Variant report

Variant	rs1264299
Chromosome Location	chr6:30883920-30883921
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:7)
CpG islands
(count:0)
Chromatin interactive
region (count:11)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:7 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	CTCF	chr6:30881367-30884041	SK-N-SH	brain:	n/a	chr6:30883455-30883476 chr6:30883454-30883470
2	POLR2A	chr6:30883417-30884112	K562	blood:	n/a	n/a
3	POLR2A	chr6:30881436-30884176	HepG2	liver:	n/a	n/a
4	RAD21	chr6:30882942-30884015	SK-N-SH	brain:	n/a	chr6:30883454-30883473
5	CTCF	chr6:30883860-30884010	HPF	lung:	n/a	n/a
6	CTCF	chr6:30882830-30883937	HCT-116	colon:	n/a	chr6:30883455-30883476 chr6:30883454-30883470
7	SMC3	chr6:30882823-30884061	SK-N-SH	brain:	n/a	n/a

No data

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

No.	Distal block	Cell Line	Cell type
1	chr6:30883403..30884976-chr6:30908264..30911485,3	MCF-7	breast:
2	chr6:30883149..30883983-chr6:31038127..31038765,2	MCF-7	breast:
3	chr6:30793814..30798702-chr6:30880453..30884092,5	K562	blood:
4	chr6:30847750..30854588-chr6:30880214..30885422,8	K562	blood:
5	chr6:30523025..30525668-chr6:30880813..30884106,3	K562	blood:
6	chr6:30882943..30883998-chr6:31010336..31011408,3	MCF-7	breast:
7	chr6:30882042..30885135-chr6:30886350..30889389,4	MCF-7	breast:
8	chr6:30883250..30883934-chr6:31010475..31011616,5	MCF-7	breast:
9	chr6:30881968..30885056-chr6:30885339..30888267,3	MCF-7	breast:
10	chr6:30882829..30883945-chr6:31036385..31037390,5	MCF-7	breast:
11	chr6:30854396..30859063-chr6:30880954..30884819,5	K562	blood:

No data

Variant related genes	Relation type
VARS2	TF binding region
ENSG00000214894	Chromatin interaction
ENSG00000204576	Chromatin interaction
ENSG00000168631	Chromatin interaction
ENSG00000204580	Chromatin interaction
ENSG00000264594	Chromatin interaction
ENSG00000137411	Chromatin interaction
ENSG00000204590	Chromatin interaction

Extended variants
information (count: 87 )
Associated
traits (count: 7 )

rSNPs within LD-proxies of this variant (count:79)

rs_ID	r²[population]
rs1264297	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1264298	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1264300	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1264301	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1264302	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1264303	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1264305	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1264307	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1264309	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1264317	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1264320	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1264332	1.00[AFR][1000 genomes];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1264342	0.87[AFR][1000 genomes];0.90[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs17189763	0.80[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs2074506	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2240804	0.83[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs2249459	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2252760	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2252856	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2252863	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2394856	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2517449	0.93[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs2517457	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2517461	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2517462	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2517463	0.93[AFR][1000 genomes];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2517466	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2517468	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2517573	0.91[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2517575	0.91[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2517577	0.93[AFR][1000 genomes];0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2517582	0.86[EUR][1000 genomes]
rs2532920	0.87[AFR][1000 genomes];0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2532921	0.93[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2532927	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2532928	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2532929	0.90[EUR][1000 genomes]
rs2532930	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2532933	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2532935	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2532936	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2532937	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2532938	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2532939	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2532940	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2532942	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2532943	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2535325	1.00[AFR][1000 genomes];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2535326	0.92[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2535327	0.80[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs2535329	0.80[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs2535330	1.00[AFR][1000 genomes];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2535331	1.00[AFR][1000 genomes];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2535335	0.92[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2535336	0.92[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2535337	1.00[AFR][1000 genomes];0.89[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2535339	1.00[AFR][1000 genomes];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2844652	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2844654	1.00[AFR][1000 genomes];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2844655	0.80[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs2844658	1.00[AFR][1000 genomes];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2844662	0.91[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2844663	0.91[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2844664	0.91[AFR][1000 genomes];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2844698	0.85[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2844699	0.93[AFR][1000 genomes];0.95[AMR][1000 genomes];0.91[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2844702	0.93[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs3130657	1.00[AFR][1000 genomes];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs753726	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7738138	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7756286	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs887381	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9262288	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9262289	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9262290	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9262291	0.88[AFR][1000 genomes];0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9262292	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9262293	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9262294	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:8 , 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
8	nsv523346	chr6:30882513-30893941	Flanking Active TSS Enhancers Transcr. at gene 5' and 3' Strong transcription Weak transcription Active TSS Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region	20 gene(s)	inside rSNPs	diseases

mRNA abundance (count:7)

SNP	Gene	Cis/trans	Tissue	Source
rs1264299	VARS2	cis	multi-tissue	Pritchard
rs1264299	GRM4	cis	parietal	SCAN
rs1264299	HIST1H2BL	cis	parietal	SCAN
rs1264299	VARSL	cis	uninvolved skin	skin_eQTL
rs1264299	VARSL	cis	normal skin	skin_eQTL
rs1264299	HCG22	cis	lymphoblastoid	seeQTL
rs1264299	GTF2H4///VARS2	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:126 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:30881400-30884200	Active TSS	Esophagus	oesophagus
2	chr6:30882200-30884000	Flanking Active TSS	Skeletal Muscle Female	skeletal muscle
3	chr6:30882600-30884000	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
4	chr6:30882600-30884000	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
5	chr6:30882600-30884000	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
6	chr6:30882600-30884800	Weak transcription	Aorta	Aorta
7	chr6:30882600-30885000	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
8	chr6:30882600-30885000	Enhancers	Lung	lung
9	chr6:30882600-30886800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
10	chr6:30882800-30884000	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
11	chr6:30882800-30884000	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
12	chr6:30882800-30884000	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
13	chr6:30882800-30884000	Enhancers	Left Ventricle	heart
14	chr6:30882800-30884000	Enhancers	Spleen	Spleen
15	chr6:30882800-30884200	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
16	chr6:30882800-30884200	Enhancers	Cortex derived primary cultured neurospheres	brain
17	chr6:30882800-30884200	Enhancers	Fetal Brain Male	brain
18	chr6:30882800-30884600	Weak transcription	H9 Cell Line	embryonic stem cell
19	chr6:30882800-30884600	Enhancers	Primary mononuclear cells fromperipheralblood	Blood
20	chr6:30882800-30884600	Weak transcription	Ovary	ovary
21	chr6:30882800-30884800	Enhancers	HUVEC	blood vessel
22	chr6:30882800-30890200	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
23	chr6:30882800-30890200	Strong transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
24	chr6:30883000-30884000	Weak transcription	H1 Cell Line	embryonic stem cell
25	chr6:30883000-30884000	Enhancers	Primary hematopoietic stem cells short term culture	blood
26	chr6:30883000-30884000	Enhancers	Brain Angular Gyrus	brain
27	chr6:30883000-30884000	Enhancers	Fetal Adrenal Gland	Adrenal Gland
28	chr6:30883000-30884000	Genic enhancers	Fetal Stomach	stomach
29	chr6:30883000-30884000	Enhancers	Pancreas	Pancrea
30	chr6:30883000-30884000	Enhancers	NHDF-Ad	bronchial
31	chr6:30883000-30884200	Genic enhancers	Fetal Intestine Small	intestine
32	chr6:30883000-30884200	Enhancers	HMEC	breast
33	chr6:30883000-30884200	Enhancers	HSMM	muscle
34	chr6:30883000-30884400	Enhancers	Brain Dorsolateral Prefrontal Cortex	brain
35	chr6:30883000-30884600	Weak transcription	iPS-15b Cell Line	embryonic stem cell
36	chr6:30883000-30885000	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
37	chr6:30883000-30889000	Weak transcription	Pancreatic Islets	Pancreatic Islet
38	chr6:30883200-30884000	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
39	chr6:30883200-30884000	Enhancers	Brain Germinal Matrix	brain
40	chr6:30883200-30884000	Enhancers	Brain Inferior Temporal Lobe	brain
41	chr6:30883200-30884200	Enhancers	Fetal Heart	heart
42	chr6:30883200-30884400	Weak transcription	Primary hematopoietic stem cells	blood
43	chr6:30883200-30885400	Weak transcription	Primary neutrophils fromperipheralblood	blood
44	chr6:30883200-30888400	Weak transcription	Small Intestine	intestine
45	chr6:30883400-30884000	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
46	chr6:30883400-30884000	Genic enhancers	Muscle Satellite Cultured Cells	--
47	chr6:30883400-30884000	Enhancers	Rectal Smooth Muscle	rectum
48	chr6:30883400-30884000	Enhancers	GM12878-XiMat	blood
49	chr6:30883400-30884200	Enhancers	Breast Myoepithelial Primary Cells	Breast
50	chr6:30883400-30884200	Enhancers	Liver	Liver

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