Variant report

Variant	rs11988552
Chromosome Location	chr8:90738200-90738201
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:297)
CpG islands
(count:0)
Chromatin interactive
region (count:14)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:297 , 50 per page) page: 1 2 3 4 5 6

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	FOXM1	chr8:90737946-90738607	GM12878	blood:	n/a	n/a
2	CTCF	chr8:90738090-90738329	Medullo	brain:	n/a	n/a
3	CTCF	chr8:90738100-90738250	NHLF	lung:	n/a	n/a
4	GTF2F1	chr8:90738033-90738375	H1-hESC	embryonic stem cell:	n/a	n/a
5	RAD21	chr8:90737981-90738463	GM12878	blood:	n/a	n/a
6	RAD21	chr8:90737967-90738488	SK-N-SH_RA	brain:	n/a	n/a
7	RAD21	chr8:90737980-90738494	ECC-1	luminal epithelium:	n/a	n/a
8	CTCF	chr8:90737930-90738479	MCF-7	breast:	n/a	n/a
9	CTCF	chr8:90737989-90738444	GM12878	blood:	n/a	n/a
10	RELA	chr8:90737869-90738404	GM19099	blood:	n/a	n/a
11	CTCF	chr8:90738140-90738290	HepG2	liver:	n/a	n/a
12	CTCF	chr8:90738057-90738325	Lung_OC	lung:	n/a	n/a
13	MTA3	chr8:90737943-90738557	GM12878	blood:	n/a	n/a
14	CTCF	chr8:90738120-90738270	GM12871	blood:	n/a	n/a
15	SMC3	chr8:90738008-90738438	Hela-S3	cervix:	n/a	n/a
16	PML	chr8:90737912-90738662	GM12878	blood:	n/a	n/a
17	RAD21	chr8:90738019-90738449	HepG2	liver:	n/a	n/a
18	CTCF	chr8:90738140-90738290	GM12869	blood:	n/a	n/a
19	FOXM1	chr8:90737827-90738535	GM12878	blood:	n/a	n/a
20	ATF1	chr8:90738051-90738334	K562	blood:	n/a	n/a
21	RUNX3	chr8:90737952-90738522	GM12878	blood:	n/a	n/a
22	CTCF	chr8:90738100-90738250	MCF-7	breast:	n/a	n/a
23	CTCF	chr8:90738140-90738290	HA-sp	spinal cord:	n/a	n/a
24	SPI1	chr8:90737981-90738365	HL-60	blood:	n/a	chr8:90738124-90738133 chr8:90738122-90738135 chr8:90738123-90738136
25	CTCF	chr8:90738100-90738250	HEK293	kidney:	n/a	n/a
26	CTCF	chr8:90738103-90738289	Kidney_OC	kidney:	n/a	n/a
27	STAT3	chr8:90738083-90738374	MCF10A-Er-Src	breast:	n/a	n/a
28	SPI1	chr8:90737925-90738300	GM12878	blood:	n/a	chr8:90738124-90738133 chr8:90738122-90738135 chr8:90738123-90738136
29	CTCF	chr8:90738140-90738290	GM12864	blood:	n/a	n/a
30	BACH1	chr8:90738096-90738310	K562	blood:	n/a	n/a
31	NFIC	chr8:90737864-90738868	GM12878	blood:	n/a	n/a
32	YY1	chr8:90737955-90738463	GM12878	blood:	n/a	n/a
33	NFATC1	chr8:90737929-90738484	GM12878	blood:	n/a	n/a
34	CTCF	chr8:90738160-90738310	WERI-Rb-1	eye:	n/a	n/a
35	CTCF	chr8:90738124-90738294	HepG2	liver:	n/a	n/a
36	CTCF	chr8:90738140-90738290	AoAF	blood vessel:	n/a	n/a
37	POLR2A	chr8:90737966-90738356	Raji	blood:	n/a	n/a
38	RAD21	chr8:90738047-90738399	K562	blood:	n/a	n/a
39	CTCF	chr8:90738137-90738240	GM19240	blood:	n/a	n/a
40	CTCF	chr8:90737975-90738460	A549	lung:	n/a	n/a
41	CTCF	chr8:90738120-90738270	GM12864	blood:	n/a	n/a
42	ELF1	chr8:90737989-90738437	GM12878	blood:	n/a	n/a
43	ELF1	chr8:90738015-90738211	K562	blood:	n/a	n/a
44	CTCF	chr8:90738120-90738270	HRPEpiC	eye:	n/a	n/a
45	BCLAF1	chr8:90737861-90738551	GM12878	blood:	n/a	chr8:90738122-90738131 chr8:90737903-90737912
46	CTCF	chr8:90738095-90738399	GM10248	blood:	n/a	n/a
47	CTCF	chr8:90738100-90738250	AG10803	skin:	n/a	n/a
48	ATF2	chr8:90737929-90738551	GM12878	blood:	n/a	n/a
49	CTCF	chr8:90738117-90738297	Gliobla	brain:	n/a	n/a
50	CTCF	chr8:90738124-90738283	Pancreas_OC	pancreas:	n/a	n/a

No data

(count:14 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr8:90737750..90738653-chr8:90995891..90997375,11	MCF-7	breast:
2	chr8:90737820..90738670-chr8:90996630..90997353,4	K562	blood:
3	chr8:90736815..90743993-chr8:90765696..90773918,18	MCF-7	breast:
4	chr8:90732834..90736227-chr8:90736670..90741646,5	MCF-7	breast:
5	chr8:90737986..90738708-chr8:90849422..90850036,2	MCF-7	breast:
6	chr8:90737773..90739680-chr8:90867503..90870182,2	MCF-7	breast:
7	chr8:90737934..90739593-chr8:90739830..90742161,2	K562	blood:
8	chr8:90714137..90717056-chr8:90737564..90740115,2	K562	blood:
9	chr8:90735002..90740593-chr8:90994599..90998168,11	MCF-7	breast:
10	chr8:90737113..90738638-chr8:90994961..90997124,2	K562	blood:
11	chr8:90734885..90744209-chr8:90767977..90774247,14	MCF-7	breast:
12	chr8:90735826..90740064-chr8:90995306..90998250,3	MCF-7	breast:
13	chr8:90737440..90740963-chr8:90912985..90916304,5	MCF-7	breast:
14	chr8:90737819..90738602-chr8:90996411..90997232,4	MCF-7	breast:

No data

Variant related genes	Relation type
ENSG00000251136	TF binding region
ENSG00000164823	Chromatin interaction
ENSG00000207359	Chromatin interaction
ENSG00000104312	Chromatin interaction
ENSG00000251136	Chromatin interaction
ENSG00000104320	Chromatin interaction

Extended variants
information (count: 24 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:13)

rs_ID	r²[population]
rs10956227	0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10956271	0.91[YRI][hapmap];0.85[AFR][1000 genomes];1.00[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs11984756	1.00[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs11988253	0.83[AMR][1000 genomes];0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11995005	0.94[MKK][hapmap];0.90[YRI][hapmap];1.00[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs12540972	0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12542577	0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1397305	0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs16893139	0.90[YRI][hapmap]
rs2293808	1.00[YRI][hapmap];0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs2293809	0.90[YRI][hapmap];1.00[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs719324	0.93[EUR][1000 genomes]
rs7834416	0.90[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:11 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv831389	chr8:90575517-90753120	Enhancers Weak transcription Active TSS Strong transcription Flanking Active TSS Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	28 gene(s)	inside rSNPs	diseases
2	nsv1031578	chr8:90670102-90757821	Enhancers Strong transcription Flanking Active TSS Weak transcription Genic enhancers ZNF genes & repeats Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	diseases
3	nsv891180	chr8:90697810-90802491	Enhancers Active TSS Flanking Active TSS Weak transcription Strong transcription Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	45 gene(s)	inside rSNPs	diseases
4	nsv933502	chr8:90702392-91049100	Weak transcription Enhancers Active TSS Strong transcription Genic enhancers Flanking Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	62 gene(s)	inside rSNPs	diseases
5	nsv6294	chr8:90705780-90750101	Enhancers Active TSS ZNF genes & repeats Weak transcription Flanking Active TSS Genic enhancers Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	diseases
6	nsv934114	chr8:90720182-90999106	Active TSS Weak transcription Enhancers Flanking Active TSS Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	58 gene(s)	inside rSNPs	diseases
7	esv3479599	chr8:90736894-90741021	Weak transcription Enhancers Genic enhancers Flanking Active TSS Strong transcription	TF binding region Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
8	esv3479598	chr8:90736917-90741003	Weak transcription Enhancers Genic enhancers Strong transcription Flanking Active TSS	TF binding region Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
9	esv3479600	chr8:90736917-90741003	Enhancers Weak transcription Strong transcription Flanking Active TSS Genic enhancers	TF binding region Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
10	nsv891181	chr8:90737258-90819998	Strong transcription Flanking Active TSS Enhancers Active TSS Weak transcription ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	36 gene(s)	inside rSNPs	diseases
11	esv2762759	chr8:90738200-90739480	Weak transcription Enhancers Flanking Active TSS	TF binding region Chromatin interactive region	5 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:103 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr8:90713200-90741200	Weak transcription	Left Ventricle	heart
2	chr8:90713600-90756200	Weak transcription	Pancreas	Pancrea
3	chr8:90714200-90741400	Weak transcription	Right Ventricle	heart
4	chr8:90714400-90741000	Weak transcription	Gastric	stomach
5	chr8:90715400-90741200	Weak transcription	Rectal Mucosa Donor 29	rectum
6	chr8:90717200-90741000	Weak transcription	Stomach Smooth Muscle	stomach
7	chr8:90717800-90747800	Weak transcription	Ovary	ovary
8	chr8:90720800-90742400	Weak transcription	Fetal Lung	lung
9	chr8:90721000-90740000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
10	chr8:90721400-90740400	Weak transcription	Fetal Intestine Large	intestine
11	chr8:90721800-90738400	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
12	chr8:90725200-90740400	Weak transcription	Small Intestine	intestine
13	chr8:90726600-90741400	Weak transcription	Esophagus	oesophagus
14	chr8:90726800-90738200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
15	chr8:90731000-90738200	Weak transcription	K562	blood
16	chr8:90731000-90738400	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
17	chr8:90731800-90738600	Weak transcription	Placenta Amnion	Placenta Amnion
18	chr8:90732000-90738200	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
19	chr8:90732200-90738200	Weak transcription	HSMMtube	muscle
20	chr8:90732200-90738400	Weak transcription	HSMM	muscle
21	chr8:90733600-90741200	Weak transcription	Sigmoid Colon	Sigmoid Colon
22	chr8:90734000-90741200	Weak transcription	Liver	Liver
23	chr8:90734200-90738200	Weak transcription	Aorta	Aorta
24	chr8:90734200-90738200	Weak transcription	Brain Anterior Caudate	brain
25	chr8:90734200-90739800	Weak transcription	Fetal Stomach	stomach
26	chr8:90734200-90741200	Weak transcription	Placenta	Placenta
27	chr8:90734400-90738400	Weak transcription	Breast Myoepithelial Primary Cells	Breast
28	chr8:90734400-90740800	Weak transcription	Primary hematopoietic stem cells short term culture	blood
29	chr8:90735200-90738400	Enhancers	GM12878-XiMat	blood
30	chr8:90735400-90741200	Weak transcription	Primary T cells from cord blood	blood
31	chr8:90735800-90740800	Weak transcription	Duodenum Smooth Muscle	Duodenum
32	chr8:90736000-90740800	Enhancers	HUES48 Cell Line	embryonic stem cell
33	chr8:90736200-90739400	Enhancers	iPS-20b Cell Line	embryonic stem cell
34	chr8:90736200-90740000	Enhancers	iPS-15b Cell Line	embryonic stem cell
35	chr8:90736400-90738400	Enhancers	H1 Cell Line	embryonic stem cell
36	chr8:90736400-90739200	Enhancers	ES-I3 Cell Line	embryonic stem cell
37	chr8:90736400-90739400	Enhancers	HUES6 Cell Line	embryonic stem cell
38	chr8:90736400-90739400	Enhancers	iPS-18 Cell Line	embryonic stem cell
39	chr8:90736400-90739600	Enhancers	HUES64 Cell Line	embryonic stem cell
40	chr8:90736800-90739000	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
41	chr8:90737000-90740200	Weak transcription	Fetal Muscle Trunk	muscle
42	chr8:90737000-90741000	Weak transcription	Adipose Nuclei	Adipose
43	chr8:90737000-90741400	Weak transcription	Fetal Muscle Leg	muscle
44	chr8:90737200-90738200	Weak transcription	H9 Cell Line	embryonic stem cell
45	chr8:90737200-90741400	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
46	chr8:90737400-90738600	Enhancers	Monocytes-CD14+_RO01746	blood
47	chr8:90737600-90738200	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
48	chr8:90737600-90738400	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
49	chr8:90737600-90738600	Enhancers	ES-WA7 Cell Line	embryonic stem cell
50	chr8:90737600-90738600	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived

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