Variant report

Variant	rs12003440
Chromosome Location	chr9:95732832-95732833
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	TCF12	chr9:95732719-95732986	H1-hESC	embryonic stem cell:	n/a	n/a
2	FOS	chr9:95732661-95732935	MCF10A-Er-Src	breast:	n/a	n/a
3	NFYB	chr9:95732648-95732980	Hela-S3	cervix:	n/a	chr9:95732790-95732805
4	SP2	chr9:95732582-95732953	H1-hESC	embryonic stem cell:	n/a	n/a
5	MAX	chr9:95732598-95733163	H1-hESC	embryonic stem cell:	n/a	chr9:95733048-95733058 chr9:95733062-95733072
6	FOS	chr9:95732606-95732935	MCF10A-Er-Src	breast:	n/a	n/a
7	USF1	chr9:95732639-95733057	H1-hESC	embryonic stem cell:	n/a	n/a
8	NFYB	chr9:95732677-95733000	GM12878	blood:	n/a	chr9:95732790-95732805
9	FOXA1	chr9:95732522-95732976	T-47D	breast:	n/a	n/a
10	E2F6	chr9:95732446-95733339	H1-hESC	embryonic stem cell:	n/a	n/a
11	TEAD4	chr9:95732449-95733204	H1-hESC	embryonic stem cell:	n/a	n/a
12	SP1	chr9:95732467-95733178	H1-hESC	embryonic stem cell:	n/a	n/a
13	TEAD4	chr9:95732424-95733214	ECC-1	luminal epithelium:	n/a	n/a
14	MAX	chr9:95732805-95733154	NB4	blood:	n/a	chr9:95733048-95733058 chr9:95733062-95733072
15	FOXA1	chr9:95732453-95732970	T-47D	breast:	n/a	n/a
16	SP1	chr9:95732662-95733038	GM12878	blood:	n/a	n/a
17	TEAD4	chr9:95732457-95733216	H1-hESC	embryonic stem cell:	n/a	n/a
18	NFYB	chr9:95732636-95733000	K562	blood:	n/a	chr9:95732790-95732805
19	FOS	chr9:95732663-95732863	MCF10A-Er-Src	breast:	n/a	n/a
20	MAX	chr9:95732690-95733204	H1-hESC	embryonic stem cell:	n/a	chr9:95733048-95733058 chr9:95733062-95733072
21	SP1	chr9:95732617-95732909	GM12878	blood:	n/a	n/a
22	USF1	chr9:95732719-95733160	ECC-1	luminal epithelium:	n/a	n/a
23	GTF2F1	chr9:95732692-95732884	H1-hESC	embryonic stem cell:	n/a	n/a
24	USF1	chr9:95732525-95733211	ECC-1	luminal epithelium:	n/a	n/a
25	MAX	chr9:95732399-95733170	ECC-1	luminal epithelium:	n/a	chr9:95733048-95733058 chr9:95733062-95733072
26	MAX	chr9:95732473-95733264	MCF-7	breast:	n/a	chr9:95733048-95733058 chr9:95733062-95733072
27	NANOG	chr9:95732626-95733000	H1-hESC	embryonic stem cell:	n/a	n/a
28	TEAD4	chr9:95732575-95733166	ECC-1	luminal epithelium:	n/a	n/a
29	USF1	chr9:95732709-95733127	H1-hESC	embryonic stem cell:	n/a	n/a
30	EP300	chr9:95732407-95732884	T-47D	breast:	n/a	n/a
31	TCF12	chr9:95732693-95733010	H1-hESC	embryonic stem cell:	n/a	n/a
32	POLR2A	chr9:95732770-95732961	H1-hESC	embryonic stem cell:	n/a	n/a
33	POLR2A	chr9:95732472-95732973	H1-hESC	embryonic stem cell:	n/a	n/a
34	MAX	chr9:95732672-95733154	ECC-1	luminal epithelium:	n/a	chr9:95733048-95733058 chr9:95733062-95733072
35	CHD2	chr9:95732517-95733089	H1-hESC	embryonic stem cell:	n/a	n/a
36	JUND	chr9:95732384-95733367	H1-hESC	embryonic stem cell:	n/a	chr9:95733315-95733324
37	USF2	chr9:95732767-95733098	H1-hESC	embryonic stem cell:	n/a	n/a
38	TBP	chr9:95732557-95733214	H1-hESC	embryonic stem cell:	n/a	n/a
39	ESR1	chr9:95732281-95732834	T-47D	breast:	n/a	n/a
40	NFYA	chr9:95732664-95732928	K562	blood:	n/a	chr9:95732784-95732802
41	NFYA	chr9:95732685-95732914	Hela-S3	cervix:	n/a	chr9:95732784-95732802
42	MAX	chr9:95732432-95733218	H1-hESC	embryonic stem cell:	n/a	chr9:95733048-95733058 chr9:95733062-95733072
43	SP1	chr9:95732486-95733130	H1-hESC	embryonic stem cell:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr9:95731583..95735118-chr9:95737800..95740218,3	K562	blood:
2	chr9:95731272..95732964-chr9:95895470..95897455,2	MCF-7	breast:
3	chr9:95725342..95729207-chr9:95729946..95733070,3	K562	blood:
4	chr9:95617721..95619432-chr9:95731199..95733428,2	MCF-7	breast:
5	chr9:95637654..95640681-chr9:95731798..95734856,3	MCF-7	breast:

Variant related genes	Relation type
FGD3	TF binding region
ENSG00000127084	Chromatin interaction
ENSG00000131669	Chromatin interaction
ENSG00000127081	Chromatin interaction

Extended variants
information (count: 38 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:37)

rs_ID	r²[population]
rs10123843	0.81[CHB][hapmap];0.84[JPT][hapmap]
rs1022833	0.81[CHB][hapmap];0.84[JPT][hapmap]
rs10739933	0.81[CHB][hapmap];0.84[JPT][hapmap]
rs10739934	0.81[CHB][hapmap];0.84[JPT][hapmap]
rs10821030	0.81[CHB][hapmap];0.84[JPT][hapmap]
rs10821035	0.81[CHB][hapmap];0.84[JPT][hapmap]
rs10992489	0.80[CHB][hapmap];0.82[JPT][hapmap]
rs12003885	0.83[AFR][1000 genomes];0.90[ASN][1000 genomes]
rs12336022	0.81[CHB][hapmap];0.84[JPT][hapmap]
rs12337654	0.84[JPT][hapmap]
rs13284600	0.84[ASN][1000 genomes]
rs13293147	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.89[AFR][1000 genomes];0.97[ASN][1000 genomes]
rs13294147	0.91[CHB][hapmap];1.00[JPT][hapmap];0.84[ASN][1000 genomes]
rs17886128	0.90[AFR][1000 genomes];0.97[ASN][1000 genomes]
rs2296060	0.81[CHB][hapmap];0.84[JPT][hapmap]
rs34405247	0.87[AMR][1000 genomes];0.92[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs34739544	0.92[AFR][1000 genomes];0.93[ASN][1000 genomes]
rs34953814	0.85[AFR][1000 genomes];0.90[ASN][1000 genomes]
rs35449185	0.84[ASN][1000 genomes]
rs35721889	0.89[AFR][1000 genomes];0.97[ASN][1000 genomes]
rs4074836	0.91[AFR][1000 genomes];0.90[ASN][1000 genomes]
rs4078292	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.92[AFR][1000 genomes];0.95[ASN][1000 genomes]
rs4260949	0.91[AFR][1000 genomes];0.97[ASN][1000 genomes]
rs4744150	0.80[CHB][hapmap];0.82[JPT][hapmap]
rs4744151	0.80[CHB][hapmap];0.82[JPT][hapmap]
rs4744160	0.97[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs58264693	0.91[AFR][1000 genomes];0.97[ASN][1000 genomes]
rs6479434	0.80[CHB][hapmap];0.82[JPT][hapmap]
rs7024752	0.84[ASN][1000 genomes]
rs7032277	0.81[CHB][hapmap];0.84[JPT][hapmap]
rs7035881	1.00[CEU][hapmap];0.90[CHB][hapmap];1.00[JPT][hapmap];0.94[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7039812	0.81[CHB][hapmap];0.84[JPT][hapmap]
rs7040645	0.81[CHB][hapmap];0.84[JPT][hapmap]
rs7043469	1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.91[AFR][1000 genomes];0.97[ASN][1000 genomes]
rs7856681	0.87[ASN][1000 genomes]
rs7859461	0.91[AFR][1000 genomes];0.93[ASN][1000 genomes]
rs7873125	0.87[ASN][1000 genomes]

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

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv526296	chr9:95708192-96030392	Enhancers Bivalent/Poised TSS Weak transcription Active TSS Flanking Active TSS Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	30 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:88 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:95725600-95734000	Flanking Active TSS	Primary T helper cells fromperipheralblood	blood
2	chr9:95728000-95733800	Weak transcription	Right Atrium	heart
3	chr9:95728200-95739600	Weak transcription	Fetal Stomach	stomach
4	chr9:95728600-95733200	Genic enhancers	Spleen	Spleen
5	chr9:95728800-95733600	Weak transcription	Brain Hippocampus Middle	brain
6	chr9:95728800-95733800	Genic enhancers	Primary B cells from peripheral blood	blood
7	chr9:95728800-95739400	Weak transcription	Gastric	stomach
8	chr9:95728800-95739600	Weak transcription	Rectal Mucosa Donor 31	rectum
9	chr9:95728800-95740600	Weak transcription	Small Intestine	intestine
10	chr9:95729000-95733800	Genic enhancers	Primary Natural Killer cells fromperipheralblood	blood
11	chr9:95729000-95734000	Genic enhancers	Primary monocytes fromperipheralblood	blood
12	chr9:95729000-95735000	Weak transcription	Adipose Nuclei	Adipose
13	chr9:95729000-95739400	Weak transcription	Sigmoid Colon	Sigmoid Colon
14	chr9:95729000-95741400	Weak transcription	Right Ventricle	heart
15	chr9:95729200-95733800	Genic enhancers	Thymus	Thymus
16	chr9:95729200-95734000	Genic enhancers	Fetal Thymus	thymus
17	chr9:95729200-95739200	Weak transcription	Colonic Mucosa	Colon
18	chr9:95729400-95733800	Flanking Active TSS	Primary T helper cells PMA-I stimulated	--
19	chr9:95729600-95734200	Genic enhancers	Primary B cells from cord blood	blood
20	chr9:95730000-95733600	Flanking Active TSS	Primary T killer naive cells fromperipheralblood	blood
21	chr9:95730200-95733000	Genic enhancers	Monocytes-CD14+_RO01746	blood
22	chr9:95730400-95733800	Genic enhancers	Primary neutrophils fromperipheralblood	blood
23	chr9:95730600-95733400	Enhancers	Brain Germinal Matrix	brain
24	chr9:95730600-95733800	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
25	chr9:95731000-95733200	Flanking Active TSS	Primary T helper memory cells from peripheral blood 2	blood
26	chr9:95731000-95733200	Flanking Active TSS	Primary T helper 17 cells PMA-I stimulated	--
27	chr9:95731000-95734000	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
28	chr9:95731000-95734200	Enhancers	HUES6 Cell Line	embryonic stem cell
29	chr9:95731200-95733000	Enhancers	iPS-15b Cell Line	embryonic stem cell
30	chr9:95731200-95733000	Enhancers	iPS-20b Cell Line	embryonic stem cell
31	chr9:95731200-95733600	Enhancers	H9 Cell Line	embryonic stem cell
32	chr9:95731200-95733600	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
33	chr9:95731200-95733800	Enhancers	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
34	chr9:95731200-95733800	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
35	chr9:95731200-95733800	Enhancers	iPS DF 6.9 Cell Line	embryonic stem cell
36	chr9:95731200-95734000	Enhancers	H1 Cell Line	embryonic stem cell
37	chr9:95731200-95735000	Enhancers	ES-I3 Cell Line	embryonic stem cell
38	chr9:95731400-95733000	Transcr. at gene 5' and 3'	Primary T cells from cord blood	blood
39	chr9:95731400-95733200	Bivalent Enhancer	Fetal Muscle Trunk	muscle
40	chr9:95731400-95733400	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
41	chr9:95731400-95733600	Enhancers	Duodenum Mucosa	Duodenum
42	chr9:95731400-95733800	Enhancers	HUES48 Cell Line	embryonic stem cell
43	chr9:95731400-95733800	Enhancers	Cortex derived primary cultured neurospheres	brain
44	chr9:95731400-95734000	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
45	chr9:95731400-95734200	Enhancers	HUES64 Cell Line	embryonic stem cell
46	chr9:95731400-95735400	Enhancers	iPS-18 Cell Line	embryonic stem cell
47	chr9:95731600-95733600	Enhancers	HSMMtube	muscle
48	chr9:95731600-95733800	Transcr. at gene 5' and 3'	Primary T helper naive cells fromperipheralblood	blood
49	chr9:95731600-95736800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
50	chr9:95731800-95733000	Enhancers	Placenta	Placenta

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