Variant report

Variant	rs1771220
Chromosome Location	chr9:116163645-116163646
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	FOXP2	chr9:116163460-116163945	SK-N-MC	brain:	n/a	n/a
2	MAX	chr9:116163314-116164036	ECC-1	luminal epithelium:	n/a	chr9:116163567-116163577 chr9:116163677-116163687
3	TCF12	chr9:116163106-116163789	ECC-1	luminal epithelium:	n/a	chr9:116163208-116163215 chr9:116163276-116163283
4	FOSL2	chr9:116163429-116163938	A549	lung:	n/a	chr9:116163569-116163578
5	NFIC	chr9:116163560-116164040	HepG2	liver:	n/a	n/a
6	EGR1	chr9:116163385-116164015	ECC-1	luminal epithelium:	n/a	chr9:116163625-116163639 chr9:116163680-116163690 chr9:116163604-116163619 chr9:116163678-116163692 chr9:116163676-116163690 chr9:116163605-116163618 chr9:116163605-116163618 chr9:116163602-116163616 chr9:116163566-116163579 chr9:116163606-116163616 chr9:116163679-116163692 chr9:116163477-116163490 chr9:116163677-116163687
7	TAF1	chr9:116163259-116163894	HepG2	liver:	n/a	n/a
8	POLR2A	chr9:116163302-116164052	GM15510	blood:	n/a	n/a
9	TAF1	chr9:116163335-116163689	GM12878	blood:	n/a	n/a
10	STAT1	chr9:116163362-116163944	GM12878	blood:	n/a	chr9:116163429-116163441
11	POU2F2	chr9:116163281-116163983	GM12878	blood:	n/a	n/a
12	RAD21	chr9:116163438-116164161	MCF-7	breast:	n/a	chr9:116163787-116163801 chr9:116163786-116163805
13	TAF1	chr9:116163197-116164057	ECC-1	luminal epithelium:	n/a	n/a
14	NRF1	chr9:116163326-116164098	SK-N-SH	brain:	n/a	chr9:116163757-116163768 chr9:116163678-116163687 chr9:116163754-116163768
15	NR2F2	chr9:116163122-116163962	K562	blood:	n/a	n/a
16	POLR2A	chr9:116163352-116163956	IMR90	lung:	n/a	n/a
17	POLR2A	chr9:116163309-116163655	A549	lung:	n/a	n/a
18	CEBPD	chr9:116163316-116163783	K562	blood:	n/a	n/a
19	CTCF	chr9:116163613-116163945	GM19238	blood:	n/a	chr9:116163790-116163800 chr9:116163787-116163808 chr9:116163788-116163801 chr9:116163786-116163802 chr9:116163785-116163803 chr9:116163788-116163801
20	POLR2A	chr9:116163298-116164049	GM18505	blood:	n/a	n/a
21	CTCF	chr9:116163458-116164054	K562	blood:	n/a	chr9:116163790-116163800 chr9:116163787-116163808 chr9:116163788-116163801 chr9:116163786-116163802 chr9:116163785-116163803 chr9:116163788-116163801
22	MYC	chr9:116163562-116163908	MCF10A-Er-Src	breast:	n/a	chr9:116163567-116163577 chr9:116163677-116163687
23	NFYA	chr9:116163308-116163970	Hela-S3	cervix:	n/a	n/a
24	POLR2A	chr9:116163296-116164066	Raji	blood:	n/a	n/a
25	PAX5	chr9:116163175-116163874	GM12892	blood:	n/a	n/a
26	POLR2A	chr9:116163316-116164045	NB4	blood:	n/a	n/a
27	TEAD4	chr9:116163617-116164065	H1-hESC	embryonic stem cell:	n/a	n/a
28	RAD21	chr9:116163277-116164151	HCT-116	colon:	n/a	chr9:116163787-116163801 chr9:116163786-116163805
29	GABPA	chr9:116163193-116164010	K562	blood:	n/a	chr9:116163678-116163687 chr9:116163754-116163768
30	CTCF	chr9:116163607-116164011	H1-hESC	embryonic stem cell:	n/a	chr9:116163790-116163800 chr9:116163787-116163808 chr9:116163788-116163801 chr9:116163786-116163802 chr9:116163785-116163803 chr9:116163788-116163801
31	EGR1	chr9:116163458-116163856	GM12878	blood:	n/a	chr9:116163625-116163639 chr9:116163680-116163690 chr9:116163604-116163619 chr9:116163678-116163692 chr9:116163676-116163690 chr9:116163605-116163618 chr9:116163605-116163618 chr9:116163602-116163616 chr9:116163566-116163579 chr9:116163606-116163616 chr9:116163679-116163692 chr9:116163477-116163490 chr9:116163677-116163687
32	ZNF143	chr9:116163352-116163958	Hela-S3	cervix:	n/a	chr9:116163477-116163487 chr9:116163464-116163483 chr9:116163794-116163804
33	CTCF	chr9:116163638-116163949	GM12878	blood:	n/a	chr9:116163790-116163800 chr9:116163787-116163808 chr9:116163788-116163801 chr9:116163786-116163802 chr9:116163785-116163803 chr9:116163788-116163801
34	POLR2A	chr9:116163283-116164020	K562	blood:	n/a	n/a
35	ELF1	chr9:116163233-116163986	GM12878	blood:	n/a	chr9:116163581-116163592 chr9:116163747-116163759 chr9:116163582-116163591 chr9:116163579-116163592
36	POLR2A	chr9:116163269-116163672	U87	brain:	n/a	n/a
37	ZNF143	chr9:116163401-116164027	GM12878	blood:	n/a	chr9:116163477-116163487 chr9:116163464-116163483 chr9:116163794-116163804
38	SIN3AK20	chr9:116163219-116163668	K562	blood:	n/a	n/a
39	ELF1	chr9:116163049-116164159	MCF-7	breast:	n/a	chr9:116163581-116163592 chr9:116163747-116163759 chr9:116163582-116163591 chr9:116163579-116163592
40	SP1	chr9:116163368-116163985	GM12878	blood:	n/a	chr9:116163677-116163687 chr9:116163626-116163636 chr9:116163625-116163637 chr9:116163676-116163687 chr9:116163676-116163688 chr9:116163677-116163686 chr9:116163678-116163687 chr9:116163676-116163688 chr9:116163677-116163691 chr9:116163428-116163437 chr9:116163626-116163636 chr9:116163677-116163687 chr9:116163625-116163637
41	GABPA	chr9:116163132-116163920	SK-N-SH	brain:	n/a	chr9:116163678-116163687 chr9:116163754-116163768
42	POLR2A	chr9:116163171-116164208	PBDE	blood:	n/a	n/a
43	POLR2A	chr9:116163319-116164113	MCF10A-Er-Src	breast:	n/a	n/a
44	RCOR1	chr9:116163248-116164064	Hela-S3	cervix:	n/a	n/a
45	SMC3	chr9:116163394-116164009	K562	blood:	n/a	chr9:116163787-116163801
46	SP1	chr9:116163282-116164054	H1-hESC	embryonic stem cell:	n/a	chr9:116163677-116163687 chr9:116163626-116163636 chr9:116163625-116163637 chr9:116163676-116163687 chr9:116163676-116163688 chr9:116163677-116163686 chr9:116163678-116163687 chr9:116163676-116163688 chr9:116163677-116163691 chr9:116163428-116163437 chr9:116163626-116163636 chr9:116163677-116163687 chr9:116163625-116163637
47	POLR2A	chr9:116163187-116163959	K562	blood:	n/a	n/a
48	POLR2A	chr9:116163243-116164010	ECC-1	luminal epithelium:	n/a	n/a
49	ELK1	chr9:116163348-116164185	K562	blood:	n/a	n/a
50	SIN3AK20	chr9:116163244-116163843	SK-N-SH	brain:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr9:116156284..116160950-chr9:116161266..116165857,7	MCF-7	breast:
2	chr9:116036323..116039598-chr9:116161482..116165034,3	MCF-7	breast:
3	chr9:116137664..116140470-chr9:116160302..116166802,9	MCF-7	breast:
4	chr9:116148030..116156107-chr9:116161914..116166950,9	MCF-7	breast:
5	chr9:116111778..116112420-chr9:116163200..116164122,2	MCF-7	breast:
6	chr9:116040629..116042415-chr9:116163599..116165929,2	MCF-7	breast:
7	chr9:116063542..116066515-chr9:116162468..116165263,2	K562	blood:
8	chr9:116162231..116166322-chr9:116170436..116174778,10	MCF-7	breast:
9	chr9:116109902..116113383-chr9:116162345..116166968,8	MCF-7	breast:
10	chr9:116138257..116141960-chr9:116162197..116164966,3	K562	blood:
11	chr9:116109912..116111859-chr9:116161206..116163943,2	K562	blood:
12	chr9:116139132..116139813-chr9:116162815..116163745,2	MCF-7	breast:
13	chr9:116036224..116039468-chr9:116162090..116165920,4	MCF-7	breast:
14	chr6:30709801..30712369-chr9:116163469..116165342,2	MCF-7	breast:
15	chr9:116129674..116142040-chr9:116159218..116175468,34	MCF-7	breast:

Variant related genes	Relation type
ALAD	TF binding region
ENSG00000119411	Chromatin interaction
ENSG00000136875	Chromatin interaction
ENSG00000148218	Chromatin interaction
ENSG00000148229	Chromatin interaction
ENSG00000137331	Chromatin interaction
ENSG00000165188	Chromatin interaction
ENSG00000176386	Chromatin interaction
ENSG00000119431	Chromatin interaction
ENSG00000272273	Chromatin interaction
ENSG00000137312	Chromatin interaction
ENSG00000157653	Chromatin interaction

Extended variants
information (count: 9 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:6)

rs_ID	r²[population]
rs10733605	0.84[CEU][hapmap]
rs818684	1.00[CHB][hapmap]
rs818686	1.00[CHB][hapmap]
rs818687	1.00[CHB][hapmap]
rs818689	1.00[CHB][hapmap]
rs818694	1.00[CEU][hapmap];0.84[AMR][1000 genomes];0.91[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv530949	chr9:115821128-116487796	Flanking Active TSS Enhancers Active TSS Weak transcription Genic enhancers Strong transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	71 gene(s)	inside rSNPs	diseases
2	nsv1042663	chr9:115920158-116167140	Weak transcription Active TSS Strong transcription Enhancers Flanking Active TSS Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	43 gene(s)	inside rSNPs	diseases
3	nsv893744	chr9:115934852-116170227	Active TSS Weak transcription Enhancers Strong transcription Flanking Active TSS Bivalent/Poised TSS 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	40 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs1771220	ALAD	Cis_1M	lymphoblastoid	RTeQTL

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:116161400-116164000	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
2	chr9:116162200-116163800	Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
3	chr9:116162200-116164000	Active TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
4	chr9:116162400-116163800	Active TSS	HUES6 Cell Line	embryonic stem cell
5	chr9:116162400-116163800	Active TSS	Fetal Stomach	stomach
6	chr9:116162400-116164000	Active TSS	Primary T cells from cord blood	blood
7	chr9:116162600-116163800	Active TSS	H9 Cell Line	embryonic stem cell
8	chr9:116162600-116163800	Active TSS	HUES48 Cell Line	embryonic stem cell
9	chr9:116162600-116163800	Active TSS	Foreskin Melanocyte Primary Cells skin03	Skin
10	chr9:116162600-116163800	Active TSS	Gastric	stomach
11	chr9:116162600-116163800	Active TSS	A549	lung
12	chr9:116162600-116163800	Active TSS	NHLF	lung
13	chr9:116162600-116163800	Active TSS	Osteobl	bone
14	chr9:116162600-116164000	Active TSS	HUES64 Cell Line	embryonic stem cell
15	chr9:116162600-116164000	Active TSS	Brain Angular Gyrus	brain
16	chr9:116162600-116164000	Active TSS	Fetal Brain Female	brain
17	chr9:116162600-116164200	Active TSS	iPS-20b Cell Line	embryonic stem cell
18	chr9:116162600-116164400	Active TSS	Pancreatic Islets	Pancreatic Islet
19	chr9:116162800-116163800	Active TSS	H9 Derived Neuron Cultured Cells	ES cell derived
20	chr9:116162800-116163800	Active TSS	ES-UCSF4 Cell Line	embryonic stem cell
21	chr9:116162800-116163800	Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
22	chr9:116162800-116163800	Active TSS	Primary mononuclear cells fromperipheralblood	Blood
23	chr9:116162800-116163800	Active TSS	Liver	Liver
24	chr9:116162800-116163800	Active TSS	Brain Cingulate Gyrus	brain
25	chr9:116162800-116163800	Active TSS	Brain Inferior Temporal Lobe	brain
26	chr9:116162800-116163800	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
27	chr9:116162800-116163800	Active TSS	Colon Smooth Muscle	Colon
28	chr9:116162800-116163800	Active TSS	Fetal Intestine Small	intestine
29	chr9:116162800-116163800	Active TSS	Fetal Lung	lung
30	chr9:116162800-116163800	Active TSS	Rectal Mucosa Donor 29	rectum
31	chr9:116162800-116163800	Active TSS	GM12878-XiMat	blood
32	chr9:116162800-116163800	Active TSS	HSMM	muscle
33	chr9:116162800-116163800	Active TSS	HSMMtube	muscle
34	chr9:116162800-116164000	Active TSS	H1 Cell Line	embryonic stem cell
35	chr9:116162800-116164000	Active TSS	iPS DF 19.11 Cell Line	embryonic stem cell
36	chr9:116162800-116164000	Active TSS	Breast Myoepithelial Primary Cells	Breast
37	chr9:116162800-116164000	Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
38	chr9:116162800-116164000	Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
39	chr9:116162800-116164000	Active TSS	Brain Hippocampus Middle	brain
40	chr9:116162800-116164000	Active TSS	Duodenum Smooth Muscle	Duodenum
41	chr9:116162800-116164000	Active TSS	Left Ventricle	heart
42	chr9:116162800-116164000	Active TSS	HepG2	liver
43	chr9:116162800-116164000	Active TSS	HMEC	breast
44	chr9:116162800-116164000	Active TSS	NHDF-Ad	bronchial
45	chr9:116162800-116164200	Active TSS	Psoas Muscle	Psoas
46	chr9:116162800-116164400	Flanking Active TSS	Primary B cells from cord blood	blood
47	chr9:116162800-116164400	Active TSS	Esophagus	oesophagus
48	chr9:116163000-116163800	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
49	chr9:116163000-116163800	Active TSS	iPS-18 Cell Line	embryonic stem cell
50	chr9:116163000-116163800	Active TSS	iPS DF 6.9 Cell Line	embryonic stem cell

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