Variant report

Variant	rs11089487
Chromosome Location	chr22:31477361-31477362
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:254)
CpG islands
(count:61)
Chromatin interactive
region (count:17)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:254 , 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	POLR2A	chr22:31476902-31478202	MCF10A-Er-Src	breast:	n/a	n/a
2	TCF7L2	chr22:31476686-31477522	PANC-1	pancreas:	n/a	chr22:31476734-31476741
3	TBL1XR1	chr22:31477198-31477398	K562	blood:	n/a	n/a
4	MTA3	chr22:31476303-31477642	GM12878	blood:	n/a	n/a
5	TCF7L2	chr22:31476606-31477514	HCT-116	colon:	n/a	chr22:31476734-31476741
6	CREB1	chr22:31476341-31477662	HepG2	liver:	n/a	n/a
7	POLR2A	chr22:31476547-31478177	Hela-S3	cervix:	n/a	n/a
8	E2F4	chr22:31476859-31477432	MCF10A-Er-Src	breast:	n/a	chr22:31477259-31477269
9	BHLHE40	chr22:31476844-31477411	GM12878	blood:	n/a	n/a
10	CREB1	chr22:31476643-31477582	H1-hESC	embryonic stem cell:	n/a	n/a
11	POLR2A	chr22:31476846-31477636	HUVEC	blood vessel:	n/a	n/a
12	POLR2A	chr22:31476814-31477563	K562	blood:	n/a	n/a
13	POLR2A	chr22:31476687-31477581	GM12892	blood:	n/a	n/a
14	CHD2	chr22:31476784-31477523	Hela-S3	cervix:	n/a	n/a
15	POLR2A	chr22:31476687-31477540	GM18505	blood:	n/a	n/a
16	POLR2A	chr22:31476545-31477519	H1-neurons	neurons:	n/a	n/a
17	POLR2A	chr22:31476500-31480070	HUVEC	blood vessel:	n/a	n/a
18	RFX5	chr22:31477009-31477380	HepG2	liver:	n/a	n/a
19	CHD2	chr22:31476758-31477496	GM12878	blood:	n/a	n/a
20	POLR2A	chr22:31476722-31479551	HUVEC	blood vessel:	n/a	n/a
21	CTCF	chr22:31477260-31477410	HCT-116	colon:	n/a	n/a
22	PBX3	chr22:31477255-31477405	GM12878	blood:	n/a	n/a
23	POLR2A	chr22:31477006-31477477	A549	lung:	n/a	n/a
24	POLR2A	chr22:31476749-31479505	HUVEC	blood vessel:	n/a	n/a
25	SP1	chr22:31476701-31477524	H1-hESC	embryonic stem cell:	n/a	chr22:31477153-31477162 chr22:31477152-31477161 chr22:31477256-31477265 chr22:31477151-31477163 chr22:31477153-31477162 chr22:31477254-31477266 chr22:31477151-31477163 chr22:31477152-31477162 chr22:31477254-31477266 chr22:31477171-31477181 chr22:31477151-31477162 chr22:31477251-31477265 chr22:31477148-31477162 chr22:31477152-31477162
26	POLR2A	chr22:31476756-31481293	K562	blood:	n/a	n/a
27	TAF1	chr22:31477044-31477498	PFSK-1	brain:	n/a	n/a
28	GTF2F1	chr22:31477103-31477415	Hela-S3	cervix:	n/a	n/a
29	CTCF	chr22:31477320-31477470	AG09319	gingival:	n/a	n/a
30	ELF1	chr22:31476973-31477484	K562	blood:	n/a	n/a
31	TAF1	chr22:31477033-31477575	HepG2	liver:	n/a	n/a
32	SIN3A	chr22:31476923-31477638	GM12878	blood:	n/a	chr22:31477469-31477478 chr22:31477251-31477262
33	POLR2A	chr22:31476607-31477754	K562	blood:	n/a	n/a
34	RCOR1	chr22:31476714-31477592	K562	blood:	n/a	n/a
35	TBP	chr22:31476768-31477510	K562	blood:	n/a	n/a
36	POLR2A	chr22:31477010-31477544	A549	lung:	n/a	n/a
37	TAF1	chr22:31477069-31477453	K562	blood:	n/a	n/a
38	POLR2A	chr22:31476742-31479351	U87	brain:	n/a	n/a
39	POLR2A	chr22:31476707-31479351	U87	brain:	n/a	n/a
40	POLR2A	chr22:31477093-31477496	K562	blood:	n/a	n/a
41	MAX	chr22:31476965-31477628	K562	blood:	n/a	n/a
42	MYC	chr22:31476792-31477546	K562	blood:	n/a	n/a
43	POLR2A	chr22:31476589-31477637	PANC-1	pancreas:	n/a	n/a
44	CTCF	chr22:31477361-31477363	GM12892	blood:	n/a	n/a
45	MAX	chr22:31477249-31477410	K562	blood:	n/a	n/a
46	TAF1	chr22:31477028-31477690	A549	lung:	n/a	n/a
47	ZNF143	chr22:31476693-31477381	H1-hESC	embryonic stem cell:	n/a	n/a
48	POLR2A	chr22:31476610-31478212	ECC-1	luminal epithelium:	n/a	n/a
49	POLR2A	chr22:31476619-31477676	MCF-7	breast:	n/a	n/a
50	PAX5	chr22:31477073-31477535	GM12892	blood:	n/a	n/a

(count:61 , 50 per page) page: 1 2

No.	Chromosome Location	Cell Line	Cell type	Cell Stage
1	chr22:31477330-31477380	PrEC	prostate:	n/a
2	chr22:31477330-31477380	MCF10A-Er-Src	breast:	n/a
3	chr22:31477330-31477380	HRCEpiC	kidney:	n/a
4	chr22:31477330-31477380	AG04449	skin:	fetal
5	chr22:31477330-31477380	NT2-D1	testis:	n/a
6	chr22:31477330-31477380	SAEC	small airway:	n/a
7	chr22:31477330-31477380	PANC-1	pancreas:	n/a
8	chr22:31477330-31477380	ECC-1	luminal epithelium:	n/a
9	chr22:31477330-31477380	U87	brain:	n/a
10	chr22:31477330-31477380	SK-N-SH	brain:	n/a
11	chr22:31477330-31477380	HNPCEpiC	eye:	n/a
12	chr22:31477330-31477380	BE2_C	brain:	n/a
13	chr22:31477330-31477380	HIPEpiC	eye:	n/a
14	chr22:31477330-31477380	HCM	heart:	n/a
15	chr22:31477330-31477380	GM12892	blood:	n/a
16	chr22:31477330-31477380	HepG2	liver:	n/a
17	chr22:31477330-31477380	NB4	blood:	n/a
18	chr22:31477330-31477380	PFSK-1	brain:	n/a
19	chr22:31477330-31477380	Hepatocyte	liver:	n/a
20	chr22:31477330-31477380	AG04450	lung:	fetal
21	chr22:31477330-31477380	SK-N-MC	brain:	n/a
22	chr22:31477330-31477380	GM19239	blood:	n/a
23	chr22:31477330-31477380	AG09319	gingival:	n/a
24	chr22:31477330-31477380	GM12891	blood:	n/a
25	chr22:31477330-31477380	A549	lung:	n/a
26	chr22:31477330-31477380	HPAEpiC	pulmonary alveolar:	n/a
27	chr22:31477330-31477380	ProgFib	skin:	n/a
28	chr22:31477330-31477380	NHBE	bronchial:	n/a
29	chr22:31477330-31477380	IMR90	lung:	fetal
30	chr22:31477330-31477380	BJ	skin:	n/a
31	chr22:31477330-31477380	HUVEC	blood vessel:	n/a
32	chr22:31477330-31477380	HAEpiC	amniotic membrane:	n/a
33	chr22:31477330-31477380	HMEC	breast:	n/a
34	chr22:31477330-31477380	H1-hESC	embryonic stem cell:	embryo
35	chr22:31477330-31477380	HRPEpiC	eye:	n/a
36	chr22:31477330-31477380	HCF	heart:	n/a
37	chr22:31477330-31477380	Jurkat	blood:	n/a
38	chr22:31477330-31477380	HL-60	blood:	n/a
39	chr22:31477330-31477380	LNCaP	prostate:	n/a
40	chr22:31477330-31477380	GM06990	blood:	n/a
41	chr22:31477330-31477380	K562	blood:	n/a
42	chr22:31477330-31477380	AG10803	skin:	n/a
43	chr22:31477330-31477380	SK-N-SH_RA	brain:	n/a
44	chr22:31477330-31477380	T-47D	breast:	n/a
45	chr22:31477330-31477380	HCPEpiC	choroid plexus:	n/a
46	chr22:31477330-31477380	HEK293	kidney:	embryo
47	chr22:31477330-31477380	RPTEC	kidney:	n/a
48	chr22:31477330-31477380	NHDF-neo	bronchial:	n/a
49	chr22:31477330-31477380	AoSMC	blood vessel:	n/a
50	chr22:31477330-31477380	MCF-7	breast:	n/a

(count:17 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr22:31475364..31478247-chr22:31499584..31502277,3	MCF-7	breast:
2	chr22:31476077..31485695-chr22:31490616..31506508,29	K562	blood:
3	chr22:31360911..31371148-chr22:31475052..31483145,24	K562	blood:
4	chr17:56736226..56737884-chr22:31477314..31478907,2	MCF-7	breast:
5	chr22:31360045..31368675-chr22:31475412..31482694,29	K562	blood:
6	chr22:31455769..31462183-chr22:31475245..31482356,13	K562	blood:
7	chr22:31354949..31372607-chr22:31475365..31485377,53	MCF-7	breast:
8	chr15:71407229..71409255-chr22:31476063..31478842,2	MCF-7	breast:
9	chr22:31458274..31462644-chr22:31476246..31482425,10	K562	blood:
10	chr22:31455775..31461842-chr22:31476267..31480955,13	MCF-7	breast:
11	chr22:31358868..31372302-chr22:31474097..31485545,64	MCF-7	breast:
12	chr22:31477195..31479122-chr22:31617258..31619966,2	MCF-7	breast:
13	chr22:31476560..31478859-chr22:31533468..31537086,3	MCF-7	breast:
14	chr22:31477105..31478805-chr22:31616514..31618888,2	MCF-7	breast:
15	chr22:31475291..31477772-chr3:161087457..161089639,2	MCF-7	breast:
16	chr22:31457775..31462699-chr22:31474304..31478789,5	MCF-7	breast:
17	chr22:31275930..31278516-chr22:31475630..31478083,2	K562	blood:

No data

Variant related genes	Relation type
SMTN	TF binding region
SMTN	CpG island
ENSG00000100078	Chromatin interaction
ENSG00000199695	Chromatin interaction
ENSG00000253352	Chromatin interaction
ENSG00000225362	Chromatin interaction
ENSG00000183963	Chromatin interaction
ENSG00000133422	Chromatin interaction
ENSG00000240186	Chromatin interaction
ENSG00000196542	Chromatin interaction
ENSG00000202077	Chromatin interaction
ENSG00000184792	Chromatin interaction
ENSG00000198832	Chromatin interaction

Extended variants
information (count: 23 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:18)

rs_ID	r²[population]
rs1004243	0.91[CEU][hapmap];1.00[CHB][hapmap];0.94[AMR][1000 genomes];0.84[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs11089488	0.82[AMR][1000 genomes]
rs12330010	0.84[AMR][1000 genomes]
rs12484046	0.82[CEU][hapmap]
rs13054770	0.82[AMR][1000 genomes]
rs1558023	0.80[CEU][hapmap]
rs35657209	0.80[AMR][1000 genomes]
rs35685997	0.83[AMR][1000 genomes]
rs4281997	0.95[AMR][1000 genomes];0.86[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs4820934	0.81[AMR][1000 genomes]
rs7284108	0.82[AMR][1000 genomes]
rs7284757	0.82[CEU][hapmap]
rs737930	0.82[AMR][1000 genomes]
rs8135353	0.80[CEU][hapmap];0.82[AMR][1000 genomes]
rs9621173	0.82[AMR][1000 genomes]
rs9621184	0.83[CEU][hapmap];0.83[AMR][1000 genomes]
rs9621185	0.84[CEU][hapmap];0.83[AMR][1000 genomes]
rs9621187	0.94[AMR][1000 genomes];0.86[EUR][1000 genomes];0.81[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv9896	chr22:31369204-31513933	Strong transcription Enhancers Genic enhancers Flanking Active TSS Active TSS Weak transcription ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	35 gene(s)	inside rSNPs	diseases
2	nsv524366	chr22:31440703-31480069	Flanking Active TSS Enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Weak transcription Active TSS Strong transcription Bivalent Enhancer Genic enhancers ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	18 gene(s)	inside rSNPs	diseases
3	nsv829173	chr22:31450043-31543956	Enhancers Weak transcription Flanking Active TSS Strong transcription Transcr. at gene 5' and 3' Active TSS Genic enhancers Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	30 gene(s)	inside rSNPs	diseases
4	nsv914975	chr22:31466083-31514477	Active TSS Flanking Active TSS Strong transcription Enhancers Weak transcription Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer Genic enhancers Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	28 gene(s)	inside rSNPs	diseases
5	nsv914976	chr22:31475307-31543260	Active TSS Enhancers Flanking Active TSS Weak transcription Transcr. at gene 5' and 3' Strong transcription Flanking Bivalent TSS/Enh Genic enhancers Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	30 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:127 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr22:31476400-31477400	Active TSS	Primary hematopoietic stem cells short term culture	blood
2	chr22:31476400-31477600	Active TSS	iPS-20b Cell Line	embryonic stem cell
3	chr22:31476400-31477800	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
4	chr22:31476400-31477800	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
5	chr22:31476400-31478000	Active TSS	Muscle Satellite Cultured Cells	--
6	chr22:31476400-31478200	Active TSS	HUES64 Cell Line	embryonic stem cell
7	chr22:31476400-31478400	Active TSS	HSMM	muscle
8	chr22:31476400-31478800	Active TSS	Pancreatic Islets	Pancreatic Islet
9	chr22:31476400-31479200	Active TSS	Fetal Kidney	kidney
10	chr22:31476600-31477400	Active TSS	ES-I3 Cell Line	embryonic stem cell
11	chr22:31476600-31477400	Active TSS	Primary T killer naive cells fromperipheralblood	blood
12	chr22:31476600-31477400	Active TSS	Primary T killer memory cells from peripheral blood	blood
13	chr22:31476600-31477600	Active TSS	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
14	chr22:31476600-31477800	Active TSS	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
15	chr22:31476600-31477800	Active TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
16	chr22:31476600-31477800	Flanking Active TSS	Primary monocytes fromperipheralblood	blood
17	chr22:31476600-31477800	Flanking Active TSS	Primary Natural Killer cells fromperipheralblood	blood
18	chr22:31476600-31477800	Flanking Active TSS	Liver	Liver
19	chr22:31476600-31477800	Active TSS	Brain Cingulate Gyrus	brain
20	chr22:31476600-31478000	Flanking Active TSS	Primary B cells from cord blood	blood
21	chr22:31476600-31478000	Flanking Active TSS	Primary T regulatory cells fromperipheralblood	blood
22	chr22:31476600-31478200	Active TSS	H9 Cell Line	embryonic stem cell
23	chr22:31476600-31478200	Active TSS	HUES48 Cell Line	embryonic stem cell
24	chr22:31476600-31478200	Flanking Active TSS	Primary neutrophils fromperipheralblood	blood
25	chr22:31476600-31478200	Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
26	chr22:31476600-31478400	Flanking Active TSS	Primary T helper naive cells fromperipheralblood	blood
27	chr22:31476600-31478800	Flanking Active TSS	Placenta	Placenta
28	chr22:31476600-31478800	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
29	chr22:31476600-31479200	Active TSS	Aorta	Aorta
30	chr22:31476600-31479200	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
31	chr22:31476600-31479600	Flanking Active TSS	Skeletal Muscle Male	skeletal muscle
32	chr22:31476600-31480400	Active TSS	Brain Angular Gyrus	brain
33	chr22:31476800-31477400	Active TSS	iPS-15b Cell Line	embryonic stem cell
34	chr22:31476800-31477400	Active TSS	iPS-18 Cell Line	embryonic stem cell
35	chr22:31476800-31477400	Active TSS	ES-UCSF4 Cell Line	embryonic stem cell
36	chr22:31476800-31477400	Active TSS	Primary hematopoietic stem cells	blood
37	chr22:31476800-31477400	Active TSS	Primary T helper memory cells from peripheral blood 2	blood
38	chr22:31476800-31477400	Active TSS	Brain Hippocampus Middle	brain
39	chr22:31476800-31477400	Active TSS	Fetal Brain Female	brain
40	chr22:31476800-31477400	Active TSS	Fetal Thymus	thymus
41	chr22:31476800-31477400	Active TSS	Thymus	Thymus
42	chr22:31476800-31477600	Active TSS	iPS DF 19.11 Cell Line	embryonic stem cell
43	chr22:31476800-31477600	Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
44	chr22:31476800-31477600	Active TSS	Brain Germinal Matrix	brain
45	chr22:31476800-31477600	Enhancers	Fetal Heart	heart
46	chr22:31476800-31477600	Active TSS	Rectal Mucosa Donor 29	rectum
47	chr22:31476800-31477600	Active TSS	Stomach Mucosa	stomach
48	chr22:31476800-31477600	Active TSS	Hela-S3	cervix
49	chr22:31476800-31477800	Active TSS	ES-WA7 Cell Line	embryonic stem cell
50	chr22:31476800-31477800	Active TSS	H1 Cell Line	embryonic stem cell

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