Variant report

Variant	rs7049095
Chromosome Location	chr9:12774691-12774692
allele	A/T
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	chr9:12774654-12777141	A549	lung:	n/a	chr9:12776538-12776548
2	MAX	chr9:12774649-12777128	A549	lung:	n/a	n/a
3	ZNF143	chr9:12774559-12775017	K562	blood:	n/a	n/a
4	EP300	chr9:12774649-12775293	A549	lung:	n/a	n/a
5	MAFK	chr9:12774688-12775349	Hela-S3	cervix:	n/a	n/a
6	TEAD4	chr9:12774635-12775203	A549	lung:	n/a	n/a
7	YY1	chr9:12774682-12775557	SK-N-SH_RA	brain:	n/a	n/a
8	SP1	chr9:12774675-12775287	A549	lung:	n/a	n/a
9	TBP	chr9:12774671-12775459	Hela-S3	cervix:	n/a	n/a
10	REST	chr9:12774565-12776484	H1-neurons	neurons:	n/a	n/a
11	CTCF	chr9:12774571-12777307	A549	lung:	n/a	chr9:12774974-12774987 chr9:12776466-12776482 chr9:12776170-12776180
12	RAD21	chr9:12774592-12777718	SK-N-SH	brain:	n/a	chr9:12775612-12775625 chr9:12776040-12776054 chr9:12776188-12776201 chr9:12776038-12776052 chr9:12776171-12776181
13	SP1	chr9:12774669-12775297	A549	lung:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr9:12770939..12774696-chr9:12774747..12779041,5	MCF-7	breast:
2	chr19:32895532..32897847-chr9:12774427..12776236,2	MCF-7	breast:
3	chr9:12774109..12791345-chr9:12812800..12822770,37	MCF-7	breast:
4	chr9:12773974..12784053-chr9:12813051..12820453,19	MCF-7	breast:

Variant related genes	Relation type
LURAP1L	TF binding region
ENSG00000153714	Chromatin interaction
ENSG00000178904	Chromatin interaction
ENSG00000269093	Chromatin interaction
ENSG00000267213	Chromatin interaction
ENSG00000235448	Chromatin interaction

Extended variants
information (count: 33 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:22)

rs_ID	r²[population]
rs10115741	0.81[ASN][1000 genomes]
rs1041175	0.91[ASN][1000 genomes]
rs10733246	0.82[ASN][1000 genomes]
rs10733247	0.87[ASN][1000 genomes]
rs10756408	0.97[ASN][1000 genomes]
rs10809838	0.91[ASN][1000 genomes]
rs10960780	0.89[ASN][1000 genomes]
rs10960786	0.93[ASN][1000 genomes]
rs1326781	0.82[ASN][1000 genomes]
rs1326794	0.91[ASN][1000 genomes]
rs1326796	0.86[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1409631	1.00[ASN][1000 genomes]
rs1409633	0.93[ASN][1000 genomes]
rs1887176	1.00[ASN][1000 genomes]
rs1887177	0.88[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2209273	0.97[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs2209274	0.93[ASN][1000 genomes]
rs2382362	0.82[ASN][1000 genomes]
rs4996096	0.87[ASN][1000 genomes]
rs7025099	0.95[ASN][1000 genomes]
rs7037828	0.96[ASN][1000 genomes]
rs9696885	0.92[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:11 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv2759671	chr9:12235048-12784092	Flanking Active TSS Flanking Bivalent TSS/Enh Enhancers Active TSS Strong transcription Weak transcription Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer Genic enhancers Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases
2	nsv1034393	chr9:12278703-12798236	Enhancers Weak transcription Bivalent/Poised TSS Flanking Active TSS Flanking Bivalent TSS/Enh Active TSS Bivalent Enhancer Strong transcription Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases
3	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
4	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
5	nsv1029415	chr9:12424340-12794623	Bivalent/Poised TSS Enhancers Flanking Active TSS Weak transcription Transcr. at gene 5' and 3' Active TSS ZNF genes & repeats Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
6	nsv540064	chr9:12424340-12794623	Transcr. at gene 5' and 3' Enhancers Weak transcription Flanking Active TSS Active TSS Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats Strong transcription Genic enhancers Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
7	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
8	esv2758182	chr9:12621991-12784092	Enhancers Weak transcription Flanking Active TSS Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3' Strong transcription Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
9	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
10	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
11	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

No data

Chromatin state (count:41 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:12761600-12774800	Weak transcription	NHLF	lung
2	chr9:12766800-12774800	Weak transcription	Rectal Mucosa Donor 29	rectum
3	chr9:12766800-12774800	Weak transcription	HSMMtube	muscle
4	chr9:12770400-12774800	Weak transcription	Fetal Intestine Small	intestine
5	chr9:12770600-12774800	Weak transcription	Rectal Mucosa Donor 31	rectum
6	chr9:12771400-12774800	Weak transcription	Fetal Intestine Large	intestine
7	chr9:12772200-12774800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
8	chr9:12772400-12774800	Weak transcription	HUVEC	blood vessel
9	chr9:12772600-12774800	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
10	chr9:12772800-12774800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
11	chr9:12772800-12774800	Weak transcription	Hela-S3	cervix
12	chr9:12772800-12774800	Weak transcription	HSMM	muscle
13	chr9:12773000-12774800	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
14	chr9:12773000-12774800	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
15	chr9:12773000-12774800	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
16	chr9:12773000-12774800	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
17	chr9:12773000-12774800	Weak transcription	Adipose Nuclei	Adipose
18	chr9:12773200-12774800	Weak transcription	HMEC	breast
19	chr9:12773200-12774800	Weak transcription	NHEK	skin
20	chr9:12774000-12774800	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
21	chr9:12774200-12776600	Active TSS	Fetal Lung	lung
22	chr9:12774400-12775000	Weak transcription	Liver	Liver
23	chr9:12774600-12774800	Bivalent Enhancer	HUES64 Cell Line	embryonic stem cell
24	chr9:12774600-12774800	Flanking Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
25	chr9:12774600-12774800	Flanking Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
26	chr9:12774600-12774800	Flanking Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
27	chr9:12774600-12774800	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
28	chr9:12774600-12774800	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
29	chr9:12774600-12774800	Enhancers	Muscle Satellite Cultured Cells	--
30	chr9:12774600-12774800	Enhancers	Colon Smooth Muscle	Colon
31	chr9:12774600-12774800	Flanking Active TSS	A549	lung
32	chr9:12774600-12774800	Enhancers	HepG2	liver
33	chr9:12774600-12774800	Enhancers	Osteobl	bone
34	chr9:12774600-12775000	Flanking Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
35	chr9:12774600-12775200	Flanking Active TSS	H9 Derived Neuron Cultured Cells	ES cell derived
36	chr9:12774600-12775400	Active TSS	Duodenum Smooth Muscle	Duodenum
37	chr9:12774600-12776600	Active TSS	Brain Cingulate Gyrus	brain
38	chr9:12774600-12776600	Active TSS	Fetal Kidney	kidney
39	chr9:12774600-12776600	Active TSS	NH-A	brain
40	chr9:12774600-12776800	Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
41	chr9:12774600-12778000	Active TSS	NHDF-Ad	bronchial

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