Variant report

Variant	rs10257172
Chromosome Location	chr7:22397187-22397188
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	MAX	chr7:22395826-22397740	ECC-1	luminal epithelium:	n/a	chr7:22396400-22396409 chr7:22396401-22396408 chr7:22396247-22396257
2	TEAD4	chr7:22396927-22398028	HepG2	liver:	n/a	n/a
3	E2F6	chr7:22396744-22397636	H1-hESC	embryonic stem cell:	n/a	n/a
4	HDAC2	chr7:22396556-22397247	HepG2	liver:	n/a	n/a
5	POLR2A	chr7:22395920-22397909	HepG2	liver:	n/a	n/a
6	MAX	chr7:22395733-22398023	HepG2	liver:	n/a	chr7:22396400-22396409 chr7:22396401-22396408 chr7:22396247-22396257
7	MAX	chr7:22395821-22397345	H1-hESC	embryonic stem cell:	n/a	chr7:22396400-22396409 chr7:22396401-22396408 chr7:22396247-22396257
8	STAT3	chr7:22396607-22397791	MCF10A-Er-Src	breast:	n/a	chr7:22397019-22397033 chr7:22397177-22397189 chr7:22397419-22397430 chr7:22397022-22397030 chr7:22397509-22397517
9	SIN3AK20	chr7:22397031-22397877	MCF-7	breast:	n/a	n/a
10	MAX	chr7:22396532-22397762	ECC-1	luminal epithelium:	n/a	n/a
11	BHLHE40	chr7:22395948-22397776	HepG2	liver:	n/a	chr7:22396791-22396807
12	MYBL2	chr7:22396969-22397731	HepG2	liver:	n/a	n/a
13	SMC3	chr7:22397167-22397765	HepG2	liver:	n/a	chr7:22397504-22397514
14	HA-E2F1	chr7:22396589-22397706	MCF-7	breast:	n/a	chr7:22396694-22396704
15	HEY1	chr7:22396317-22398005	HepG2	liver:	n/a	chr7:22396714-22396729
16	NR2F2	chr7:22397141-22397685	MCF-7	breast:	n/a	n/a
17	E2F4	chr7:22396756-22397637	MCF10A-Er-Src	breast:	n/a	n/a
18	STAT3	chr7:22397082-22397666	MCF10A-Er-Src	breast:	n/a	chr7:22397177-22397189 chr7:22397419-22397430 chr7:22397509-22397517
19	MYC	chr7:22396558-22397616	MCF10A-Er-Src	breast:	n/a	n/a
20	TEAD4	chr7:22397023-22397786	ECC-1	luminal epithelium:	n/a	n/a
21	MBD4	chr7:22396886-22397820	HepG2	liver:	n/a	n/a
22	STAT3	chr7:22397071-22397599	MCF10A-Er-Src	breast:	n/a	chr7:22397177-22397189 chr7:22397419-22397430 chr7:22397509-22397517
23	FOS	chr7:22397138-22397677	MCF10A-Er-Src	breast:	n/a	chr7:22397480-22397491
24	CHD2	chr7:22397048-22397625	HepG2	liver:	n/a	n/a
25	ZEB1	chr7:22396466-22397931	HepG2	liver:	n/a	chr7:22397008-22397019
26	MAX	chr7:22396342-22397654	HepG2	liver:	n/a	chr7:22396400-22396409 chr7:22396401-22396408
27	ARID3A	chr7:22397040-22397640	HepG2	liver:	n/a	n/a
28	POLR2A	chr7:22396478-22398049	HepG2	liver:	n/a	n/a
29	NFIC	chr7:22396573-22397786	ECC-1	luminal epithelium:	n/a	n/a
30	TCF12	chr7:22396445-22397841	ECC-1	luminal epithelium:	n/a	n/a
31	FOXA1	chr7:22397184-22397967	HepG2	liver:	n/a	n/a
32	MXI1	chr7:22396373-22397788	HepG2	liver:	n/a	n/a
33	TCF12	chr7:22397065-22397875	ECC-1	luminal epithelium:	n/a	n/a
34	E2F6	chr7:22396538-22397402	H1-hESC	embryonic stem cell:	n/a	chr7:22396694-22396704
35	REST	chr7:22396843-22397220	HepG2	liver:	n/a	n/a
36	POLR2A	chr7:22396889-22397975	HepG2	liver:	n/a	n/a
37	USF2	chr7:22397187-22397312	HepG2	liver:	n/a	n/a
38	MXI1	chr7:22395172-22397746	SK-N-SH	brain:	n/a	n/a
39	POLR2A	chr7:22396873-22397698	HepG2	liver:	n/a	n/a
40	NFIC	chr7:22396685-22397737	ECC-1	luminal epithelium:	n/a	n/a
41	POLR2A	chr7:22396913-22397794	HepG2	liver:	n/a	n/a
42	MAX	chr7:22397008-22397472	H1-hESC	embryonic stem cell:	n/a	n/a
43	EP300	chr7:22396885-22397895	ECC-1	luminal epithelium:	n/a	chr7:22397252-22397262
44	MAX	chr7:22395602-22398083	HepG2	liver:	n/a	chr7:22396400-22396409 chr7:22396401-22396408 chr7:22396247-22396257
45	POLR2A	chr7:22396512-22397743	MCF10A-Er-Src	breast:	n/a	n/a
46	MAX	chr7:22396569-22397377	H1-hESC	embryonic stem cell:	n/a	n/a
47	MYC	chr7:22397143-22397629	MCF10A-Er-Src	breast:	n/a	n/a
48	RCOR1	chr7:22396957-22397465	HepG2	liver:	n/a	n/a
49	MYBL2	chr7:22397025-22397945	HepG2	liver:	n/a	n/a
50	POLR2A	chr7:22394994-22398094	HepG2	liver:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr7:22397116..22399145-chr7:22400776..22403703,2	MCF-7	breast:
2	chr7:22396965..22399007-chr7:22400295..22402165,2	K562	blood:

Variant related genes	Relation type
RAPGEF5	TF binding region

Extended variants
information (count: 9 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:5)

rs_ID	r²[population]
rs12539362	0.96[CEU][hapmap];0.95[CHB][hapmap];0.87[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.89[LWK][hapmap];0.95[MEX][hapmap];0.98[TSI][hapmap];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs17720371	0.82[YRI][hapmap]
rs4632961	0.85[CEU][hapmap];0.86[CHB][hapmap];0.89[JPT][hapmap];0.80[MEX][hapmap]
rs6976502	0.95[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.86[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7778401	0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.84[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	nsv830923	chr7:22316841-22494973	Enhancers Flanking Active TSS Strong transcription Weak transcription Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
2	esv3437848	chr7:22395252-22397800	Bivalent/Poised TSS Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Enhancers Weak transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
3	esv3375885	chr7:22395502-22397825	Flanking Bivalent TSS/Enh Active TSS Enhancers Flanking Active TSS Bivalent Enhancer Weak transcription Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
4	esv3445637	chr7:22395652-22398200	Enhancers Weak transcription Bivalent Enhancer Flanking Active TSS Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs10257172	ITGB8	cis	parietal	SCAN

Chromatin state (count:102 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:22394400-22397600	Active TSS	Duodenum Mucosa	Duodenum
2	chr7:22395000-22397200	Active TSS	Sigmoid Colon	Sigmoid Colon
3	chr7:22395000-22397600	Active TSS	Brain Cingulate Gyrus	brain
4	chr7:22395400-22397200	Active TSS	H9 Cell Line	embryonic stem cell
5	chr7:22395400-22397400	Active TSS	Thymus	Thymus
6	chr7:22395800-22397200	Bivalent/Poised TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
7	chr7:22395800-22397200	Active TSS	Gastric	stomach
8	chr7:22395800-22397400	Bivalent/Poised TSS	Stomach Smooth Muscle	stomach
9	chr7:22396000-22397200	Active TSS	iPS DF 6.9 Cell Line	embryonic stem cell
10	chr7:22396000-22397200	Active TSS	Brain Hippocampus Middle	brain
11	chr7:22396000-22397200	Active TSS	Fetal Brain Female	brain
12	chr7:22396000-22397400	Active TSS	Primary T cells from cord blood	blood
13	chr7:22396000-22397400	Active TSS	Pancreatic Islets	Pancreatic Islet
14	chr7:22396200-22397200	Active TSS	iPS DF 19.11 Cell Line	embryonic stem cell
15	chr7:22396200-22397200	Active TSS	Breast Myoepithelial Primary Cells	Breast
16	chr7:22396200-22397400	Active TSS	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
17	chr7:22396200-22397400	Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
18	chr7:22396200-22397400	Active TSS	Rectal Smooth Muscle	rectum
19	chr7:22396200-22397800	Enhancers	Fetal Brain Male	brain
20	chr7:22396600-22397200	Bivalent/Poised TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
21	chr7:22396800-22397200	Bivalent Enhancer	IMR90 fetal lung fibroblasts Cell Line	lung
22	chr7:22396800-22397200	Bivalent Enhancer	Foreskin Melanocyte Primary Cells skin03	Skin
23	chr7:22396800-22397400	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
24	chr7:22396800-22397400	Enhancers	Primary B cells from peripheral blood	blood
25	chr7:22396800-22397400	Flanking Bivalent TSS/Enh	Foreskin Fibroblast Primary Cells skin01	Skin
26	chr7:22396800-22397400	Enhancers	Fetal Heart	heart
27	chr7:22396800-22397800	Bivalent Enhancer	H9 Derived Neuron Cultured Cells	ES cell derived
28	chr7:22397000-22397200	Flanking Bivalent TSS/Enh	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
29	chr7:22397000-22397200	Flanking Bivalent TSS/Enh	H1 Derived Mesenchymal Stem Cells	ES cell derived
30	chr7:22397000-22397200	Flanking Active TSS	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
31	chr7:22397000-22397200	Flanking Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
32	chr7:22397000-22397200	Flanking Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
33	chr7:22397000-22397200	Bivalent/Poised TSS	HUES48 Cell Line	embryonic stem cell
34	chr7:22397000-22397200	Bivalent/Poised TSS	iPS-15b Cell Line	embryonic stem cell
35	chr7:22397000-22397200	Flanking Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
36	chr7:22397000-22397200	Flanking Active TSS	Primary B cells from cord blood	blood
37	chr7:22397000-22397200	Bivalent Enhancer	Primary T cells fromperipheralblood	blood
38	chr7:22397000-22397200	Flanking Active TSS	Primary hematopoietic stem cells	blood
39	chr7:22397000-22397200	Bivalent/Poised TSS	Primary hematopoietic stem cells short term culture	blood
40	chr7:22397000-22397200	Bivalent Enhancer	Primary Natural Killer cells fromperipheralblood	blood
41	chr7:22397000-22397200	Flanking Bivalent TSS/Enh	Primary hematopoietic stem cells G-CSF-mobilized Female	--
42	chr7:22397000-22397200	Flanking Bivalent TSS/Enh	Primary hematopoietic stem cells G-CSF-mobilized Male	--
43	chr7:22397000-22397200	Flanking Bivalent TSS/Enh	Muscle Satellite Cultured Cells	--
44	chr7:22397000-22397200	Flanking Bivalent TSS/Enh	Cortex derived primary cultured neurospheres	brain
45	chr7:22397000-22397200	Flanking Bivalent TSS/Enh	Foreskin Fibroblast Primary Cells skin02	Skin
46	chr7:22397000-22397200	Flanking Active TSS	Brain Angular Gyrus	brain
47	chr7:22397000-22397200	Flanking Active TSS	Colonic Mucosa	Colon
48	chr7:22397000-22397200	Flanking Bivalent TSS/Enh	Fetal Muscle Trunk	muscle
49	chr7:22397000-22397200	Flanking Bivalent TSS/Enh	Fetal Muscle Leg	muscle
50	chr7:22397000-22397200	Flanking Bivalent TSS/Enh	Fetal Stomach	stomach

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