Variant report

Variant	rs221798
Chromosome Location	chr7:100287495-100287496
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	CTCF	chr7:100287380-100287530	MCF-7	breast:	n/a	chr7:100287426-100287434
2	CTCF	chr7:100287360-100287510	GM12867	blood:	n/a	chr7:100287426-100287434
3	CTCF	chr7:100287398-100287526	HepG2	liver:	n/a	chr7:100287426-100287434
4	CTCF	chr7:100287332-100287503	MCF-7	breast:	n/a	chr7:100287426-100287434
5	CTCF	chr7:100287380-100287530	GM12865	blood:	n/a	chr7:100287426-100287434
6	CTCF	chr7:100287380-100287530	HCT-116	colon:	n/a	chr7:100287426-100287434
7	EBF1	chr7:100287155-100287533	GM12878	blood:	n/a	chr7:100287336-100287347 chr7:100287337-100287347 chr7:100287338-100287347 chr7:100287336-100287349
8	CTCF	chr7:100287332-100287520	MCF-7	breast:	n/a	chr7:100287426-100287434
9	CTCF	chr7:100287420-100287570	GM12871	blood:	n/a	chr7:100287426-100287434
10	CTCF	chr7:100287308-100287513	GM19238	blood:	n/a	chr7:100287426-100287434
11	CTCF	chr7:100287359-100287503	MCF-7	breast:	n/a	chr7:100287426-100287434
12	POLR2A	chr7:100287339-100287757	HepG2	liver:	n/a	n/a
13	CTCF	chr7:100287420-100287570	GM12867	blood:	n/a	chr7:100287426-100287434
14	POLR2A	chr7:100287128-100287503	H1-hESC	embryonic stem cell:	n/a	n/a
15	CTCF	chr7:100287380-100287530	WERI-Rb-1	eye:	n/a	chr7:100287426-100287434
16	EBF1	chr7:100287184-100287550	GM12878	blood:	n/a	chr7:100287336-100287347 chr7:100287337-100287347 chr7:100287338-100287347 chr7:100287336-100287349
17	CTCF	chr7:100287318-100287508	GM12891	blood:	n/a	chr7:100287426-100287434
18	CTCF	chr7:100287360-100287510	BE2_C	brain:	n/a	chr7:100287426-100287434
19	CTCF	chr7:100287323-100287506	HepG2	liver:	n/a	chr7:100287426-100287434
20	CTCF	chr7:100287276-100287570	GM12878	blood:	n/a	chr7:100287426-100287434
21	CTCF	chr7:100287460-100287610	GM12870	blood:	n/a	n/a
22	CTCF	chr7:100287380-100287530	HepG2	liver:	n/a	chr7:100287426-100287434
23	CTCF	chr7:100287420-100287570	GM12873	blood:	n/a	chr7:100287426-100287434
24	POLR2A	chr7:100287200-100287563	MCF-7	breast:	n/a	n/a
25	CTCF	chr7:100287480-100287630	NB4	blood:	n/a	n/a
26	CTCF	chr7:100287360-100287510	GM12873	blood:	n/a	chr7:100287426-100287434
27	POLR2A	chr7:100279071-100287739	K562	blood:	n/a	n/a
28	CTCF	chr7:100287420-100287570	GM12872	blood:	n/a	chr7:100287426-100287434
29	CTCF	chr7:100287375-100287505	K562	blood:	n/a	chr7:100287426-100287434
30	CTCF	chr7:100287380-100287530	HEEpiC	esophagus:	n/a	chr7:100287426-100287434
31	CTCF	chr7:100287380-100287530	BE2_C	brain:	n/a	chr7:100287426-100287434
32	POLR2A	chr7:100287329-100287554	K562	blood:	n/a	n/a
33	CTCF	chr7:100287317-100287536	K562	blood:	n/a	chr7:100287426-100287434
34	CTCF	chr7:100287440-100287590	HBMEC	blood vessel:	n/a	n/a
35	CTCF	chr7:100287323-100287507	MCF-7	breast:	n/a	chr7:100287426-100287434
36	POLR2A	chr7:100286649-100288004	K562	blood:	n/a	n/a
37	CTCF	chr7:100287420-100287570	K562	blood:	n/a	chr7:100287426-100287434
38	CTCF	chr7:100287360-100287510	GM12872	blood:	n/a	chr7:100287426-100287434
39	CTCF	chr7:100287400-100287550	Hela-S3	cervix:	n/a	chr7:100287426-100287434
40	CTCF	chr7:100287380-100287530	GM12866	blood:	n/a	chr7:100287426-100287434
41	CTCF	chr7:100287349-100287536	GM19240	blood:	n/a	chr7:100287426-100287434
42	CTCF	chr7:100287380-100287530	GM12869	blood:	n/a	chr7:100287426-100287434
43	CTCF	chr7:100287360-100287510	Caco-2	colon:	n/a	chr7:100287426-100287434
44	CTCF	chr7:100287420-100287570	HMEC	breast:	n/a	chr7:100287426-100287434
45	CTCF	chr7:100287460-100287690	GM06990	blood:	n/a	n/a
46	POLR2A	chr7:100286922-100287812	SK-N-MC	brain:	n/a	n/a
47	CTCF	chr7:100287380-100287530	GM12874	blood:	n/a	chr7:100287426-100287434
48	CTCF	chr7:100287380-100287530	HRPEpiC	eye:	n/a	chr7:100287426-100287434
49	CTCF	chr7:100287369-100287529	GM12878	blood:	n/a	chr7:100287426-100287434
50	CTCF	chr7:100287328-100287502	MCF-7	breast:	n/a	chr7:100287426-100287434

No.	Chromosome Location	Cell Line	Cell type	Cell Stage
1	chr7:100287481-100287531	Hela-S3	cervix:	n/a
2	chr7:100287481-100287531	CMK	blood:	n/a
3	chr7:100287481-100287531	PANC-1	pancreas:	n/a
4	chr7:100287481-100287531	GM12878	blood:	n/a
5	chr7:100287481-100287531	IMR90	lung:	fetal
6	chr7:100287481-100287531	AG04449	skin:	fetal
7	chr7:100287481-100287531	Hepatocyte	liver:	n/a
8	chr7:100287481-100287531	LNCaP	prostate:	n/a
9	chr7:100287481-100287531	HL-60	blood:	n/a
10	chr7:100287481-100287531	HRPEpiC	eye:	n/a
11	chr7:100287481-100287531	HUVEC	blood vessel:	n/a
12	chr7:100287481-100287531	RPTEC	kidney:	n/a
13	chr7:100287481-100287531	SKMC	muscle:	n/a
14	chr7:100287481-100287531	H1-hESC	embryonic stem cell:	embryo
15	chr7:100287481-100287531	BE2_C	brain:	n/a
16	chr7:100287481-100287531	NH-A	brain:	n/a
17	chr7:100287481-100287531	Jurkat	blood:	n/a
18	chr7:100287481-100287531	Caco-2	colon:	n/a
19	chr7:100287481-100287531	SAEC	small airway:	n/a
20	chr7:100287481-100287531	HAEpiC	amniotic membrane:	n/a
21	chr7:100287481-100287531	AG09319	gingival:	n/a
22	chr7:100287481-100287531	HCF	heart:	n/a
23	chr7:100287481-100287531	K562	blood:	n/a
24	chr7:100287481-100287531	PrEC	prostate:	n/a
25	chr7:100287481-100287531	AG10803	skin:	n/a
26	chr7:100287481-100287531	HRCEpiC	kidney:	n/a
27	chr7:100287481-100287531	SK-N-SH	brain:	n/a
28	chr7:100287481-100287531	AoSMC	blood vessel:	n/a
29	chr7:100287481-100287531	HCPEpiC	choroid plexus:	n/a
30	chr7:100287481-100287531	MCF10A-Er-Src	breast:	n/a
31	chr7:100287481-100287531	NHBE	bronchial:	n/a
32	chr7:100287481-100287531	NB4	blood:	n/a
33	chr7:100287481-100287531	U87	brain:	n/a
34	chr7:100287481-100287531	HMEC	breast:	n/a
35	chr7:100287481-100287531	HepG2	liver:	n/a
36	chr7:100287481-100287531	HEK293	kidney:	embryo
37	chr7:100287481-100287531	ECC-1	luminal epithelium:	n/a
38	chr7:100287481-100287531	NHDF-neo	bronchial:	n/a
39	chr7:100287481-100287531	PFSK-1	brain:	n/a
40	chr7:100287481-100287531	ProgFib	skin:	n/a
41	chr7:100287481-100287531	HRE	kidney:	n/a
42	chr7:100287481-100287531	ovcar-3	ovarian:	n/a
43	chr7:100287481-100287531	GM12891	blood:	n/a
44	chr7:100287481-100287531	MCF-7	breast:	n/a
45	chr7:100287481-100287531	AG04450	lung:	fetal
46	chr7:100287481-100287531	GM06990	blood:	n/a
47	chr7:100287481-100287531	SK-N-SH_RA	brain:	n/a
48	chr7:100287481-100287531	GM12892	blood:	n/a
49	chr7:100287481-100287531	SK-N-MC	brain:	n/a
50	chr7:100287481-100287531	HCT-116	colon:	n/a

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	chr7:100200773..100203323-chr7:100286656..100289565,2	MCF-7	breast:
4	chr7:100239138..100241612-chr7:100287076..100289093,2	K562	blood:
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	chr7:100287211..100289558-chr7:100423705..100426047,3	K562	blood:
9	chr7:100025899..100028913-chr7:100286592..100288668,3	K562	blood:
10	chr7:100284400..100287604-chr7:100471903..100474319,4	MCF-7	breast:
11	chr7:100180869..100184882-chr7:100287482..100291355,9	MCF-7	breast:

Variant related genes	Relation type
GIGYF1	TF binding region
GIGYF1	CpG island
ENSG00000146834	Chromatin interaction
ENSG00000146828	Chromatin interaction
ENSG00000196411	Chromatin interaction
ENSG00000077454	Chromatin interaction
ENSG00000106333	Chromatin interaction
ENSG00000224729	Chromatin interaction
ENSG00000106327	Chromatin interaction
ENSG00000087087	Chromatin interaction
ENSG00000106336	Chromatin interaction
ENSG00000078487	Chromatin interaction

Extended variants
information (count: 36 )
Associated
traits (count: 1 )

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

rs_ID	r²[population]
rs1734907	1.00[ASN][1000 genomes]
rs221770	0.84[AFR][1000 genomes];0.86[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs221774	0.94[AFR][1000 genomes];0.86[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs221778	0.89[AFR][1000 genomes];0.94[EUR][1000 genomes]
rs221779	0.84[EUR][1000 genomes]
rs221780	0.84[AFR][1000 genomes];0.93[ASN][1000 genomes]
rs221781	0.86[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs221783	0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs221784	0.87[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs221786	0.81[AMR][1000 genomes];0.91[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs221789	0.87[ASN][1000 genomes]
rs221792	0.81[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs221793	0.84[EUR][1000 genomes]
rs221794	0.84[AFR][1000 genomes];0.96[ASN][1000 genomes]
rs221796	0.81[AMR][1000 genomes];0.96[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs221797	0.81[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs221800	0.86[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs221803	0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2432929	0.85[AFR][1000 genomes];0.86[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4727462	0.91[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs492430	1.00[ASN][1000 genomes]
rs506597	0.88[AFR][1000 genomes];0.86[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs534043	0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs564449	0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]

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
rs221798	GIGYF1	cis	Nerve Tibial	GTEx

Chromatin state (count:126 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:100274200-100287600	Strong transcription	Placenta Amnion	Placenta Amnion
2	chr7:100274200-100288800	Genic enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
3	chr7:100274200-100289200	Weak transcription	Fetal Kidney	kidney
4	chr7:100274200-100290400	Weak transcription	HSMMtube	muscle
5	chr7:100274400-100287600	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
6	chr7:100274400-100287800	Strong transcription	iPS-15b Cell Line	embryonic stem cell
7	chr7:100274400-100287800	Strong transcription	iPS-20b Cell Line	embryonic stem cell
8	chr7:100274400-100287800	Strong transcription	Primary hematopoietic stem cells short term culture	blood
9	chr7:100274400-100288000	Strong transcription	HUES64 Cell Line	embryonic stem cell
10	chr7:100274400-100288000	Strong transcription	Rectal Mucosa Donor 29	rectum
11	chr7:100274400-100288600	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
12	chr7:100274600-100287600	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
13	chr7:100274600-100287800	Weak transcription	Fetal Brain Male	brain
14	chr7:100274600-100288200	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
15	chr7:100274800-100288600	Strong transcription	HUES48 Cell Line	embryonic stem cell
16	chr7:100275600-100287800	Strong transcription	Duodenum Mucosa	Duodenum
17	chr7:100276000-100287600	Strong transcription	Gastric	stomach
18	chr7:100276400-100288800	Strong transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
19	chr7:100276400-100290000	Weak transcription	Pancreatic Islets	Pancreatic Islet
20	chr7:100277400-100287600	Strong transcription	iPS DF 6.9 Cell Line	embryonic stem cell
21	chr7:100277400-100288000	Strong transcription	iPS-18 Cell Line	embryonic stem cell
22	chr7:100278400-100287800	Strong transcription	Cortex derived primary cultured neurospheres	brain
23	chr7:100278400-100287800	Strong transcription	Fetal Intestine Small	intestine
24	chr7:100278400-100288400	Strong transcription	Fetal Intestine Large	intestine
25	chr7:100278600-100288000	Strong transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
26	chr7:100278800-100287600	Strong transcription	Primary monocytes fromperipheralblood	blood
27	chr7:100278800-100288000	Strong transcription	Monocytes-CD14+_RO01746	blood
28	chr7:100279400-100288400	Strong transcription	Fetal Stomach	stomach
29	chr7:100279800-100288400	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
30	chr7:100280000-100288800	Weak transcription	NHDF-Ad	bronchial
31	chr7:100280400-100288000	Strong transcription	HUES6 Cell Line	embryonic stem cell
32	chr7:100280400-100289600	Weak transcription	HUVEC	blood vessel
33	chr7:100281600-100290600	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
34	chr7:100283000-100288400	Weak transcription	Psoas Muscle	Psoas
35	chr7:100283000-100289000	Strong transcription	NHEK	skin
36	chr7:100283400-100288800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
37	chr7:100284000-100290400	Weak transcription	Small Intestine	intestine
38	chr7:100284200-100287600	Transcr. at gene 5' and 3'	Foreskin Fibroblast Primary Cells skin01	Skin
39	chr7:100284200-100287600	Transcr. at gene 5' and 3'	Foreskin Fibroblast Primary Cells skin02	Skin
40	chr7:100284400-100287600	Strong transcription	Brain Angular Gyrus	brain
41	chr7:100284400-100288200	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
42	chr7:100284600-100287800	Strong transcription	K562	blood
43	chr7:100284600-100289000	Weak transcription	Primary hematopoietic stem cells	blood
44	chr7:100284800-100287600	Genic enhancers	Foreskin Melanocyte Primary Cells skin01	Skin
45	chr7:100285400-100287800	Enhancers	Primary T killer naive cells fromperipheralblood	blood
46	chr7:100285400-100288800	Genic enhancers	Spleen	Spleen
47	chr7:100285400-100289800	Enhancers	Fetal Heart	heart
48	chr7:100285600-100287600	Genic enhancers	Right Ventricle	heart
49	chr7:100285600-100287600	Enhancers	HMEC	breast
50	chr7:100285600-100287800	Genic enhancers	Brain Inferior Temporal Lobe	brain

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