Variant report

Variant	rs3130797
Chromosome Location	chr6:30846088-30846089
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:11)
CpG islands
(count:0)
Chromatin interactive
region (count:22)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:11 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	CTCF	chr6:30846060-30846210	NHLF	lung:	n/a	n/a
2	CTCF	chr6:30846060-30846210	WI-38	lung:	n/a	n/a
3	RAD21	chr6:30845215-30846113	HCT-116	colon:	n/a	chr6:30845661-30845680 chr6:30845665-30845679
4	CTCF	chr6:30846060-30846210	HPF	lung:	n/a	n/a
5	TEAD4	chr6:30845013-30846183	K562	blood:	n/a	n/a
6	ZNF263	chr6:30845441-30846703	HEK293-T-REx	kidney:	n/a	chr6:30846273-30846282
7	SMC3	chr6:30844866-30846228	SK-N-SH	brain:	n/a	chr6:30845665-30845679
8	CTCF	chr6:30845009-30846143	HCT-116	colon:	n/a	chr6:30845663-30845681 chr6:30845665-30845678 chr6:30845664-30845680
9	CBX3	chr6:30845020-30846174	K562	blood:	n/a	n/a
10	RAD21	chr6:30845036-30846095	HCT-116	colon:	n/a	chr6:30845665-30845679 chr6:30845661-30845680
11	CTCF	chr6:30845202-30846095	A549	lung:	n/a	chr6:30845663-30845681 chr6:30845665-30845678 chr6:30845664-30845680

No data

(count:22 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr6:30845452..30847676-chr6:30880865..30882821,3	MCF-7	breast:
2	chr6:30795972..30797365-chr6:30845047..30846130,14	MCF-7	breast:
3	chr6:30844198..30846831-chr6:30855109..30857991,4	K562	blood:
4	chr6:30581875..30586807-chr6:30843879..30846748,7	K562	blood:
5	chr6:30794393..30796248-chr6:30844324..30846676,2	K562	blood:
6	chr6:30582174..30584970-chr6:30843879..30846723,2	K562	blood:
7	chr6:30709419..30712490-chr6:30846004..30847673,3	K562	blood:
8	chr6:30844233..30846807-chr6:30875461..30877284,2	MCF-7	breast:
9	chr6:30844224..30847170-chr6:30875754..30878478,2	K562	blood:
10	chr6:30794216..30799803-chr6:30838849..30846731,16	K562	blood:
11	chr6:30707945..30712505-chr6:30840794..30847673,9	K562	blood:
12	chr6:30705171..30717521-chr6:30843972..30856100,74	MCF-7	breast:
13	chr6:30845163..30847158-chr6:30883257..30885343,2	K562	blood:
14	chr6:30795918..30796957-chr6:30845184..30846122,7	MCF-7	breast:
15	chr6:30704403..30722478-chr6:30842859..30858629,100	MCF-7	breast:
16	chr6:30792427..30796566-chr6:30845190..30846951,4	MCF-7	breast:
17	chr6:30795677..30797852-chr6:30845172..30846174,17	K562	blood:
18	chr6:30845624..30847125-chr6:31037029..31038938,2	MCF-7	breast:
19	chr6:30845624..30847168-chr6:30875817..30877416,2	K562	blood:
20	chr6:30844121..30846194-chr6:30880539..30883879,3	K562	blood:
21	chr6:30780598..30803497-chr6:30842531..30855110,80	MCF-7	breast:
22	chr6:30845522..30846299-chr6:30881480..30882160,2	MCF-7	breast:

No data

Variant related genes	Relation type
DDR1-AS1	TF binding region
DDR1	TF binding region
ENSG00000137312	Chromatin interaction
ENSG00000204568	Chromatin interaction
ENSG00000213780	Chromatin interaction
ENSG00000137331	Chromatin interaction
ENSG00000263608	Chromatin interaction
ENSG00000214894	Chromatin interaction
ENSG00000204569	Chromatin interaction
ENSG00000222894	Chromatin interaction
ENSG00000272273	Chromatin interaction
ENSG00000137411	Chromatin interaction
ENSG00000204580	Chromatin interaction

Extended variants
information (count: 23 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:14)

rs_ID	r²[population]
rs2253705	0.90[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2517459	0.92[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2532932	0.92[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2894059	0.91[AFR][1000 genomes];0.95[AMR][1000 genomes];0.87[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs3094108	0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3094719	0.92[AMR][1000 genomes];0.87[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs3095345	0.96[ASN][1000 genomes]
rs3130648	0.83[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs3130779	0.85[AMR][1000 genomes];0.92[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs3130780	0.88[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs3130788	0.86[AMR][1000 genomes];0.92[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs3131028	0.84[EUR][1000 genomes]
rs3131032	0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3131034	0.85[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[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	esv3519970	chr6:30382942-31378788	Genic enhancers Weak transcription Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Enhancers Transcr. at gene 5' and 3' Strong transcription Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	1030 gene(s)	inside rSNPs	diseases
2	esv3519971	chr6:30382942-31378788	Bivalent Enhancer Flanking Active TSS Active TSS Weak transcription Enhancers Transcr. at gene 5' and 3' Strong transcription Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	1030 gene(s)	inside rSNPs	diseases
3	nsv601481	chr6:30422632-31284253	Weak transcription Genic enhancers Transcr. at gene 5' and 3' Flanking Active TSS Strong transcription Enhancers Active TSS Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	1012 gene(s)	inside rSNPs	diseases
4	nsv1015372	chr6:30704734-31582152	Active TSS Flanking Active TSS Enhancers Weak transcription Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Strong transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	334 gene(s)	inside rSNPs	diseases
5	nsv538173	chr6:30704734-31582152	Flanking Active TSS Enhancers Weak transcription Active TSS Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Strong transcription Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	334 gene(s)	inside rSNPs	diseases
6	nsv884109	chr6:30824532-30872203	Strong transcription Weak transcription Enhancers Flanking Active TSS Bivalent Enhancer Active TSS Transcr. at gene 5' and 3' Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	31 gene(s)	inside rSNPs	diseases
7	nsv884110	chr6:30845563-30856463	Active TSS Transcr. at gene 5' and 3' Flanking Active TSS Weak transcription Enhancers Flanking Bivalent TSS/Enh Strong transcription Genic enhancers Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	29 gene(s)	inside rSNPs	diseases
8	nsv884111	chr6:30845563-30864279	Active TSS Weak transcription Enhancers Flanking Active TSS Strong transcription Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA	29 gene(s)	inside rSNPs	diseases
9	nsv884112	chr6:30845563-30866618	Flanking Active TSS Enhancers Genic enhancers Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Strong transcription Weak transcription Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA	29 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:110 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:30843200-30846800	Enhancers	Cortex derived primary cultured neurospheres	brain
2	chr6:30843600-30848400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
3	chr6:30844200-30846200	Enhancers	Fetal Heart	heart
4	chr6:30844200-30848600	Enhancers	Fetal Thymus	thymus
5	chr6:30844200-30850200	Weak transcription	Spleen	Spleen
6	chr6:30844400-30846400	Enhancers	Fetal Stomach	stomach
7	chr6:30844600-30846600	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
8	chr6:30844600-30846600	Enhancers	Esophagus	oesophagus
9	chr6:30844800-30846200	Enhancers	Fetal Muscle Leg	muscle
10	chr6:30845000-30846200	Enhancers	iPS-20b Cell Line	embryonic stem cell
11	chr6:30845000-30846200	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
12	chr6:30845000-30846800	Enhancers	HUES6 Cell Line	embryonic stem cell
13	chr6:30845200-30846200	Enhancers	H1 Cell Line	embryonic stem cell
14	chr6:30845200-30846200	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
15	chr6:30845200-30846200	Enhancers	Primary B cells from peripheral blood	blood
16	chr6:30845200-30846200	Flanking Active TSS	Skeletal Muscle Male	skeletal muscle
17	chr6:30845200-30846200	Flanking Bivalent TSS/Enh	HepG2	liver
18	chr6:30845200-30846400	Enhancers	iPS-18 Cell Line	embryonic stem cell
19	chr6:30845200-30846600	Enhancers	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
20	chr6:30845200-30848000	Enhancers	Brain Germinal Matrix	brain
21	chr6:30845400-30848400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
22	chr6:30845400-30848600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
23	chr6:30845600-30846200	Enhancers	Brain Dorsolateral Prefrontal Cortex	brain
24	chr6:30845600-30846200	Enhancers	Psoas Muscle	Psoas
25	chr6:30845600-30846200	Enhancers	NHLF	lung
26	chr6:30845600-30846600	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
27	chr6:30845600-30846800	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
28	chr6:30845600-30847600	Weak transcription	Fetal Kidney	kidney
29	chr6:30845600-30847800	Weak transcription	Fetal Brain Male	brain
30	chr6:30845600-30848000	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
31	chr6:30845600-30848400	Weak transcription	Pancreatic Islets	Pancreatic Islet
32	chr6:30845600-30848400	Weak transcription	Placenta Amnion	Placenta Amnion
33	chr6:30845600-30848600	Weak transcription	NH-A	brain
34	chr6:30845800-30846200	Enhancers	Primary T cells fromperipheralblood	blood
35	chr6:30845800-30846200	Enhancers	Primary T helper cells PMA-I stimulated	--
36	chr6:30845800-30846200	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
37	chr6:30845800-30846200	Enhancers	Primary T regulatory cells fromperipheralblood	blood
38	chr6:30845800-30846200	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
39	chr6:30845800-30846200	Enhancers	Brain Hippocampus Middle	brain
40	chr6:30845800-30846400	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
41	chr6:30845800-30846400	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
42	chr6:30845800-30846600	Enhancers	Adipose Nuclei	Adipose
43	chr6:30845800-30846800	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
44	chr6:30845800-30846800	Enhancers	Fetal Muscle Trunk	muscle
45	chr6:30845800-30847000	Enhancers	Breast Myoepithelial Primary Cells	Breast
46	chr6:30845800-30849800	Weak transcription	Colonic Mucosa	Colon
47	chr6:30845800-30849800	Weak transcription	Right Atrium	heart
48	chr6:30845800-30850000	Weak transcription	Primary B cells from cord blood	blood
49	chr6:30845800-30850800	Weak transcription	Primary T cells from cord blood	blood
50	chr6:30845800-30851200	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood

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