs28757437	0.83[AMR][1000 genomes];0.85[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs4458584	0.83[EUR][1000 genomes]
rs60992195	0.87[ASN][1000 genomes]
rs6882209	0.83[EUR][1000 genomes]
rs7731783	0.80[EUR][1000 genomes]
rs901379	0.87[AMR][1000 genomes];0.83[EUR][1000 genomes];0.90[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:8 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv916108	chr5:176688459-177078723	Weak transcription Genic enhancers Strong transcription Enhancers Active TSS Transcr. at gene 5' and 3' Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	138 gene(s)	inside rSNPs	diseases
2	nsv1024444	chr5:176751921-177427715	Weak transcription Transcr. at gene 5' and 3' Enhancers Flanking Active TSS Genic enhancers Flanking Bivalent TSS/Enh Strong transcription Bivalent Enhancer Active TSS Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	142 gene(s)	inside rSNPs	diseases
3	esv2752795	chr5:176898619-177488281	Active TSS Strong transcription Flanking Active TSS Enhancers Weak transcription Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	78 gene(s)	inside rSNPs	diseases
4	nsv1022630	chr5:176975746-177028082	Weak transcription Flanking Active TSS Transcr. at gene 5' and 3' Active TSS Strong transcription Enhancers Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	24 gene(s)	inside rSNPs	diseases
5	nsv537966	chr5:176975746-177028082	Genic enhancers Strong transcription Flanking Active TSS Enhancers Active TSS Transcr. at gene 5' and 3' Weak transcription Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	24 gene(s)	inside rSNPs	diseases
6	nsv883181	chr5:176978496-177034786	Bivalent/Poised TSS Active TSS Weak transcription Enhancers Genic enhancers Bivalent Enhancer Strong transcription Flanking Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	24 gene(s)	inside rSNPs	diseases
7	nsv883182	chr5:176980995-177322056	Active TSS Transcr. at gene 5' and 3' Strong transcription Weak transcription Enhancers Flanking Active TSS Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	33 gene(s)	inside rSNPs	diseases
8	nsv883183	chr5:177019379-177030351	Flanking Active TSS Strong transcription Active TSS Weak transcription Transcr. at gene 5' and 3' Enhancers Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	21 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs28707336	B4GALT7	cis	Whole Blood	GTEx
rs28707336	FAM153A	cis	Heart Left Ventricle	GTEx
rs28707336	RP11-1101H11.1	cis	Heart Left Ventricle	GTEx

Chromatin state (count:127 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:177025600-177027600	Active TSS	Duodenum Mucosa	Duodenum
2	chr5:177025600-177027800	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
3	chr5:177025600-177027800	Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
4	chr5:177026000-177027600	Active TSS	Primary T cells effector/memory enriched fromperipheralblood	blood
5	chr5:177026000-177027600	Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
6	chr5:177026000-177027600	Active TSS	Rectal Mucosa Donor 31	rectum
7	chr5:177026000-177027800	Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
8	chr5:177026200-177027400	Active TSS	Primary T helper naive cells fromperipheralblood	blood
9	chr5:177026200-177027600	Active TSS	H9 Cell Line	embryonic stem cell
10	chr5:177026200-177027600	Active TSS	iPS-18 Cell Line	embryonic stem cell
11	chr5:177026200-177027600	Active TSS	Breast Myoepithelial Primary Cells	Breast
12	chr5:177026200-177027600	Active TSS	Primary T cells from cord blood	blood
13	chr5:177026200-177027600	Active TSS	Primary T helper memory cells from peripheral blood 1	blood
14	chr5:177026200-177027600	Active TSS	Primary T killer naive cells fromperipheralblood	blood
15	chr5:177026200-177027600	Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
16	chr5:177026200-177027600	Active TSS	Brain Angular Gyrus	brain
17	chr5:177026200-177027600	Active TSS	Brain Cingulate Gyrus	brain
18	chr5:177026200-177027600	Active TSS	Brain Germinal Matrix	brain
19	chr5:177026200-177027600	Active TSS	Brain Inferior Temporal Lobe	brain
20	chr5:177026200-177027600	Active TSS	Colonic Mucosa	Colon
21	chr5:177026200-177027600	Active TSS	Colon Smooth Muscle	Colon
22	chr5:177026200-177027600	Active TSS	Rectal Mucosa Donor 29	rectum
23	chr5:177026200-177027600	Active TSS	Rectal Smooth Muscle	rectum
24	chr5:177026200-177027600	Active TSS	K562	blood
25	chr5:177026200-177027600	Active TSS	NH-A	brain
26	chr5:177026200-177027800	Active TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
27	chr5:177026200-177027800	Active TSS	HUES48 Cell Line	embryonic stem cell
28	chr5:177026200-177027800	Active TSS	IMR90 fetal lung fibroblasts Cell Line	lung
29	chr5:177026200-177027800	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
30	chr5:177026200-177027800	Active TSS	Fetal Brain Female	brain
31	chr5:177026200-177027800	Active TSS	Fetal Kidney	kidney
32	chr5:177026200-177027800	Active TSS	Thymus	Thymus
33	chr5:177026200-177027800	Active TSS	NHDF-Ad	bronchial
34	chr5:177026200-177028000	Active TSS	ES-I3 Cell Line	embryonic stem cell
35	chr5:177026200-177028000	Flanking Active TSS	Primary mononuclear cells fromperipheralblood	Blood
36	chr5:177026200-177028200	Active TSS	iPS-15b Cell Line	embryonic stem cell
37	chr5:177026200-177028200	Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
38	chr5:177026200-177028200	Active TSS	Pancreatic Islets	Pancreatic Islet
39	chr5:177026200-177028200	Active TSS	Psoas Muscle	Psoas
40	chr5:177026400-177027200	Active TSS	Primary neutrophils fromperipheralblood	blood
41	chr5:177026400-177027400	Active TSS	Primary B cells from cord blood	blood
42	chr5:177026400-177027400	Active TSS	Primary T helper cells fromperipheralblood	blood
43	chr5:177026400-177027400	Active TSS	Primary T regulatory cells fromperipheralblood	blood
44	chr5:177026400-177027400	Active TSS	Brain Substantia Nigra	brain
45	chr5:177026400-177027400	Active TSS	HepG2	liver
46	chr5:177026400-177027600	Active TSS	H1 Cell Line	embryonic stem cell
47	chr5:177026400-177027600	Active TSS	H9 Derived Neuron Cultured Cells	ES cell derived
48	chr5:177026400-177027600	Active TSS	HUES6 Cell Line	embryonic stem cell
49	chr5:177026400-177027600	Active TSS	Primary T helper memory cells from peripheral blood 2	blood
50	chr5:177026400-177027600	Active TSS	Primary T helper naive cells from peripheral blood	blood

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