Variant report

Variant	rs3218825
Chromosome Location	chr6:30881031-30881032
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:8)
CpG islands
(count:0)
Chromatin interactive
region (count:21)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:8 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr6:30880670-30881232	H1-hESC	embryonic stem cell:	n/a	n/a
2	TAF7	chr6:30880774-30881270	H1-hESC	embryonic stem cell:	n/a	n/a
3	POLR2A	chr6:30880977-30881047	HepG2	liver:	n/a	n/a
4	NRF1	chr6:30880936-30882491	SK-N-SH	brain:	n/a	chr6:30881557-30881566 chr6:30882016-30882027 chr6:30881990-30882001
5	POLR2A	chr6:30880818-30881219	K562	blood:	n/a	n/a
6	POLR2A	chr6:30880849-30881088	H1-hESC	embryonic stem cell:	n/a	n/a
7	POLR2A	chr6:30880923-30881194	H1-hESC	embryonic stem cell:	n/a	n/a
8	POLR2A	chr6:30880807-30881235	H1-hESC	embryonic stem cell:	n/a	n/a

No data

(count:21 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr6:30847750..30851239-chr6:30880214..30883075,5	K562	blood:
2	chr6:30850549..30855941-chr6:30880357..30883667,13	MCF-7	breast:
3	chr6:30793814..30798702-chr6:30880453..30884092,5	K562	blood:
4	chr6:30682386..30686066-chr6:30878897..30882722,4	K562	blood:
5	chr6:30847750..30854588-chr6:30880214..30885422,8	K562	blood:
6	chr6:30581497..30584727-chr6:30876949..30882098,5	K562	blood:
7	chr6:30583221..30584727-chr6:30879043..30881958,2	K562	blood:
8	chr6:30583713..30586617-chr6:30879172..30881064,2	MCF-7	breast:
9	chr6:30684320..30686534-chr6:30879167..30882068,2	MCF-7	breast:
10	chr6:30880736..30883349-chr6:30890122..30892611,2	MCF-7	breast:
11	chr6:30523025..30525668-chr6:30880813..30884106,3	K562	blood:
12	chr6:30843411..30845774-chr6:30879579..30881795,2	MCF-7	breast:
13	chr6:30850840..30855328-chr6:30877838..30882665,10	MCF-7	breast:
14	chr6:30844121..30846194-chr6:30880539..30883879,3	K562	blood:
15	chr6:30735539..30738504-chr6:30880365..30881967,2	MCF-7	breast:
16	chr6:30843383..30845810-chr6:30880379..30882936,3	K562	blood:
17	chr6:30709669..30712213-chr6:30880810..30882538,2	MCF-7	breast:
18	chr6:30583267..30585351-chr6:30880366..30882119,2	MCF-7	breast:
19	chr6:30854396..30859063-chr6:30880954..30884819,5	K562	blood:
20	chr6:30707880..30713865-chr6:30880456..30883497,7	MCF-7	breast:
21	chr6:30683565..30685674-chr6:30879957..30882271,2	K562	blood:

No data

Variant related genes	Relation type
VARS2	TF binding region
ENSG00000272273	Chromatin interaction
ENSG00000204568	Chromatin interaction
ENSG00000214894	Chromatin interaction
ENSG00000237775	Chromatin interaction
ENSG00000264594	Chromatin interaction
ENSG00000204576	Chromatin interaction
ENSG00000204569	Chromatin interaction
ENSG00000137331	Chromatin interaction
ENSG00000222894	Chromatin interaction
ENSG00000137411	Chromatin interaction
ENSG00000204590	Chromatin interaction
ENSG00000204580	Chromatin interaction
ENSG00000137312	Chromatin interaction
ENSG00000137337	Chromatin interaction

Extended variants
information (count: 28 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:21)

rs_ID	r²[population]
rs10947109	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11759918	0.82[ASN][1000 genomes]
rs17189749	0.94[ASN][1000 genomes]
rs17196123	0.87[ASN][1000 genomes]
rs17840009	0.82[ASN][1000 genomes]
rs2894054	0.91[ASN][1000 genomes]
rs3218804	0.82[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs45627239	0.94[ASN][1000 genomes]
rs55697712	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs59124304	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6926224	0.84[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs6926723	0.84[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs6940037	0.94[ASN][1000 genomes]
rs73727104	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs73727106	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs73727107	0.85[ASN][1000 genomes]
rs73727480	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7747800	0.87[ASN][1000 genomes]
rs7761138	0.85[ASN][1000 genomes]
rs7770596	0.84[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs7772269	0.82[ASN][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	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	nsv1031677	chr6:30857542-30972865	Flanking Active TSS Weak transcription Bivalent Enhancer Genic enhancers Enhancers Active TSS Bivalent/Poised TSS Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	32 gene(s)	inside rSNPs	diseases
7	nsv525438	chr6:30864829-30933975	Weak transcription Strong transcription Enhancers Transcr. at gene 5' and 3' Active TSS Flanking Active TSS Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	30 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:125 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:30876800-30881400	Weak transcription	Right Atrium	heart
2	chr6:30876800-30881600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
3	chr6:30876800-30881800	Weak transcription	Small Intestine	intestine
4	chr6:30877000-30881200	Weak transcription	Primary T helper naive cells from peripheral blood	blood
5	chr6:30877000-30881200	Weak transcription	Fetal Heart	heart
6	chr6:30877000-30881200	Weak transcription	Stomach Mucosa	stomach
7	chr6:30877000-30881200	Weak transcription	A549	lung
8	chr6:30877000-30881400	Weak transcription	Pancreatic Islets	Pancreatic Islet
9	chr6:30877200-30881200	Strong transcription	HUES64 Cell Line	embryonic stem cell
10	chr6:30877200-30881200	Strong transcription	iPS-20b Cell Line	embryonic stem cell
11	chr6:30877200-30881200	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
12	chr6:30877200-30881200	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
13	chr6:30877200-30881400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
14	chr6:30877200-30881400	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
15	chr6:30877200-30881400	Weak transcription	Primary T killer memory cells from peripheral blood	blood
16	chr6:30877200-30881400	Weak transcription	HSMM	muscle
17	chr6:30877400-30881200	Strong transcription	HUES48 Cell Line	embryonic stem cell
18	chr6:30877400-30881400	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
19	chr6:30877400-30881400	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
20	chr6:30877400-30881400	Strong transcription	Primary hematopoietic stem cells short term culture	blood
21	chr6:30877400-30881400	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
22	chr6:30877400-30881400	Strong transcription	Fetal Stomach	stomach
23	chr6:30877400-30881600	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
24	chr6:30877400-30881600	Strong transcription	K562	blood
25	chr6:30877600-30881200	Strong transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
26	chr6:30877600-30881200	Strong transcription	iPS-18 Cell Line	embryonic stem cell
27	chr6:30877600-30881200	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
28	chr6:30877600-30881200	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
29	chr6:30877600-30881200	Strong transcription	Foreskin Fibroblast Primary Cells skin01	Skin
30	chr6:30877600-30881200	Strong transcription	Fetal Muscle Leg	muscle
31	chr6:30877600-30881400	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
32	chr6:30877600-30881400	Strong transcription	Osteobl	bone
33	chr6:30877800-30881200	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
34	chr6:30877800-30881200	Strong transcription	HMEC	breast
35	chr6:30877800-30881200	Strong transcription	HUVEC	blood vessel
36	chr6:30877800-30881400	Strong transcription	Muscle Satellite Cultured Cells	--
37	chr6:30878000-30881200	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
38	chr6:30878000-30881400	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
39	chr6:30878000-30881400	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
40	chr6:30878200-30881200	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
41	chr6:30878400-30881200	Strong transcription	NH-A	brain
42	chr6:30878600-30881400	Strong transcription	Hela-S3	cervix
43	chr6:30878800-30881400	Weak transcription	Primary B cells from cord blood	blood
44	chr6:30879000-30881200	Weak transcription	Fetal Kidney	kidney
45	chr6:30879200-30881200	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
46	chr6:30879200-30881400	Weak transcription	NHDF-Ad	bronchial
47	chr6:30879400-30881400	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
48	chr6:30879400-30881600	Weak transcription	Aorta	Aorta
49	chr6:30879600-30881400	Weak transcription	Brain Angular Gyrus	brain
50	chr6:30879800-30881400	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood

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