Variant report

Variant	rs901379
Chromosome Location	chr5:177030573-177030574
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:6)
CpG islands
(count:61)
Chromatin interactive
region (count:2)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:6 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	FOXA2	chr5:177030448-177030749	A549	lung:	n/a	n/a
2	POLR2A	chr5:177030469-177030768	HepG2	liver:	n/a	n/a
3	FOXA2	chr5:177030511-177030792	A549	lung:	n/a	n/a
4	MAX	chr5:177030562-177031998	HCT-116	colon:	n/a	chr5:177031553-177031563 chr5:177031549-177031559 chr5:177031143-177031153
5	POLR2A	chr5:177030311-177030617	HepG2	liver:	n/a	n/a
6	HCFC1	chr5:177030490-177031569	Hela-S3	cervix:	n/a	n/a

(count:61 , 50 per page) page: 1 2

No.	Chromosome Location	Cell Line	Cell type	Cell Stage
1	chr5:177030568-177030618	ECC-1	luminal epithelium:	n/a
2	chr5:177030568-177030618	HCPEpiC	choroid plexus:	n/a
3	chr5:177030568-177030618	Hepatocyte	liver:	n/a
4	chr5:177030568-177030618	NB4	blood:	n/a
5	chr5:177030568-177030618	GM19239	blood:	n/a
6	chr5:177030568-177030618	SK-N-SH	brain:	n/a
7	chr5:177030568-177030618	AG04449	skin:	fetal
8	chr5:177030568-177030618	HRE	kidney:	n/a
9	chr5:177030568-177030618	GM12891	blood:	n/a
10	chr5:177030568-177030618	BE2_C	brain:	n/a
11	chr5:177030568-177030618	NHBE	bronchial:	n/a
12	chr5:177030568-177030618	HepG2	liver:	n/a
13	chr5:177030568-177030618	ovcar-3	ovarian:	n/a
14	chr5:177030568-177030618	HL-60	blood:	n/a
15	chr5:177030568-177030618	HCF	heart:	n/a
16	chr5:177030568-177030618	PrEC	prostate:	n/a
17	chr5:177030568-177030618	GM12892	blood:	n/a
18	chr5:177030568-177030618	NT2-D1	testis:	n/a
19	chr5:177030568-177030618	HIPEpiC	eye:	n/a
20	chr5:177030568-177030618	SKMC	muscle:	n/a
21	chr5:177030568-177030618	HMEC	breast:	n/a
22	chr5:177030568-177030618	AG09309	skin:	n/a
23	chr5:177030568-177030618	Jurkat	blood:	n/a
24	chr5:177030568-177030618	HRPEpiC	eye:	n/a
25	chr5:177030568-177030618	HPAEpiC	pulmonary alveolar:	n/a
26	chr5:177030568-177030618	NHDF-neo	bronchial:	n/a
27	chr5:177030568-177030618	K562	blood:	n/a
28	chr5:177030568-177030618	MCF-7	breast:	n/a
29	chr5:177030568-177030618	AG09319	gingival:	n/a
30	chr5:177030568-177030618	Caco-2	colon:	n/a
31	chr5:177030568-177030618	HEEpiC	esophagus:	n/a
32	chr5:177030568-177030618	PANC-1	pancreas:	n/a
33	chr5:177030568-177030618	HAEpiC	amniotic membrane:	n/a
34	chr5:177030568-177030618	AG04450	lung:	fetal
35	chr5:177030568-177030618	NH-A	brain:	n/a
36	chr5:177030568-177030618	A549	lung:	n/a
37	chr5:177030568-177030618	AG10803	skin:	n/a
38	chr5:177030568-177030618	Hela-S3	cervix:	n/a
39	chr5:177030568-177030618	GM06990	blood:	n/a
40	chr5:177030568-177030618	PFSK-1	brain:	n/a
41	chr5:177030568-177030618	T-47D	breast:	n/a
42	chr5:177030568-177030618	MCF10A-Er-Src	breast:	n/a
43	chr5:177030568-177030618	SK-N-SH_RA	brain:	n/a
44	chr5:177030568-177030618	RPTEC	kidney:	n/a
45	chr5:177030568-177030618	AoSMC	blood vessel:	n/a
46	chr5:177030568-177030618	HUVEC	blood vessel:	n/a
47	chr5:177030568-177030618	HCT-116	colon:	n/a
48	chr5:177030568-177030618	HRCEpiC	kidney:	n/a
49	chr5:177030568-177030618	H1-hESC	embryonic stem cell:	embryo
50	chr5:177030568-177030618	IMR90	lung:	fetal

(count:2 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr5:177028879..177031069-chr5:177037476..177041584,3	MCF-7	breast:
2	chr5:176978227..176980470-chr5:177030532..177033432,2	MCF-7	breast:

No data

Variant related genes	Relation type
B4GALT7	TF binding region
B4GALT7	CpG island
ENSG00000146067	Chromatin interaction
ENSG00000247679	Chromatin interaction

Extended variants
information (count: 28 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:23)

rs_ID	r²[population]
rs10036396	0.87[AMR][1000 genomes];0.90[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs10040391	0.88[AMR][1000 genomes];0.88[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs1047577	0.88[AMR][1000 genomes];0.90[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs11490750	0.86[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12654617	0.81[ASN][1000 genomes]
rs13164561	0.80[AFR][1000 genomes];0.89[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs1872623	0.93[AMR][1000 genomes];0.90[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs1872624	0.99[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1963011	0.83[ASN][1000 genomes]
rs2046511	0.82[ASN][1000 genomes]
rs2334991	0.86[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs28375402	0.96[ASN][1000 genomes]
rs28579790	0.94[ASN][1000 genomes]
rs28707336	0.87[AMR][1000 genomes];0.83[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs28757437	0.81[AMR][1000 genomes];0.88[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4458584	0.89[AMR][1000 genomes];0.90[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs56981142	0.88[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs60992195	0.93[ASN][1000 genomes]
rs6882209	0.88[AMR][1000 genomes];0.91[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs6889184	0.85[ASN][1000 genomes]
rs729460	0.88[AMR][1000 genomes]
rs7703727	0.82[ASN][1000 genomes]
rs7731783	0.84[AMR][1000 genomes];0.87[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 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	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
5	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

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs901379	B4GALT7	cis	Whole Blood	GTEx
rs901379	C5orf25,LOC202181	cis	brain	BrainEAC
rs901379	FAM153A	cis	Heart Left Ventricle	GTEx
rs901379	RP11-1101H11.1	cis	Heart Left Ventricle	GTEx

Chromatin state (count:115 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:177028000-177030600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
2	chr5:177028000-177032200	Weak transcription	Aorta	Aorta
3	chr5:177028000-177034200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
4	chr5:177028000-177034200	Weak transcription	HUES48 Cell Line	embryonic stem cell
5	chr5:177028000-177040000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
6	chr5:177028200-177031400	Weak transcription	Thymus	Thymus
7	chr5:177028200-177033600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
8	chr5:177028200-177034200	Weak transcription	iPS-15b Cell Line	embryonic stem cell
9	chr5:177028200-177034400	Weak transcription	HUES64 Cell Line	embryonic stem cell
10	chr5:177028200-177035600	Weak transcription	Primary neutrophils fromperipheralblood	blood
11	chr5:177028200-177036400	Weak transcription	H9 Cell Line	embryonic stem cell
12	chr5:177028200-177038000	Weak transcription	Right Atrium	heart
13	chr5:177028400-177030600	Weak transcription	Spleen	Spleen
14	chr5:177028400-177030800	Weak transcription	Rectal Mucosa Donor 31	rectum
15	chr5:177028400-177031200	Weak transcription	Colonic Mucosa	Colon
16	chr5:177028400-177031600	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
17	chr5:177028400-177031800	Weak transcription	Primary T cells from cord blood	blood
18	chr5:177028400-177031800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
19	chr5:177028400-177032000	Weak transcription	Lung	lung
20	chr5:177028400-177032000	Weak transcription	Placenta Amnion	Placenta Amnion
21	chr5:177028400-177032200	Weak transcription	Monocytes-CD14+_RO01746	blood
22	chr5:177028400-177034000	Weak transcription	HUES6 Cell Line	embryonic stem cell
23	chr5:177028400-177034000	Weak transcription	A549	lung
24	chr5:177028400-177034200	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
25	chr5:177028400-177034200	Weak transcription	Rectal Smooth Muscle	rectum
26	chr5:177028400-177034800	Weak transcription	iPS-18 Cell Line	embryonic stem cell
27	chr5:177028400-177036600	Weak transcription	HMEC	breast
28	chr5:177028400-177040200	Weak transcription	Primary hematopoietic stem cells	blood
29	chr5:177028400-177042600	Weak transcription	Primary B cells from cord blood	blood
30	chr5:177028400-177044800	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
31	chr5:177028400-177045800	Weak transcription	Left Ventricle	heart
32	chr5:177028400-177045800	Weak transcription	Psoas Muscle	Psoas
33	chr5:177028400-177048400	Weak transcription	NH-A	brain
34	chr5:177028600-177030600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
35	chr5:177028600-177030800	Weak transcription	Fetal Intestine Large	intestine
36	chr5:177028600-177031200	Weak transcription	Brain Germinal Matrix	brain
37	chr5:177028600-177031400	Weak transcription	Primary monocytes fromperipheralblood	blood
38	chr5:177028600-177031400	Weak transcription	Fetal Muscle Leg	muscle
39	chr5:177028600-177031800	Weak transcription	NHLF	lung
40	chr5:177028600-177032000	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
41	chr5:177028600-177032200	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
42	chr5:177028600-177032600	Weak transcription	Muscle Satellite Cultured Cells	--
43	chr5:177028600-177033200	Weak transcription	Osteobl	bone
44	chr5:177028600-177034000	Weak transcription	Primary B cells from peripheral blood	blood
45	chr5:177028600-177034000	Weak transcription	Colon Smooth Muscle	Colon
46	chr5:177028600-177034200	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
47	chr5:177028600-177034200	Weak transcription	Duodenum Smooth Muscle	Duodenum
48	chr5:177028600-177034400	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
49	chr5:177028600-177034400	Weak transcription	Fetal Thymus	thymus
50	chr5:177028600-177034600	Weak transcription	Fetal Kidney	kidney

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