Variant report

Variant	rs2007680
Chromosome Location	chr6:2451052-2451053
allele	A/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	chr6:2450920-2451070	HRE	kidney:	n/a	n/a
2	GATA2	chr6:2450714-2451068	SH-SY5Y	brain:	n/a	chr6:2450979-2450988
3	NFIC	chr6:2450788-2451194	SK-N-SH	brain:	n/a	chr6:2450999-2451016
4	CTCF	chr6:2450920-2451070	HEK293	kidney:	n/a	n/a
5	CTCF	chr6:2450980-2451130	BE2_C	brain:	n/a	n/a
6	NFIC	chr6:2450644-2451272	ECC-1	luminal epithelium:	n/a	chr6:2450999-2451016
7	RAD21	chr6:2450827-2451052	SK-N-SH_RA	brain:	n/a	n/a
8	CTCF	chr6:2450920-2451070	HMEC	breast:	n/a	n/a
9	CTCF	chr6:2450940-2451090	HRE	kidney:	n/a	n/a
10	CTCF	chr6:2450960-2451110	SAEC	small airway:	n/a	n/a
11	CTCF	chr6:2450920-2451070	HEEpiC	esophagus:	n/a	n/a
12	RAD21	chr6:2450763-2451119	ECC-1	luminal epithelium:	n/a	n/a
13	NFIC	chr6:2450722-2451313	ECC-1	luminal epithelium:	n/a	chr6:2450999-2451016

Variant related genes	Relation type
GMDS-AS1	TF binding region

Extended variants
information (count: 17 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:8)

rs_ID	r²[population]
rs11242774	0.81[AMR][1000 genomes]
rs761096	0.83[CHB][hapmap];1.00[JPT][hapmap];0.93[AMR][1000 genomes]
rs7744318	0.94[AFR][1000 genomes];0.98[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7763441	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7768075	0.96[AFR][1000 genomes];0.98[AMR][1000 genomes];0.92[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs9378332	0.85[AMR][1000 genomes];0.84[ASN][1000 genomes]
rs9501843	0.89[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9503194	0.85[AMR][1000 genomes];0.84[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:9 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv531295	chr6:1773436-2724986	Enhancers Weak transcription ZNF genes & repeats Flanking Active TSS Active TSS Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	71 gene(s)	inside rSNPs	diseases
2	nsv883388	chr6:2093432-2514911	Strong transcription Enhancers ZNF genes & repeats Weak transcription Transcr. at gene 5' and 3' Active TSS Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	62 gene(s)	inside rSNPs	diseases
3	nsv883389	chr6:2093432-2776303	Weak transcription Enhancers Flanking Active TSS Active TSS ZNF genes & repeats Bivalent Enhancer Strong transcription Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	87 gene(s)	inside rSNPs	diseases
4	nsv1021573	chr6:2246721-2832408	Enhancers ZNF genes & repeats Strong transcription Active TSS Flanking Active TSS Weak transcription Bivalent/Poised TSS Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	80 gene(s)	inside rSNPs	diseases
5	nsv538102	chr6:2246721-2832408	Weak transcription Enhancers Flanking Bivalent TSS/Enh Active TSS Bivalent Enhancer ZNF genes & repeats Flanking Active TSS Strong transcription Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	80 gene(s)	inside rSNPs	diseases
6	nsv883390	chr6:2265344-2584919	Weak transcription Enhancers Strong transcription ZNF genes & repeats Bivalent Enhancer Flanking Active TSS Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	30 gene(s)	inside rSNPs	diseases
7	nsv883391	chr6:2282747-2507448	Flanking Active TSS Weak transcription Enhancers Active TSS ZNF genes & repeats Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	24 gene(s)	inside rSNPs	diseases
8	nsv1016878	chr6:2375784-2680476	Enhancers Weak transcription Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Strong transcription ZNF genes & repeats Active TSS Bivalent/Poised TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	24 gene(s)	inside rSNPs	diseases
9	nsv498004	chr6:2380300-3313587	Weak transcription Active TSS Strong transcription Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats Enhancers Bivalent Enhancer Flanking Active TSS Bivalent/Poised TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	163 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:24 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:2414600-2452000	Weak transcription	Ovary	ovary
2	chr6:2417600-2454200	Weak transcription	Pancreas	Pancrea
3	chr6:2448600-2451400	Enhancers	Hela-S3	cervix
4	chr6:2449400-2451200	Weak transcription	Skeletal Muscle Male	skeletal muscle
5	chr6:2449600-2451600	Weak transcription	HepG2	liver
6	chr6:2449600-2452400	Enhancers	Fetal Heart	heart
7	chr6:2449600-2454600	Weak transcription	Fetal Kidney	kidney
8	chr6:2449600-2455800	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
9	chr6:2449600-2460400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
10	chr6:2449600-2460400	Weak transcription	Fetal Brain Female	brain
11	chr6:2449600-2461200	Weak transcription	Stomach Smooth Muscle	stomach
12	chr6:2449800-2455200	Weak transcription	Brain Angular Gyrus	brain
13	chr6:2450200-2454000	Weak transcription	Brain Substantia Nigra	brain
14	chr6:2450200-2460400	Weak transcription	Brain Anterior Caudate	brain
15	chr6:2450400-2451400	Enhancers	Breast Myoepithelial Primary Cells	Breast
16	chr6:2450600-2451800	Enhancers	Skeletal Muscle Female	skeletal muscle
17	chr6:2450800-2452000	Enhancers	Fetal Muscle Leg	muscle
18	chr6:2451000-2451200	Bivalent Enhancer	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
19	chr6:2451000-2451200	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
20	chr6:2451000-2451200	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
21	chr6:2451000-2451200	Enhancers	Fetal Brain Male	brain
22	chr6:2451000-2451200	Bivalent Enhancer	Osteobl	bone
23	chr6:2451000-2451400	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
24	chr6:2451000-2451400	Bivalent Enhancer	HSMM	muscle

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