Variant report

Variant	rs7899948
Chromosome Location	chr10:99468978-99468979
allele	G/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	POLR2A	chr10:99466622-99471094	MCF10A-Er-Src	breast:	n/a	n/a
2	CTCF	chr10:99468860-99469010	GM06990	blood:	n/a	n/a
3	CTCF	chr10:99468960-99469110	GM12874	blood:	n/a	chr10:99469000-99469018
4	POLR2A	chr10:99468825-99469825	Hela-S3	cervix:	n/a	n/a
5	CTCF	chr10:99468966-99469877	HCT-116	colon:	n/a	chr10:99469428-99469446 chr10:99469429-99469445 chr10:99469431-99469444 chr10:99469000-99469018 chr10:99469430-99469451 chr10:99469433-99469443 chr10:99469232-99469245
6	RAD21	chr10:99468916-99469998	SK-N-SH	brain:	n/a	chr10:99469609-99469623 chr10:99469605-99469624 chr10:99469429-99469448
7	CTCF	chr10:99468960-99469110	AG09319	gingival:	n/a	chr10:99469000-99469018
8	CTCF	chr10:99468940-99469090	NB4	blood:	n/a	chr10:99469000-99469018
9	CTCF	chr10:99468840-99468990	HAc	cerebellar:	n/a	n/a
10	CTCF	chr10:99468895-99469927	A549	lung:	n/a	chr10:99469428-99469446 chr10:99469429-99469445 chr10:99469431-99469444 chr10:99469000-99469018 chr10:99469430-99469451 chr10:99469433-99469443 chr10:99469232-99469245
11	POLR2A	chr10:99468849-99469924	MCF10A-Er-Src	breast:	n/a	n/a
12	SMC3	chr10:99468873-99469815	SK-N-SH	brain:	n/a	chr10:99469430-99469444 chr10:99469002-99469016 chr10:99469434-99469444

No.	Distal block	Cell Line	Cell type
1	chr10:99467434..99470349-chr10:99491482..99494563,3	MCF-7	breast:
2	chr10:99468809..99469891-chr10:99491266..99492143,11	MCF-7	breast:
3	chr10:99464473..99466388-chr10:99467350..99469682,2	MCF-7	breast:
4	chr10:99431862..99434859-chr10:99467271..99469904,2	MCF-7	breast:
5	chr10:99468370..99471944-chr10:99473650..99476348,3	K562	blood:
6	chr10:99468891..99470130-chr10:99490908..99491797,4	K562	blood:
7	chr10:99466947..99470987-chr10:99489059..99494674,5	MCF-7	breast:

Variant related genes	Relation type
MARVELD1	TF binding region
ENSG00000155254	Chromatin interaction

Extended variants
information (count: 9 )
Associated
traits (count: 6 )

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

rs_ID	r²[population]
rs10786366	0.88[ASW][hapmap];0.95[CHB][hapmap];0.89[CHD][hapmap];1.00[JPT][hapmap];0.83[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs12265254	0.87[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs12415272	0.85[CEU][hapmap];0.85[MEX][hapmap];0.86[TSI][hapmap];0.91[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs4919131	0.84[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs4919133	0.82[AMR][1000 genomes]
rs6584147	0.89[ASW][hapmap];1.00[CEU][hapmap];0.95[CHB][hapmap];0.87[CHD][hapmap];1.00[JPT][hapmap];0.85[MEX][hapmap];0.97[TSI][hapmap];0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs6584148	0.85[CEU][hapmap];0.80[GIH][hapmap];0.85[MEX][hapmap];0.81[MKK][hapmap];0.80[TSI][hapmap];0.93[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs7913630	0.95[CHB][hapmap];1.00[JPT][hapmap]

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

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv1817777	chr10:99196035-99558169	Weak transcription Flanking Active TSS Active TSS Enhancers Genic enhancers Strong transcription Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	66 gene(s)	inside rSNPs	diseases

mRNA abundance (count:6)

SNP	Gene	Cis/trans	Tissue	Source
rs7899948	SFRP5	cis	cerebellum	SCAN
rs7899948	DHDPSL	cis	cerebellum	SCAN
rs7899948	C10orf62	cis	cerebellum	SCAN
rs7899948	PI4K2A	cis	parietal	SCAN
rs7899948	PI4K2A	cis	cerebellum	SCAN
rs7899948	FRAT2	cis	cerebellum	SCAN

Chromatin state (count:44 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr10:99462000-99472800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
2	chr10:99462200-99469000	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
3	chr10:99465200-99469000	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
4	chr10:99465200-99469000	Weak transcription	NHLF	lung
5	chr10:99466000-99472600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
6	chr10:99466400-99472600	Enhancers	Breast Myoepithelial Primary Cells	Breast
7	chr10:99467200-99469800	Enhancers	Fetal Heart	heart
8	chr10:99467200-99469800	Enhancers	Fetal Muscle Leg	muscle
9	chr10:99467200-99469800	Enhancers	Ovary	ovary
10	chr10:99467200-99471800	Weak transcription	Spleen	Spleen
11	chr10:99467400-99469000	Weak transcription	Fetal Intestine Small	intestine
12	chr10:99467400-99469800	Enhancers	Skeletal Muscle Female	skeletal muscle
13	chr10:99467400-99470000	Enhancers	Rectal Smooth Muscle	rectum
14	chr10:99467600-99469800	Enhancers	Colon Smooth Muscle	Colon
15	chr10:99467800-99469000	Weak transcription	Aorta	Aorta
16	chr10:99468000-99469800	Enhancers	Duodenum Smooth Muscle	Duodenum
17	chr10:99468400-99469000	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
18	chr10:99468400-99469000	Enhancers	Hela-S3	cervix
19	chr10:99468400-99469400	Enhancers	HepG2	liver
20	chr10:99468400-99470200	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
21	chr10:99468400-99472800	Weak transcription	Liver	Liver
22	chr10:99468600-99469000	Weak transcription	Right Atrium	heart
23	chr10:99468600-99469000	Enhancers	Stomach Smooth Muscle	stomach
24	chr10:99468600-99469400	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
25	chr10:99468600-99469600	Enhancers	Fetal Intestine Large	intestine
26	chr10:99468600-99469800	Enhancers	HSMMtube	muscle
27	chr10:99468800-99469000	Enhancers	A549	lung
28	chr10:99468800-99469200	Enhancers	Colonic Mucosa	Colon
29	chr10:99468800-99469400	Enhancers	Adipose Nuclei	Adipose
30	chr10:99468800-99469600	Enhancers	iPS DF 6.9 Cell Line	embryonic stem cell
31	chr10:99468800-99469600	Enhancers	Skeletal Muscle Male	skeletal muscle
32	chr10:99468800-99469800	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
33	chr10:99468800-99469800	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
34	chr10:99468800-99469800	Enhancers	Foreskin Melanocyte Primary Cells skin01	Skin
35	chr10:99468800-99469800	Enhancers	Placenta	Placenta
36	chr10:99468800-99469800	Enhancers	Right Ventricle	heart
37	chr10:99468800-99469800	Enhancers	NH-A	brain
38	chr10:99468800-99470000	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
39	chr10:99468800-99470000	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
40	chr10:99468800-99470000	Enhancers	Fetal Stomach	stomach
41	chr10:99468800-99470000	Enhancers	HSMM	muscle
42	chr10:99468800-99470000	Enhancers	NHDF-Ad	bronchial
43	chr10:99468800-99470000	Enhancers	Osteobl	bone
44	chr10:99468800-99470200	Enhancers	Fetal Muscle Trunk	muscle

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links