Variant report

Variant	rs7859336
Chromosome Location	chr9:12814568-12814569
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	CTCF	chr9:12814500-12814650	HA-sp	spinal cord:	n/a	n/a
2	GABPA	chr9:12814258-12814836	A549	lung:	n/a	n/a
3	CTCF	chr9:12814540-12814690	HRPEpiC	eye:	n/a	n/a
4	POLR2A	chr9:12814366-12814762	HepG2	liver:	n/a	n/a
5	BHLHE40	chr9:12814481-12814829	K562	blood:	n/a	n/a
6	TCF7L2	chr9:12814100-12814914	Hela-S3	cervix:	n/a	chr9:12814593-12814602 chr9:12814594-12814603
7	STAT3	chr9:12813904-12814992	MCF10A-Er-Src	breast:	n/a	chr9:12814593-12814602 chr9:12814805-12814813 chr9:12814953-12814964
8	REST	chr9:12814448-12814695	SK-N-SH	brain:	n/a	n/a
9	MAX	chr9:12814392-12814879	MCF-7	breast:	n/a	chr9:12814672-12814682 chr9:12814420-12814429
10	MAX	chr9:12813977-12814950	HepG2	liver:	n/a	chr9:12814672-12814682 chr9:12814420-12814429
11	FOXA1	chr9:12813818-12814728	HepG2	liver:	n/a	chr9:12814104-12814119
12	EP300	chr9:12814215-12814769	T-47D	breast:	n/a	chr9:12814418-12814432 chr9:12814594-12814603 chr9:12814543-12814557 chr9:12814499-12814508
13	CTCF	chr9:12814460-12814610	HVMF	connective:	n/a	n/a
14	CEBPB	chr9:12814170-12814794	ECC-1	luminal epithelium:	n/a	chr9:12814579-12814590
15	FOSL1	chr9:12814052-12815023	HCT-116	colon:	n/a	chr9:12814448-12814460 chr9:12814593-12814603 chr9:12814594-12814603 chr9:12814593-12814602 chr9:12814501-12814510 chr9:12814597-12814605 chr9:12814594-12814601
16	MYC	chr9:12814480-12814730	NB4	blood:	n/a	chr9:12814672-12814682
17	CTCF	chr9:12814558-12814758	K562	blood:	n/a	n/a
18	TCF12	chr9:12814191-12814921	A549	lung:	n/a	n/a
19	EP300	chr9:12814080-12814834	HepG2	liver:	n/a	chr9:12814418-12814432 chr9:12814594-12814603 chr9:12814543-12814557 chr9:12814499-12814508
20	TBP	chr9:12814000-12814837	HepG2	liver:	n/a	n/a
21	SIN3AK20	chr9:12814437-12814863	A549	lung:	n/a	n/a
22	GATA3	chr9:12814118-12815056	SK-N-SH	brain:	n/a	chr9:12814878-12814885
23	NFYA	chr9:12814095-12814885	Hela-S3	cervix:	n/a	n/a
24	MYC	chr9:12814530-12814747	HepG2	liver:	n/a	chr9:12814672-12814682
25	MAFK	chr9:12813560-12814882	HepG2	liver:	n/a	chr9:12814594-12814604 chr9:12813705-12813720
26	NR3C1	chr9:12813945-12814840	A549	lung:	n/a	n/a
27	CTCF	chr9:12814540-12814690	WI-38	lung:	n/a	n/a
28	POLR2A	chr9:12814435-12814802	SK-N-SH	brain:	n/a	n/a
29	CTCF	chr9:12814520-12814670	SAEC	small airway:	n/a	n/a
30	JUND	chr9:12814247-12814870	MCF-7	breast:	n/a	chr9:12814448-12814460 chr9:12814593-12814603 chr9:12814594-12814603 chr9:12814593-12814602 chr9:12814501-12814510 chr9:12814597-12814605 chr9:12814594-12814601 chr9:12814592-12814603
31	EP300	chr9:12814076-12815084	SK-N-SH	brain:	n/a	chr9:12814418-12814432 chr9:12814594-12814603 chr9:12814543-12814557 chr9:12814499-12814508
32	FOSL2	chr9:12814229-12814873	MCF-7	breast:	n/a	chr9:12814448-12814460 chr9:12814593-12814603 chr9:12814594-12814603 chr9:12814593-12814602 chr9:12814501-12814510 chr9:12814597-12814605 chr9:12814594-12814601
33	GTF2F1	chr9:12814108-12815050	Hela-S3	cervix:	n/a	n/a
34	POLR2A	chr9:12814029-12816382	IMR90	lung:	n/a	n/a
35	TEAD4	chr9:12814080-12815060	SK-N-SH	brain:	n/a	n/a
36	ZKSCAN1	chr9:12814107-12814803	Hela-S3	cervix:	n/a	n/a
37	USF1	chr9:12814483-12814795	SK-N-SH_RA	brain:	n/a	chr9:12814668-12814679
38	BHLHE40	chr9:12814145-12814857	A549	lung:	n/a	n/a
39	MAX	chr9:12814428-12814899	MCF-7	breast:	n/a	chr9:12814672-12814682
40	STAT3	chr9:12813582-12815077	Hela-S3	cervix:	n/a	chr9:12814593-12814602 chr9:12814805-12814813 chr9:12814953-12814964
41	CTCF	chr9:12814540-12814690	HPAF	blood vessel:	n/a	n/a
42	USF1	chr9:12814532-12814763	HepG2	liver:	n/a	chr9:12814668-12814679
43	PBX3	chr9:12814188-12814772	A549	lung:	n/a	n/a
44	JUND	chr9:12814120-12814797	T-47D	breast:	n/a	chr9:12814448-12814460 chr9:12814593-12814603 chr9:12814594-12814603 chr9:12814593-12814602 chr9:12814501-12814510 chr9:12814597-12814605 chr9:12814594-12814601 chr9:12814592-12814603
45	USF1	chr9:12814411-12814874	ECC-1	luminal epithelium:	n/a	chr9:12814668-12814679
46	FOSL2	chr9:12814209-12814945	A549	lung:	n/a	chr9:12814448-12814460 chr9:12814593-12814603 chr9:12814594-12814603 chr9:12814593-12814602 chr9:12814501-12814510 chr9:12814597-12814605 chr9:12814594-12814601
47	CTCF	chr9:12814540-12814690	AoAF	blood vessel:	n/a	n/a
48	JUND	chr9:12813946-12815294	SK-N-SH	brain:	n/a	chr9:12814448-12814460 chr9:12814593-12814603 chr9:12814594-12814603 chr9:12814593-12814602 chr9:12814501-12814510 chr9:12814597-12814605 chr9:12814594-12814601 chr9:12814592-12814603
49	JUND	chr9:12813593-12814863	Hela-S3	cervix:	n/a	chr9:12814448-12814460 chr9:12814593-12814603 chr9:12814594-12814603 chr9:12814593-12814602 chr9:12814501-12814510 chr9:12814597-12814605 chr9:12814594-12814601 chr9:12814592-12814603
50	ELF1	chr9:12814406-12814798	A549	lung:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr9:12774109..12791345-chr9:12812800..12822770,37	MCF-7	breast:
2	chr9:12773974..12784053-chr9:12813051..12820453,19	MCF-7	breast:

Variant related genes	Relation type
ENSG00000235448	TF binding region
ENSG00000153714	Chromatin interaction

Extended variants
information (count: 26 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:19)

rs_ID	r²[population]
rs10122949	0.83[EUR][1000 genomes]
rs10960800	0.84[EUR][1000 genomes]
rs10960803	0.88[EUR][1000 genomes]
rs10960804	0.88[EUR][1000 genomes]
rs10960805	0.93[AFR][1000 genomes];0.95[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs10960806	1.00[JPT][hapmap];0.91[ASN][1000 genomes]
rs10960807	0.91[ASN][1000 genomes]
rs10960808	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs10960812	0.84[CHB][hapmap];1.00[JPT][hapmap];0.87[ASN][1000 genomes]
rs10960813	0.90[CEU][hapmap];0.90[CHB][hapmap];1.00[JPT][hapmap];0.80[AMR][1000 genomes];0.88[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs1318454	0.84[EUR][1000 genomes]
rs34919266	0.88[EUR][1000 genomes]
rs4397503	0.88[EUR][1000 genomes]
rs6474732	1.00[CEU][hapmap];0.94[CHB][hapmap];0.84[JPT][hapmap];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6474733	0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6474736	0.83[CHB][hapmap];1.00[JPT][hapmap];0.86[ASN][1000 genomes]
rs71507332	0.84[EUR][1000 genomes]
rs7846724	0.83[CHB][hapmap];1.00[JPT][hapmap];0.87[ASN][1000 genomes]
rs9298684	0.88[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:7 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv869288	chr9:12286919-12816766	Enhancers Bivalent Enhancer Weak transcription Flanking Active TSS Active TSS Strong transcription Flanking Bivalent TSS/Enh Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases
2	nsv498136	chr9:12387840-12984158	Genic enhancers Enhancers Active TSS Flanking Active TSS Weak transcription Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh Strong transcription Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	13 gene(s)	inside rSNPs	diseases
3	esv2422212	chr9:12448789-13127738	Enhancers Weak transcription Strong transcription Flanking Active TSS Active TSS Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	17 gene(s)	inside rSNPs	diseases
4	nsv1030835	chr9:12717405-12840928	Enhancers Active TSS Weak transcription Flanking Active TSS Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	10 gene(s)	inside rSNPs	diseases
5	nsv892573	chr9:12730636-12874703	Enhancers Weak transcription Active TSS ZNF genes & repeats Flanking Active TSS Strong transcription Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	10 gene(s)	inside rSNPs	diseases
6	nsv892574	chr9:12754969-12918226	Weak transcription Flanking Active TSS ZNF genes & repeats Enhancers Active TSS Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	10 gene(s)	inside rSNPs	diseases
7	nsv892575	chr9:12804243-12852462	Enhancers Weak transcription Active TSS Flanking Active TSS Genic enhancers ZNF genes & repeats Strong transcription Transcr. at gene 5' and 3'	TF binding region Chromatin interactive region lncRNA miRNA target site	4 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:67 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:12792000-12817200	Weak transcription	Sigmoid Colon	Sigmoid Colon
2	chr9:12808600-12818400	Weak transcription	Fetal Brain Male	brain
3	chr9:12809200-12817200	Weak transcription	Small Intestine	intestine
4	chr9:12809200-12821400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
5	chr9:12810400-12817600	Weak transcription	Gastric	stomach
6	chr9:12812200-12816200	Enhancers	Fetal Lung	lung
7	chr9:12812200-12816400	Weak transcription	Pancreas	Pancrea
8	chr9:12812800-12814800	Active TSS	HMEC	breast
9	chr9:12812800-12815000	Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
10	chr9:12813400-12815200	Flanking Active TSS	HUVEC	blood vessel
11	chr9:12813600-12814800	Enhancers	Brain Germinal Matrix	brain
12	chr9:12813600-12815200	Flanking Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
13	chr9:12813600-12816200	Enhancers	Fetal Adrenal Gland	Adrenal Gland
14	chr9:12813800-12814800	Enhancers	Brain Dorsolateral Prefrontal Cortex	brain
15	chr9:12813800-12815200	Enhancers	Cortex derived primary cultured neurospheres	brain
16	chr9:12813800-12815200	Enhancers	Fetal Stomach	stomach
17	chr9:12813800-12815600	Enhancers	Adipose Nuclei	Adipose
18	chr9:12814000-12814600	Flanking Active TSS	Foreskin Melanocyte Primary Cells skin03	Skin
19	chr9:12814000-12814600	Flanking Active TSS	Brain Inferior Temporal Lobe	brain
20	chr9:12814000-12814600	Active TSS	Psoas Muscle	Psoas
21	chr9:12814000-12814600	Flanking Active TSS	Rectal Mucosa Donor 31	rectum
22	chr9:12814000-12814600	Active TSS	HepG2	liver
23	chr9:12814000-12814800	Active TSS	IMR90 fetal lung fibroblasts Cell Line	lung
24	chr9:12814000-12814800	Flanking Active TSS	Rectal Mucosa Donor 29	rectum
25	chr9:12814000-12814800	Active TSS	Stomach Smooth Muscle	stomach
26	chr9:12814000-12814800	Active TSS	A549	lung
27	chr9:12814000-12815000	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
28	chr9:12814000-12815000	Active TSS	Aorta	Aorta
29	chr9:12814000-12815000	Enhancers	Fetal Heart	heart
30	chr9:12814000-12815000	Flanking Active TSS	Fetal Kidney	kidney
31	chr9:12814000-12815200	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
32	chr9:12814000-12815200	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
33	chr9:12814000-12815800	Enhancers	HSMM	muscle
34	chr9:12814200-12814600	Flanking Active TSS	Brain Hippocampus Middle	brain
35	chr9:12814200-12814600	Flanking Active TSS	Duodenum Mucosa	Duodenum
36	chr9:12814200-12814600	Flanking Active TSS	Fetal Intestine Small	intestine
37	chr9:12814200-12814600	Active TSS	Right Atrium	heart
38	chr9:12814200-12814600	Enhancers	Skeletal Muscle Female	skeletal muscle
39	chr9:12814200-12814600	Flanking Active TSS	Stomach Mucosa	stomach
40	chr9:12814200-12814800	Active TSS	Hela-S3	cervix
41	chr9:12814200-12815200	Active TSS	Pancreatic Islets	Pancreatic Islet
42	chr9:12814400-12814600	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
43	chr9:12814400-12814600	Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
44	chr9:12814400-12814600	Active TSS	Brain Angular Gyrus	brain
45	chr9:12814400-12814800	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
46	chr9:12814400-12814800	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
47	chr9:12814400-12814800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
48	chr9:12814400-12814800	Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
49	chr9:12814400-12814800	Active TSS	Muscle Satellite Cultured Cells	--
50	chr9:12814400-12814800	Active TSS	Brain Cingulate Gyrus	brain

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