Variant report

Variant	rs12339889
Chromosome Location	chr9:6008989-6008990
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	NFIC	chr9:6008405-6009000	ECC-1	luminal epithelium:	n/a	n/a
2	IRF1	chr9:6008490-6009044	K562	blood:	n/a	chr9:6008518-6008532
3	MXI1	chr9:6006692-6008998	Hela-S3	cervix:	n/a	n/a
4	HCFC1	chr9:6006627-6009015	Hela-S3	cervix:	n/a	n/a
5	CTCF	chr9:6008804-6009005	K562	blood:	n/a	n/a
6	POLR2A	chr9:6007577-6009009	HUVEC	blood vessel:	n/a	n/a
7	NRF1	chr9:6007606-6009014	SK-N-SH	brain:	n/a	chr9:6008649-6008660 chr9:6008649-6008663 chr9:6008472-6008483 chr9:6008088-6008097 chr9:6008649-6008660 chr9:6007938-6007947 chr9:6008472-6008486 chr9:6008472-6008481 chr9:6008469-6008483 chr9:6008651-6008660
8	REST	chr9:6007012-6009114	H1-neurons	neurons:	n/a	chr9:6008408-6008418 chr9:6007110-6007123 chr9:6007039-6007052 chr9:6008083-6008093 chr9:6008164-6008174
9	MXI1	chr9:6005845-6009194	SK-N-SH	brain:	n/a	n/a
10	POLR2A	chr9:6008552-6009021	PBDE	blood:	n/a	n/a
11	NRF1	chr9:6008305-6009070	K562	blood:	n/a	chr9:6008649-6008660 chr9:6008649-6008663 chr9:6008472-6008483 chr9:6008649-6008660 chr9:6008472-6008486 chr9:6008472-6008481 chr9:6008469-6008483 chr9:6008651-6008660
12	PML	chr9:6006689-6009001	GM12878	blood:	n/a	n/a
13	POLR2A	chr9:6008191-6009126	GM12891	blood:	n/a	n/a
14	POLR2A	chr9:6007531-6009098	SK-N-MC	brain:	n/a	n/a
15	POLR2A	chr9:6008299-6008990	U87	brain:	n/a	n/a
16	POLR2A	chr9:6008168-6008990	U87	brain:	n/a	n/a
17	POLR2A	chr9:6007740-6009313	MCF10A-Er-Src	breast:	n/a	n/a
18	TBP	chr9:6008453-6009031	Hela-S3	cervix:	n/a	n/a
19	CREB1	chr9:6007788-6009004	GM12878	blood:	n/a	n/a
20	TBL1XR1	chr9:6008402-6009000	K562	blood:	n/a	n/a
21	POLR2A	chr9:6008201-6010366	K562	blood:	n/a	n/a
22	POLR2A	chr9:6006886-6009191	Hela-S3	cervix:	n/a	n/a
23	POLR2A	chr9:6006920-6009265	H1-hESC	embryonic stem cell:	n/a	n/a
24	TAF1	chr9:6008288-6009067	ECC-1	luminal epithelium:	n/a	n/a
25	MAX	chr9:6006726-6009282	NB4	blood:	n/a	chr9:6008187-6008197 chr9:6007888-6007898 chr9:6007990-6008000 chr9:6008504-6008514
26	TBP	chr9:6008505-6009327	GM12878	blood:	n/a	n/a
27	POLR2A	chr9:6007674-6009180	MCF10A-Er-Src	breast:	n/a	n/a
28	POLR2A	chr9:6006943-6009292	HepG2	liver:	n/a	n/a
29	POLR2A	chr9:6007909-6009104	PFSK-1	brain:	n/a	n/a
30	POLR2A	chr9:6008343-6008994	GM12892	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr9:5895944..5898513-chr9:6007926..6009577,2	K562	blood:
2	chr9:6006778..6010531-chr9:6011866..6018012,11	MCF-7	breast:
3	chr9:5832476..5834522-chr9:6008226..6010221,2	MCF-7	breast:

Variant related genes	Relation type
KIAA2026	TF binding region
ENSG00000099219	Chromatin interaction
ENSG00000137040	Chromatin interaction
ENSG00000120215	Chromatin interaction

Extended variants
information (count: 68 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:62)

rs_ID	r²[population]
rs10116214	0.95[AFR][1000 genomes];0.83[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10124484	1.00[CHB][hapmap]
rs10125832	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10975350	1.00[EUR][1000 genomes]
rs10975351	1.00[EUR][1000 genomes]
rs10975362	1.00[EUR][1000 genomes]
rs10975363	1.00[EUR][1000 genomes]
rs10975364	1.00[EUR][1000 genomes]
rs10975372	0.85[AFR][1000 genomes];0.80[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs10975377	0.84[AFR][1000 genomes];0.80[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs11506678	1.00[EUR][1000 genomes]
rs11793956	0.91[AMR][1000 genomes]
rs12337300	1.00[EUR][1000 genomes]
rs12337445	1.00[EUR][1000 genomes]
rs12337790	1.00[CHB][hapmap];1.00[MEX][hapmap];0.90[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs12339713	0.82[AFR][1000 genomes];0.80[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs12339886	0.84[AFR][1000 genomes];0.80[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs12340153	1.00[EUR][1000 genomes]
rs12340531	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12341021	1.00[CHB][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12342166	1.00[EUR][1000 genomes]
rs12342282	0.85[CHD][hapmap];1.00[MEX][hapmap];0.82[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs12343325	1.00[EUR][1000 genomes]
rs12345849	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12351533	1.00[EUR][1000 genomes]
rs12352918	0.93[AFR][1000 genomes];0.83[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs1260130	1.00[MEX][hapmap]
rs1330124	1.00[CHB][hapmap]
rs1411949	1.00[EUR][1000 genomes]
rs1776008	1.00[MEX][hapmap]
rs1993912	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[MEX][hapmap];0.91[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs2233177	0.85[CHD][hapmap]
rs2233178	0.85[CHD][hapmap]
rs28431078	1.00[EUR][1000 genomes]
rs28706504	1.00[EUR][1000 genomes]
rs380568	1.00[CHB][hapmap]
rs386775	1.00[EUR][1000 genomes]
rs57154492	0.90[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs58291302	0.82[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs60037728	0.90[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7022080	1.00[EUR][1000 genomes]
rs7029847	0.80[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73383109	0.81[AFR][1000 genomes];0.80[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73383113	0.84[AFR][1000 genomes];0.80[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73383114	0.84[AFR][1000 genomes];0.80[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73383144	0.80[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73385128	0.82[AFR][1000 genomes];0.80[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73387085	0.83[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs73389036	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73389044	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73397307	1.00[EUR][1000 genomes]
rs73397376	1.00[EUR][1000 genomes]
rs73399307	1.00[EUR][1000 genomes]
rs73639554	1.00[EUR][1000 genomes]
rs73639568	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7853706	0.91[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs7854980	0.84[AFR][1000 genomes];0.80[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7858084	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7858846	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7859471	1.00[CHB][hapmap]
rs7875607	0.84[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9299025	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv948847	chr9:5712626-6417677	Strong transcription Enhancers Weak transcription Flanking Active TSS Active TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	39 gene(s)	inside rSNPs	diseases
2	nsv1031086	chr9:5806949-6630686	Strong transcription Enhancers Weak transcription Active TSS Flanking Active TSS Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	42 gene(s)	inside rSNPs	diseases
3	nsv539967	chr9:5806949-6630686	Flanking Active TSS Enhancers Strong transcription Weak transcription Genic enhancers Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	42 gene(s)	inside rSNPs	diseases
4	nsv892155	chr9:5825768-6044937	Weak transcription Genic enhancers Enhancers Strong transcription Flanking Active TSS Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	16 gene(s)	inside rSNPs	diseases
5	nsv892156	chr9:5892375-6011757	Weak transcription Genic enhancers Strong transcription Active TSS Enhancers Flanking Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	8 gene(s)	inside rSNPs	diseases
6	nsv1015450	chr9:5915640-6114652	Enhancers Strong transcription Active TSS Weak transcription Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	11 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:124 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:6005600-6009200	Active TSS	HUES6 Cell Line	embryonic stem cell
2	chr9:6005800-6009000	Active TSS	Ovary	ovary
3	chr9:6006000-6009000	Active TSS	Right Ventricle	heart
4	chr9:6006000-6009200	Active TSS	Psoas Muscle	Psoas
5	chr9:6006000-6009200	Active TSS	Right Atrium	heart
6	chr9:6006200-6009000	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
7	chr9:6006200-6009000	Active TSS	IMR90 fetal lung fibroblasts Cell Line	lung
8	chr9:6006200-6009200	Active TSS	ES-I3 Cell Line	embryonic stem cell
9	chr9:6006200-6009200	Active TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
10	chr9:6006200-6009200	Active TSS	HUES48 Cell Line	embryonic stem cell
11	chr9:6006200-6009200	Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
12	chr9:6006200-6009200	Active TSS	Fetal Thymus	thymus
13	chr9:6006200-6009400	Active TSS	HUES64 Cell Line	embryonic stem cell
14	chr9:6006200-6009400	Active TSS	K562	blood
15	chr9:6006400-6009000	Active TSS	Breast Myoepithelial Primary Cells	Breast
16	chr9:6006400-6009000	Active TSS	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
17	chr9:6006400-6009000	Active TSS	Foreskin Melanocyte Primary Cells skin03	Skin
18	chr9:6006400-6009000	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
19	chr9:6006400-6009400	Active TSS	HSMMtube	muscle
20	chr9:6006600-6009000	Active TSS	iPS-15b Cell Line	embryonic stem cell
21	chr9:6006600-6009000	Active TSS	iPS-20b Cell Line	embryonic stem cell
22	chr9:6006600-6009000	Active TSS	Brain Cingulate Gyrus	brain
23	chr9:6006600-6009000	Active TSS	Brain Hippocampus Middle	brain
24	chr9:6006600-6009200	Active TSS	H1 Cell Line	embryonic stem cell
25	chr9:6006600-6009200	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
26	chr9:6006600-6009200	Active TSS	Brain Germinal Matrix	brain
27	chr9:6006600-6009200	Active TSS	Rectal Smooth Muscle	rectum
28	chr9:6006600-6009200	Active TSS	Thymus	Thymus
29	chr9:6006800-6009000	Active TSS	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
30	chr9:6006800-6009000	Active TSS	iPS-18 Cell Line	embryonic stem cell
31	chr9:6006800-6009000	Active TSS	Aorta	Aorta
32	chr9:6006800-6009000	Active TSS	Brain Anterior Caudate	brain
33	chr9:6006800-6009000	Active TSS	Colon Smooth Muscle	Colon
34	chr9:6006800-6009000	Active TSS	Fetal Kidney	kidney
35	chr9:6006800-6009000	Active TSS	Fetal Muscle Trunk	muscle
36	chr9:6006800-6009000	Active TSS	Fetal Stomach	stomach
37	chr9:6006800-6009000	Active TSS	Placenta Amnion	Placenta Amnion
38	chr9:6006800-6009000	Active TSS	NHEK	skin
39	chr9:6006800-6009200	Active TSS	NHLF	lung
40	chr9:6007000-6009000	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
41	chr9:6007000-6009000	Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
42	chr9:6007000-6009000	Active TSS	Brain Inferior Temporal Lobe	brain
43	chr9:6007000-6009000	Active TSS	Fetal Intestine Small	intestine
44	chr9:6007200-6009000	Active TSS	Placenta	Placenta
45	chr9:6007400-6009000	Active TSS	Fetal Muscle Leg	muscle
46	chr9:6007800-6009000	Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
47	chr9:6007800-6009000	Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
48	chr9:6007800-6009000	Active TSS	HepG2	liver
49	chr9:6008000-6014800	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
50	chr9:6008400-6013400	Weak transcription	Gastric	stomach

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