Variant report

Variant	rs10863778
Chromosome Location	chr1:209825386-209825387
allele	C/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	SMARCB1	chr1:209824459-209826866	Hela-S3	cervix:	n/a	n/a
2	POLR2A	chr1:209825255-209826864	HCT-116	colon:	n/a	n/a
3	POLR2A	chr1:209825278-209826853	Hela-S3	cervix:	n/a	n/a
4	POLR2A	chr1:209824341-209826797	Hela-S3	cervix:	n/a	n/a
5	POLR2A	chr1:209823635-209826810	Hela-S3	cervix:	n/a	n/a
6	SMARCC2	chr1:209825323-209826917	Hela-S3	cervix:	n/a	n/a
7	SPI1	chr1:209825359-209825605	GM12878	blood:	n/a	n/a
8	SP1	chr1:209825324-209827797	HCT-116	colon:	n/a	chr1:209826528-209826540 chr1:209826528-209826540 chr1:209827536-209827550
9	SPI1	chr1:209825295-209825632	GM12891	blood:	n/a	n/a
10	POLR2A	chr1:209823641-209826800	Hela-S3	cervix:	n/a	n/a
11	POLR2A	chr1:209822652-209827741	MCF10A-Er-Src	breast:	n/a	n/a
12	SMARCC1	chr1:209823905-209827566	Hela-S3	cervix:	n/a	chr1:209826912-209826921
13	EP300	chr1:209825379-209827075	ECC-1	luminal epithelium:	n/a	chr1:209825475-209825489 chr1:209825985-209826001 chr1:209826299-209826313
14	POLR2A	chr1:209821930-209827817	MCF10A-Er-Src	breast:	n/a	n/a
15	SPI1	chr1:209825336-209825637	GM12891	blood:	n/a	n/a
16	WRNIP1	chr1:209825306-209825480	GM12878	blood:	n/a	n/a
17	JUND	chr1:209825245-209826987	HCT-116	colon:	n/a	chr1:209825785-209825799 chr1:209826487-209826497 chr1:209826486-209826497 chr1:209826487-209826497 chr1:209826484-209826495
18	TFAP2A	chr1:209824362-209826859	Hela-S3	cervix:	n/a	chr1:209825637-209825649 chr1:209824794-209824809

Variant related genes	Relation type
LAMB3	TF binding region

Extended variants
information (count: 9 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:6)

rs_ID	r²[population]
rs10779510	0.87[AFR][1000 genomes];0.81[EUR][1000 genomes]
rs12089972	0.99[ASN][1000 genomes]
rs2298924	0.85[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2298927	0.87[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2298929	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.81[LWK][hapmap];0.82[MEX][hapmap];0.84[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.87[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs36051870	1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv999901	chr1:209600631-210205379	Flanking Active TSS Enhancers Weak transcription Active TSS Bivalent Enhancer Strong transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	76 gene(s)	inside rSNPs	diseases
2	nsv1014034	chr1:209759648-210501731	Enhancers Weak transcription Flanking Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Strong transcription Active TSS Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	45 gene(s)	inside rSNPs	diseases
3	esv2762140	chr1:209816331-209830347	Enhancers Strong transcription Weak transcription Active TSS Flanking Active TSS Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs10863778	SLC26A9	cis	parietal	SCAN
rs10863778	SPATC1	trans	cerebellum	SCAN
rs10863778	RD3	cis	parietal	SCAN

Chromatin state (count:97 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:209814600-209826800	Enhancers	Fetal Adrenal Gland	Adrenal Gland
2	chr1:209817000-209825400	Enhancers	Skeletal Muscle Female	skeletal muscle
3	chr1:209817800-209825800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
4	chr1:209817800-209826000	Weak transcription	Brain Angular Gyrus	brain
5	chr1:209818000-209826000	Weak transcription	Brain Inferior Temporal Lobe	brain
6	chr1:209818200-209825800	Weak transcription	Brain Cingulate Gyrus	brain
7	chr1:209818200-209826000	Weak transcription	Brain Substantia Nigra	brain
8	chr1:209819200-209825400	Enhancers	NHLF	lung
9	chr1:209819200-209827400	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
10	chr1:209819200-209831200	Enhancers	Pancreas	Pancrea
11	chr1:209820000-209825400	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
12	chr1:209820000-209825400	Enhancers	Stomach Smooth Muscle	stomach
13	chr1:209820000-209825600	Weak transcription	Fetal Brain Female	brain
14	chr1:209820000-209825800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
15	chr1:209820400-209826200	Weak transcription	HUES64 Cell Line	embryonic stem cell
16	chr1:209820800-209825800	Enhancers	Primary monocytes fromperipheralblood	blood
17	chr1:209820800-209826000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
18	chr1:209821000-209826200	Weak transcription	Fetal Brain Male	brain
19	chr1:209821600-209828000	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
20	chr1:209822400-209825800	Enhancers	Placenta	Placenta
21	chr1:209822600-209827200	Enhancers	HSMMtube	muscle
22	chr1:209823000-209826400	Weak transcription	Psoas Muscle	Psoas
23	chr1:209823000-209836200	Weak transcription	Ovary	ovary
24	chr1:209823200-209825600	Weak transcription	Brain Germinal Matrix	brain
25	chr1:209823200-209825600	Weak transcription	Fetal Heart	heart
26	chr1:209823200-209826000	Weak transcription	Fetal Kidney	kidney
27	chr1:209823200-209826200	Active TSS	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
28	chr1:209823400-209825600	Weak transcription	Brain Hippocampus Middle	brain
29	chr1:209823400-209826000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
30	chr1:209823400-209827000	Enhancers	Adipose Nuclei	Adipose
31	chr1:209823400-209827200	Weak transcription	Gastric	stomach
32	chr1:209824000-209825400	Enhancers	Right Atrium	heart
33	chr1:209824000-209825600	Weak transcription	Cortex derived primary cultured neurospheres	brain
34	chr1:209824000-209825600	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
35	chr1:209824000-209828000	Enhancers	GM12878-XiMat	blood
36	chr1:209824200-209826400	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
37	chr1:209824200-209827000	Active TSS	Breast Myoepithelial Primary Cells	Breast
38	chr1:209824200-209827800	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
39	chr1:209824400-209825800	Weak transcription	Fetal Thymus	thymus
40	chr1:209824400-209825800	Weak transcription	Spleen	Spleen
41	chr1:209824400-209826000	Weak transcription	Liver	Liver
42	chr1:209824400-209826600	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
43	chr1:209824400-209827000	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
44	chr1:209824400-209827000	Flanking Active TSS	Hela-S3	cervix
45	chr1:209824600-209825600	Enhancers	Fetal Muscle Trunk	muscle
46	chr1:209824600-209825800	Enhancers	Monocytes-CD14+_RO01746	blood
47	chr1:209824600-209826000	Weak transcription	Fetal Lung	lung
48	chr1:209824600-209826200	Enhancers	Primary neutrophils fromperipheralblood	blood
49	chr1:209824600-209826400	Weak transcription	Primary hematopoietic stem cells	blood
50	chr1:209824800-209825600	Active TSS	Sigmoid Colon	Sigmoid Colon

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