Variant report

Variant	rs221797
Chromosome Location	chr7:100285974-100285975
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:7)
CpG islands
(count:0)
Chromatin interactive
region (count:10)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:7 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr7:100282525-100286002	K562	blood:	n/a	n/a
2	POLR2A	chr7:100284828-100286626	K562	blood:	n/a	n/a
3	POLR2A	chr7:100285889-100286535	HepG2	liver:	n/a	n/a
4	POLR2A	chr7:100279071-100287739	K562	blood:	n/a	n/a
5	CHD1	chr7:100285293-100286299	IMR90	lung:	n/a	n/a
6	POLR2A	chr7:100285875-100286698	SK-N-MC	brain:	n/a	n/a
7	POLR2A	chr7:100285712-100286087	H1-hESC	embryonic stem cell:	n/a	n/a

No data

(count:10 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr7:100025163..100029050-chr7:100284721..100290800,5	MCF-7	breast:
2	chr7:100229407..100233868-chr7:100285575..100288686,3	MCF-7	breast:
3	chr7:100181696..100183356-chr7:100285003..100287484,2	K562	blood:
4	chr7:100182617..100185782-chr7:100284570..100287283,3	MCF-7	breast:
5	chr7:100222759..100227059-chr7:100284156..100289115,6	K562	blood:
6	chr7:100228701..100230503-chr7:100285337..100287602,2	K562	blood:
7	chr7:100198433..100204411-chr7:100285757..100293733,14	K562	blood:
8	chr7:100284987..100287383-chr7:100301493..100305069,3	K562	blood:
9	chr7:100284400..100287604-chr7:100471903..100474319,4	MCF-7	breast:
10	chr7:100285374..100287070-chr7:100470986..100472980,2	K562	blood:

No data

Variant related genes	Relation type
GIGYF1	TF binding region
ENSG00000106336	Chromatin interaction
ENSG00000146834	Chromatin interaction
ENSG00000078487	Chromatin interaction
ENSG00000077454	Chromatin interaction
ENSG00000106333	Chromatin interaction
ENSG00000106327	Chromatin interaction
ENSG00000172336	Chromatin interaction
ENSG00000224729	Chromatin interaction
ENSG00000087087	Chromatin interaction

Extended variants
information (count: 45 )
Associated
traits (count: 1 )

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

rs_ID	r²[population]
rs10247962	1.00[ASW][hapmap];0.85[CHB][hapmap];1.00[JPT][hapmap]
rs1052897	1.00[ASW][hapmap];0.85[CHB][hapmap];1.00[JPT][hapmap]
rs12673102	1.00[ASW][hapmap];0.85[CHB][hapmap];1.00[JPT][hapmap]
rs1734907	1.00[CHB][hapmap];0.89[CHD][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs221770	1.00[CEU][hapmap];1.00[CHB][hapmap];0.89[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.90[LWK][hapmap];0.82[MEX][hapmap];0.85[MKK][hapmap];1.00[TSI][hapmap];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs221774	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.82[MEX][hapmap];0.87[TSI][hapmap];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs221778	0.94[EUR][1000 genomes]
rs221779	0.84[EUR][1000 genomes]
rs221780	1.00[CHB][hapmap];0.89[CHD][hapmap];1.00[JPT][hapmap];0.93[ASN][1000 genomes]
rs221781	0.89[EUR][1000 genomes]
rs221783	0.84[AMR][1000 genomes];0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs221784	1.00[CHB][hapmap];0.89[CHD][hapmap];1.00[ASN][1000 genomes]
rs221786	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.82[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.82[MEX][hapmap];1.00[TSI][hapmap];0.89[AMR][1000 genomes];0.93[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs221789	0.82[CHB][hapmap];0.90[CHD][hapmap];1.00[JPT][hapmap];0.87[ASN][1000 genomes]
rs221792	1.00[ASN][1000 genomes]
rs221793	0.87[EUR][1000 genomes]
rs221794	0.96[ASN][1000 genomes]
rs221796	0.89[AMR][1000 genomes];0.96[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs221798	0.81[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs221800	0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs221803	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.89[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[TSI][hapmap];0.84[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2432929	0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3757859	1.00[ASW][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap]
rs4727457	0.85[CHB][hapmap];1.00[JPT][hapmap]
rs4727462	0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4729598	1.00[ASW][hapmap];0.85[CHB][hapmap];1.00[JPT][hapmap];0.82[MEX][hapmap];0.87[TSI][hapmap]
rs4729600	0.85[CHB][hapmap];1.00[JPT][hapmap]
rs492430	1.00[ASN][1000 genomes]
rs506597	0.92[CEU][hapmap];1.00[CHB][hapmap];0.89[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.82[MEX][hapmap];0.87[TSI][hapmap];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs534043	0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs564449	0.92[CEU][hapmap];0.89[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.82[MEX][hapmap];1.00[TSI][hapmap];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6975957	1.00[JPT][hapmap]
rs7457868	0.85[CHB][hapmap];1.00[JPT][hapmap]

Variant overlapped rSNPs/rCNVs (count:12 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv1829095	chr7:99814675-100494084	Bivalent Enhancer Active TSS Weak transcription Strong transcription Bivalent/Poised TSS Flanking Active TSS Transcr. at gene 5' and 3' Enhancers Flanking Bivalent TSS/Enh Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	393 gene(s)	inside rSNPs	diseases
2	nsv888779	chr7:100014711-100313420	Genic enhancers Transcr. at gene 5' and 3' Enhancers Weak transcription Flanking Active TSS Active TSS Bivalent/Poised TSS Strong transcription ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	321 gene(s)	inside rSNPs	diseases
3	nsv888785	chr7:100141861-100313420	Transcr. at gene 5' and 3' Weak transcription Flanking Active TSS Enhancers Flanking Bivalent TSS/Enh Genic enhancers Active TSS Bivalent Enhancer Strong transcription Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	83 gene(s)	inside rSNPs	diseases
4	nsv888786	chr7:100159567-100313420	Bivalent/Poised TSS Flanking Active TSS Weak transcription Active TSS Strong transcription Enhancers Flanking Bivalent TSS/Enh Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	83 gene(s)	inside rSNPs	diseases
5	nsv831072	chr7:100162503-100362835	Enhancers Weak transcription Strong transcription Flanking Active TSS Transcr. at gene 5' and 3' Active TSS Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	82 gene(s)	inside rSNPs	diseases
6	nsv888791	chr7:100221867-100371114	Enhancers Flanking Active TSS Active TSS Bivalent Enhancer Strong transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS Weak transcription Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	50 gene(s)	inside rSNPs	diseases
7	nsv607933	chr7:100240191-100365613	Enhancers Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Flanking Active TSS Genic enhancers Weak transcription Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	42 gene(s)	inside rSNPs	diseases
8	nsv470381	chr7:100240191-100431980	Strong transcription Active TSS Bivalent Enhancer Enhancers Flanking Active TSS Weak transcription Bivalent/Poised TSS Transcr. at gene 5' and 3' Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	49 gene(s)	inside rSNPs	diseases
9	nsv8184	chr7:100240737-100345945	Weak transcription Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS Active TSS Strong transcription Enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	40 gene(s)	inside rSNPs	diseases
10	nsv888792	chr7:100252918-100329189	Enhancers Weak transcription Genic enhancers ZNF genes & repeats Strong transcription Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	40 gene(s)	inside rSNPs	diseases
11	nsv888795	chr7:100266081-100298626	Strong transcription Genic enhancers Weak transcription Active TSS Flanking Bivalent TSS/Enh Flanking Active TSS Enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region miRNA target site	31 gene(s)	inside rSNPs	diseases
12	esv1804951	chr7:100275135-100374093	Weak transcription Flanking Active TSS Bivalent Enhancer Strong transcription Flanking Bivalent TSS/Enh Enhancers Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	38 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs221797	GIGYF1	cis	Nerve Tibial	GTEx

Chromatin state (count:125 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:100274000-100287000	Strong transcription	Lung	lung
2	chr7:100274200-100287600	Strong transcription	Placenta Amnion	Placenta Amnion
3	chr7:100274200-100288800	Genic enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
4	chr7:100274200-100289200	Weak transcription	Fetal Kidney	kidney
5	chr7:100274200-100290400	Weak transcription	HSMMtube	muscle
6	chr7:100274400-100286000	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
7	chr7:100274400-100286200	Strong transcription	Left Ventricle	heart
8	chr7:100274400-100286200	Strong transcription	Sigmoid Colon	Sigmoid Colon
9	chr7:100274400-100286400	Strong transcription	Thymus	Thymus
10	chr7:100274400-100287400	Strong transcription	Brain Cingulate Gyrus	brain
11	chr7:100274400-100287400	Strong transcription	Brain Substantia Nigra	brain
12	chr7:100274400-100287600	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
13	chr7:100274400-100287800	Strong transcription	iPS-15b Cell Line	embryonic stem cell
14	chr7:100274400-100287800	Strong transcription	iPS-20b Cell Line	embryonic stem cell
15	chr7:100274400-100287800	Strong transcription	Primary hematopoietic stem cells short term culture	blood
16	chr7:100274400-100288000	Strong transcription	HUES64 Cell Line	embryonic stem cell
17	chr7:100274400-100288000	Strong transcription	Rectal Mucosa Donor 29	rectum
18	chr7:100274400-100288600	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
19	chr7:100274600-100286400	Strong transcription	Fetal Brain Female	brain
20	chr7:100274600-100286400	Strong transcription	Skeletal Muscle Female	skeletal muscle
21	chr7:100274600-100286600	Strong transcription	Rectal Smooth Muscle	rectum
22	chr7:100274600-100287000	Strong transcription	Fetal Lung	lung
23	chr7:100274600-100287200	Strong transcription	Dnd41	blood
24	chr7:100274600-100287600	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
25	chr7:100274600-100287800	Weak transcription	Fetal Brain Male	brain
26	chr7:100274600-100288200	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
27	chr7:100274800-100286600	Strong transcription	Fetal Thymus	thymus
28	chr7:100274800-100288600	Strong transcription	HUES48 Cell Line	embryonic stem cell
29	chr7:100275000-100286800	Strong transcription	Brain Hippocampus Middle	brain
30	chr7:100275400-100286400	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
31	chr7:100275600-100287800	Strong transcription	Duodenum Mucosa	Duodenum
32	chr7:100275800-100286400	Strong transcription	Brain Germinal Matrix	brain
33	chr7:100275800-100287000	Strong transcription	Liver	Liver
34	chr7:100276000-100287600	Strong transcription	Gastric	stomach
35	chr7:100276400-100288800	Strong transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
36	chr7:100276400-100290000	Weak transcription	Pancreatic Islets	Pancreatic Islet
37	chr7:100277400-100287200	Strong transcription	Esophagus	oesophagus
38	chr7:100277400-100287600	Strong transcription	iPS DF 6.9 Cell Line	embryonic stem cell
39	chr7:100277400-100288000	Strong transcription	iPS-18 Cell Line	embryonic stem cell
40	chr7:100277600-100287200	Strong transcription	Placenta	Placenta
41	chr7:100277800-100287000	Strong transcription	Rectal Mucosa Donor 31	rectum
42	chr7:100277800-100287200	Weak transcription	Primary B cells from cord blood	blood
43	chr7:100278400-100287000	Strong transcription	Primary neutrophils fromperipheralblood	blood
44	chr7:100278400-100287400	Strong transcription	Colonic Mucosa	Colon
45	chr7:100278400-100287800	Strong transcription	Cortex derived primary cultured neurospheres	brain
46	chr7:100278400-100287800	Strong transcription	Fetal Intestine Small	intestine
47	chr7:100278400-100288400	Strong transcription	Fetal Intestine Large	intestine
48	chr7:100278600-100286200	Strong transcription	Skeletal Muscle Male	skeletal muscle
49	chr7:100278600-100286800	Strong transcription	Ovary	ovary
50	chr7:100278600-100288000	Strong transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived

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