Variant report

Variant	rs1872624
Chromosome Location	chr5:177029836-177029837
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	POLR2A	chr5:177028714-177029850	K562	blood:	n/a	n/a
2	POLR2A	chr5:177029420-177030048	HepG2	liver:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr5:176979030..176982090-chr5:177027612..177030348,3	K562	blood:
2	chr5:177028879..177031069-chr5:177037476..177041584,3	MCF-7	breast:
3	chr5:176935179..176936864-chr5:177027186..177030051,3	K562	blood:

Variant related genes	Relation type
B4GALT7	TF binding region
ENSG00000146094	Chromatin interaction
ENSG00000247679	Chromatin interaction
ENSG00000146067	Chromatin interaction
ENSG00000272459	Chromatin interaction

Extended variants
information (count: 30 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:24)

rs_ID	r²[population]
rs10036396	0.88[AMR][1000 genomes];0.94[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs10040391	0.87[AMR][1000 genomes];0.92[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs1047577	0.89[AMR][1000 genomes];0.94[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs11490750	0.80[AMR][1000 genomes];0.89[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12654617	0.80[ASN][1000 genomes]
rs13164561	0.88[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs1843633	0.81[ASN][1000 genomes]
rs1872623	0.94[AMR][1000 genomes];0.94[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs1963011	0.82[ASN][1000 genomes]
rs2046511	0.80[ASN][1000 genomes]
rs2334991	0.87[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs28375402	0.98[ASN][1000 genomes]
rs28579790	0.96[ASN][1000 genomes]
rs28707336	0.88[AMR][1000 genomes];0.86[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs28757437	0.83[AMR][1000 genomes];0.91[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4458584	0.88[AMR][1000 genomes];0.94[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs56981142	0.89[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs60992195	0.95[ASN][1000 genomes]
rs6882209	0.89[AMR][1000 genomes];0.95[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs6889184	0.84[ASN][1000 genomes]
rs729460	0.89[AMR][1000 genomes]
rs7703727	0.81[ASN][1000 genomes]
rs7731783	0.83[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs901379	0.99[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:6 , 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
6	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:4)

SNP	Gene	Cis/trans	Tissue	Source
rs1872624	B4GALT7	cis	Muscle Skeletal	GTEx
rs1872624	B4GALT7	cis	Whole Blood	GTEx
rs1872624	FAM153A	cis	Heart Left Ventricle	GTEx
rs1872624	RP11-1101H11.1	cis	Heart Left Ventricle	GTEx

Chromatin state (count:116 , 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	chr5:177028400-177030000	Enhancers	Brain Hippocampus Middle	brain
14	chr5:177028400-177030000	Enhancers	Skeletal Muscle Female	skeletal muscle
15	chr5:177028400-177030200	Weak transcription	Placenta	Placenta
16	chr5:177028400-177030200	Weak transcription	HSMMtube	muscle
17	chr5:177028400-177030400	Weak transcription	Primary hematopoietic stem cells short term culture	blood
18	chr5:177028400-177030400	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
19	chr5:177028400-177030600	Weak transcription	Spleen	Spleen
20	chr5:177028400-177030800	Weak transcription	Rectal Mucosa Donor 31	rectum
21	chr5:177028400-177031200	Weak transcription	Colonic Mucosa	Colon
22	chr5:177028400-177031600	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
23	chr5:177028400-177031800	Weak transcription	Primary T cells from cord blood	blood
24	chr5:177028400-177031800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
25	chr5:177028400-177032000	Weak transcription	Lung	lung
26	chr5:177028400-177032000	Weak transcription	Placenta Amnion	Placenta Amnion
27	chr5:177028400-177032200	Weak transcription	Monocytes-CD14+_RO01746	blood
28	chr5:177028400-177034000	Weak transcription	HUES6 Cell Line	embryonic stem cell
29	chr5:177028400-177034000	Weak transcription	A549	lung
30	chr5:177028400-177034200	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
31	chr5:177028400-177034200	Weak transcription	Rectal Smooth Muscle	rectum
32	chr5:177028400-177034800	Weak transcription	iPS-18 Cell Line	embryonic stem cell
33	chr5:177028400-177036600	Weak transcription	HMEC	breast
34	chr5:177028400-177040200	Weak transcription	Primary hematopoietic stem cells	blood
35	chr5:177028400-177042600	Weak transcription	Primary B cells from cord blood	blood
36	chr5:177028400-177044800	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
37	chr5:177028400-177045800	Weak transcription	Left Ventricle	heart
38	chr5:177028400-177045800	Weak transcription	Psoas Muscle	Psoas
39	chr5:177028400-177048400	Weak transcription	NH-A	brain
40	chr5:177028600-177030600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
41	chr5:177028600-177030800	Weak transcription	Fetal Intestine Large	intestine
42	chr5:177028600-177031200	Weak transcription	Brain Germinal Matrix	brain
43	chr5:177028600-177031400	Weak transcription	Primary monocytes fromperipheralblood	blood
44	chr5:177028600-177031400	Weak transcription	Fetal Muscle Leg	muscle
45	chr5:177028600-177031800	Weak transcription	NHLF	lung
46	chr5:177028600-177032000	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
47	chr5:177028600-177032200	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
48	chr5:177028600-177032600	Weak transcription	Muscle Satellite Cultured Cells	--
49	chr5:177028600-177033200	Weak transcription	Osteobl	bone
50	chr5:177028600-177034000	Weak transcription	Primary B cells from peripheral blood	blood

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