Variant report

Variant	rs221800
Chromosome Location	chr7:100288552-100288553
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	CTCF	chr7:100288420-100288570	HMEC	breast:	n/a	n/a
2	POLR2A	chr7:100288351-100289048	SK-N-MC	brain:	n/a	n/a
3	POLR2A	chr7:100288549-100288570	Hela-S3	cervix:	n/a	n/a
4	CTCF	chr7:100288420-100288570	NHDF-neo	bronchial:	n/a	n/a
5	CTCF	chr7:100288440-100288590	HAc	cerebellar:	n/a	n/a
6	CTCF	chr7:100288420-100288570	AoAF	blood vessel:	n/a	n/a
7	ZNF384	chr7:100288374-100288571	K562	blood:	n/a	n/a
8	SMC3	chr7:100288186-100291400	SK-N-SH	brain:	n/a	chr7:100289216-100289230 chr7:100288446-100288456 chr7:100289506-100289516 chr7:100289447-100289457 chr7:100289447-100289461
9	CTCF	chr7:100288440-100288590	GM12873	blood:	n/a	n/a
10	POLR2A	chr7:100288369-100290133	K562	blood:	n/a	n/a
11	CTCF	chr7:100288460-100288610	SK-N-SH_RA	brain:	n/a	n/a
12	CTCF	chr7:100288420-100288570	GM12878	blood:	n/a	n/a
13	CTCF	chr7:100288420-100288570	HMF	breast:	n/a	n/a
14	CTCF	chr7:100288420-100288570	HRPEpiC	eye:	n/a	n/a
15	CTCF	chr7:100288440-100288590	HEEpiC	esophagus:	n/a	n/a
16	CTCF	chr7:100288440-100288590	HMEC	breast:	n/a	n/a
17	CTCF	chr7:100288420-100288570	AG04450	lung:	n/a	n/a
18	CTCF	chr7:100288420-100288570	AG09319	gingival:	n/a	n/a
19	RAD21	chr7:100288338-100290934	SK-N-SH	brain:	n/a	chr7:100289443-100289462 chr7:100288871-100288883 chr7:100289480-100289493 chr7:100289445-100289457 chr7:100290681-100290690 chr7:100288444-100288456 chr7:100289447-100289457 chr7:100289242-100289252 chr7:100288446-100288456 chr7:100289240-100289252
20	CTCF	chr7:100288420-100288570	WERI-Rb-1	eye:	n/a	n/a
21	CTCF	chr7:100288420-100288569	MCF-7	breast:	n/a	n/a
22	CTCF	chr7:100288420-100288570	NHEK	skin:	n/a	n/a
23	CTCF	chr7:100288420-100288570	K562	blood:	n/a	n/a
24	CTCF	chr7:100288395-100288556	Hela-S3	cervix:	n/a	n/a
25	CTCF	chr7:100288440-100288590	HCFaa	heart:	n/a	n/a
26	CTCF	chr7:100288366-100288567	HepG2	liver:	n/a	n/a
27	CTCF	chr7:100288500-100288650	WI-38	lung:	n/a	n/a
28	CTCF	chr7:100288420-100288570	BE2_C	brain:	n/a	n/a
29	POLR2A	chr7:100288335-100289071	K562	blood:	n/a	n/a
30	CTCF	chr7:100288440-100288590	HBMEC	blood vessel:	n/a	n/a
31	CTCF	chr7:100288420-100288570	GM12874	blood:	n/a	n/a
32	POLR2A	chr7:100288426-100288613	H1-hESC	embryonic stem cell:	n/a	n/a
33	CTCF	chr7:100288254-100288687	K562	blood:	n/a	n/a
34	CTCF	chr7:100288420-100288570	GM12872	blood:	n/a	n/a
35	CTCF	chr7:100288440-100288590	GM12878	blood:	n/a	n/a
36	CTCF	chr7:100288460-100288610	HPF	lung:	n/a	n/a
37	CTCF	chr7:100288330-100291509	SK-N-SH	brain:	n/a	chr7:100289445-100289463 chr7:100289242-100289255 chr7:100289447-100289460 chr7:100291304-100291317 chr7:100289217-100289230 chr7:100288748-100288756 chr7:100289440-100289461
38	CTCF	chr7:100288440-100288590	HCPEpiC	choroid plexus:	n/a	n/a
39	CTCF	chr7:100288325-100289799	A549	lung:	n/a	chr7:100289445-100289463 chr7:100289242-100289255 chr7:100289447-100289460 chr7:100289217-100289230 chr7:100288748-100288756 chr7:100289440-100289461
40	CTCF	chr7:100288440-100288590	SAEC	small airway:	n/a	n/a
41	CTCF	chr7:100288326-100288580	IMR90	lung:	n/a	n/a
42	CTCF	chr7:100288440-100288590	AG09319	gingival:	n/a	n/a
43	CTCF	chr7:100288441-100288560	GM12878	blood:	n/a	n/a
44	REST	chr7:100288441-100288617	H1-hESC	embryonic stem cell:	n/a	chr7:100288462-100288475 chr7:100288471-100288491 chr7:100288566-100288575 chr7:100288474-100288487

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	chr7:100288549..100289428-chr7:100303217..100304173,2	MCF-7	breast:
4	chr7:100288321..100291208-chr7:100293573..100296644,3	K562	blood:
5	chr7:100200773..100203323-chr7:100286656..100289565,2	MCF-7	breast:
6	chr7:100239138..100241612-chr7:100287076..100289093,2	K562	blood:
7	chr7:100199658..100204753-chr7:100287607..100293733,10	K562	blood:
8	chr7:100222759..100227059-chr7:100284156..100289115,6	K562	blood:
9	chr7:100288252..100292867-chr7:100319528..100322364,4	K562	blood:
10	chr7:100199953..100202324-chr7:100288023..100291009,2	MCF-7	breast:
11	chr7:100287688..100293699-chr7:100300603..100306359,15	MCF-7	breast:
12	chr7:100162910..100168606-chr7:100287546..100292436,6	MCF-7	breast:
13	chr7:100198433..100204411-chr7:100285757..100293733,14	K562	blood:
14	chr7:100287211..100289558-chr7:100423705..100426047,3	K562	blood:
15	chr7:100025899..100028913-chr7:100286592..100288668,3	K562	blood:
16	chr7:100288044..100289593-chr7:100290175..100291688,2	K562	blood:
17	chr7:100180869..100184882-chr7:100287482..100291355,9	MCF-7	breast:
18	chr7:100207033..100212293-chr7:100287661..100294075,8	MCF-7	breast:
19	chr7:100027286..100029611-chr7:100288264..100290842,2	MCF-7	breast:
20	chr7:100288390..100292044-chr7:100484527..100487788,3	MCF-7	breast:

Variant related genes	Relation type
GIGYF1	TF binding region
ENSG00000106330	Chromatin interaction
ENSG00000078487	Chromatin interaction
ENSG00000106336	Chromatin interaction
ENSG00000176125	Chromatin interaction
ENSG00000106327	Chromatin interaction
ENSG00000106333	Chromatin interaction
ENSG00000184414	Chromatin interaction
ENSG00000077454	Chromatin interaction
ENSG00000146834	Chromatin interaction
ENSG00000172336	Chromatin interaction
ENSG00000224729	Chromatin interaction
ENSG00000146828	Chromatin interaction
ENSG00000196411	Chromatin interaction
ENSG00000087087	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	0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs221774	0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs221778	0.94[EUR][1000 genomes]
rs221779	0.84[EUR][1000 genomes]
rs221780	0.93[ASN][1000 genomes]
rs221781	0.89[EUR][1000 genomes]
rs221783	0.89[AMR][1000 genomes];0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs221784	1.00[ASN][1000 genomes]
rs221786	0.94[AMR][1000 genomes];0.93[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs221789	0.87[ASN][1000 genomes]
rs221792	1.00[ASN][1000 genomes]
rs221793	0.87[EUR][1000 genomes]
rs221794	0.96[ASN][1000 genomes]
rs221796	0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs221797	0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs221798	0.86[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs221803	0.89[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2432929	0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4727462	0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs492430	1.00[ASN][1000 genomes]
rs506597	0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs534043	0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs564449	0.97[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
rs221800	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	chr7:100274200-100288800	Genic enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
2	chr7:100274200-100289200	Weak transcription	Fetal Kidney	kidney
3	chr7:100274200-100290400	Weak transcription	HSMMtube	muscle
4	chr7:100274400-100288600	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
5	chr7:100274800-100288600	Strong transcription	HUES48 Cell Line	embryonic stem cell
6	chr7:100276400-100288800	Strong transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
7	chr7:100276400-100290000	Weak transcription	Pancreatic Islets	Pancreatic Islet
8	chr7:100280000-100288800	Weak transcription	NHDF-Ad	bronchial
9	chr7:100280400-100289600	Weak transcription	HUVEC	blood vessel
10	chr7:100281600-100290600	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
11	chr7:100283000-100289000	Strong transcription	NHEK	skin
12	chr7:100283400-100288800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
13	chr7:100284000-100290400	Weak transcription	Small Intestine	intestine
14	chr7:100284600-100289000	Weak transcription	Primary hematopoietic stem cells	blood
15	chr7:100285400-100288800	Genic enhancers	Spleen	Spleen
16	chr7:100285400-100289800	Enhancers	Fetal Heart	heart
17	chr7:100285600-100288800	Weak transcription	Stomach Mucosa	stomach
18	chr7:100285800-100288600	Weak transcription	Duodenum Smooth Muscle	Duodenum
19	chr7:100285800-100290600	Weak transcription	Aorta	Aorta
20	chr7:100286000-100288600	Genic enhancers	Primary Natural Killer cells fromperipheralblood	blood
21	chr7:100286000-100289200	Genic enhancers	Primary T cells fromperipheralblood	blood
22	chr7:100286200-100288600	Genic enhancers	Skeletal Muscle Male	skeletal muscle
23	chr7:100286200-100289000	Genic enhancers	Primary T helper cells fromperipheralblood	blood
24	chr7:100286200-100289400	Weak transcription	Sigmoid Colon	Sigmoid Colon
25	chr7:100286200-100289600	Weak transcription	HSMM	muscle
26	chr7:100286400-100288600	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
27	chr7:100286400-100288600	Genic enhancers	Brain Germinal Matrix	brain
28	chr7:100286400-100288800	Genic enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
29	chr7:100286400-100288800	Genic enhancers	Fetal Brain Female	brain
30	chr7:100286400-100289000	Genic enhancers	Primary B cells from peripheral blood	blood
31	chr7:100286400-100289000	Weak transcription	Osteobl	bone
32	chr7:100286400-100289200	Weak transcription	NH-A	brain
33	chr7:100286600-100288800	Weak transcription	Muscle Satellite Cultured Cells	--
34	chr7:100286600-100289000	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
35	chr7:100286600-100289000	Weak transcription	Rectal Smooth Muscle	rectum
36	chr7:100286600-100289200	Genic enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
37	chr7:100286600-100289400	Genic enhancers	Fetal Thymus	thymus
38	chr7:100287000-100288600	Weak transcription	H9 Cell Line	embryonic stem cell
39	chr7:100287000-100288600	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
40	chr7:100287000-100288800	Weak transcription	Primary neutrophils fromperipheralblood	blood
41	chr7:100287000-100288800	Weak transcription	Rectal Mucosa Donor 31	rectum
42	chr7:100287000-100288800	Strong transcription	Thymus	Thymus
43	chr7:100287000-100289200	Weak transcription	Fetal Lung	lung
44	chr7:100287000-100289400	Enhancers	Primary T helper cells PMA-I stimulated	--
45	chr7:100287000-100289400	Weak transcription	A549	lung
46	chr7:100287000-100289800	Enhancers	Colon Smooth Muscle	Colon
47	chr7:100287200-100288800	Genic enhancers	Dnd41	blood
48	chr7:100287200-100289200	Genic enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
49	chr7:100287200-100289200	Genic enhancers	Fetal Adrenal Gland	Adrenal Gland
50	chr7:100287200-100289400	Enhancers	Adipose Nuclei	Adipose

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