Variant report

Variant	rs10903248
Chromosome Location	chr5:179566817-179566818
allele	C/G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:0)
CpG islands
(count:61)
Chromatin interactive
region (count:1)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:61 , 50 per page) page: 1 2

No.	Chromosome Location	Cell Line	Cell type	Cell Stage
1	chr5:179566792-179566842	HMEC	breast:	n/a
2	chr5:179566792-179566842	ECC-1	luminal epithelium:	n/a
3	chr5:179566792-179566842	NHBE	bronchial:	n/a
4	chr5:179566792-179566842	PFSK-1	brain:	n/a
5	chr5:179566792-179566842	ProgFib	skin:	n/a
6	chr5:179566792-179566842	GM12892	blood:	n/a
7	chr5:179566792-179566842	H1-hESC	embryonic stem cell:	embryo
8	chr5:179566792-179566842	IMR90	lung:	fetal
9	chr5:179566792-179566842	HCT-116	colon:	n/a
10	chr5:179566792-179566842	A549	lung:	n/a
11	chr5:179566792-179566842	HRCEpiC	kidney:	n/a
12	chr5:179566792-179566842	Hela-S3	cervix:	n/a
13	chr5:179566792-179566842	GM19239	blood:	n/a
14	chr5:179566792-179566842	HRE	kidney:	n/a
15	chr5:179566792-179566842	PANC-1	pancreas:	n/a
16	chr5:179566792-179566842	NB4	blood:	n/a
17	chr5:179566792-179566842	AG04449	skin:	fetal
18	chr5:179566792-179566842	HUVEC	blood vessel:	n/a
19	chr5:179566792-179566842	GM12878	blood:	n/a
20	chr5:179566792-179566842	LNCaP	prostate:	n/a
21	chr5:179566792-179566842	AG10803	skin:	n/a
22	chr5:179566792-179566842	CMK	blood:	n/a
23	chr5:179566792-179566842	SAEC	small airway:	n/a
24	chr5:179566792-179566842	MCF10A-Er-Src	breast:	n/a
25	chr5:179566792-179566842	U87	brain:	n/a
26	chr5:179566792-179566842	HepG2	liver:	n/a
27	chr5:179566792-179566842	Hepatocyte	liver:	n/a
28	chr5:179566792-179566842	K562	blood:	n/a
29	chr5:179566792-179566842	GM12891	blood:	n/a
30	chr5:179566792-179566842	SK-N-MC	brain:	n/a
31	chr5:179566792-179566842	T-47D	breast:	n/a
32	chr5:179566792-179566842	MCF-7	breast:	n/a
33	chr5:179566792-179566842	SK-N-SH	brain:	n/a
34	chr5:179566792-179566842	AoSMC	blood vessel:	n/a
35	chr5:179566792-179566842	HCM	heart:	n/a
36	chr5:179566792-179566842	HL-60	blood:	n/a
37	chr5:179566792-179566842	HIPEpiC	eye:	n/a
38	chr5:179566792-179566842	AG09319	gingival:	n/a
39	chr5:179566792-179566842	SK-N-SH_RA	brain:	n/a
40	chr5:179566792-179566842	GM06990	blood:	n/a
41	chr5:179566792-179566842	BE2_C	brain:	n/a
42	chr5:179566792-179566842	NHDF-neo	bronchial:	n/a
43	chr5:179566792-179566842	PrEC	prostate:	n/a
44	chr5:179566792-179566842	Caco-2	colon:	n/a
45	chr5:179566792-179566842	HEK293	kidney:	embryo
46	chr5:179566792-179566842	SKMC	muscle:	n/a
47	chr5:179566792-179566842	HEEpiC	esophagus:	n/a
48	chr5:179566792-179566842	NH-A	brain:	n/a
49	chr5:179566792-179566842	AG09309	skin:	n/a
50	chr5:179566792-179566842	HCPEpiC	choroid plexus:	n/a

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

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr5:179561122..179566111-chr5:179566279..179570642,6	MCF-7	breast:

No data

Variant related genes	Relation type
RASGEF1C	CpG island
ENSG00000146090	Chromatin interaction

Extended variants
information (count: 24 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:13)

rs_ID	r²[population]
rs10067359	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs10072480	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs10903249	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs4700715	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs4700878	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs4700879	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs6601084	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs6601085	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs6878491	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs6878835	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs6882752	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs6897364	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs7707107	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:11 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv531997	chr5:179107599-179588082	Enhancers Strong transcription Flanking Active TSS ZNF genes & repeats Weak transcription Genic enhancers Flanking Bivalent TSS/Enh Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	339 gene(s)	inside rSNPs	diseases
2	nsv1030437	chr5:179235423-179649944	Enhancers Strong transcription Flanking Active TSS Active TSS Weak transcription ZNF genes & repeats Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	189 gene(s)	inside rSNPs	diseases
3	nsv537982	chr5:179235423-179649944	Active TSS Weak transcription Flanking Active TSS Genic enhancers Strong transcription Bivalent/Poised TSS Enhancers Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	189 gene(s)	inside rSNPs	diseases
4	nsv948909	chr5:179249099-179772640	Weak transcription Active TSS Flanking Active TSS Enhancers Strong transcription ZNF genes & repeats Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	175 gene(s)	inside rSNPs	diseases
5	nsv1033706	chr5:179402769-179806356	Strong transcription Weak transcription Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Enhancers Flanking Bivalent TSS/Enh Flanking Active TSS Active TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	165 gene(s)	inside rSNPs	diseases
6	nsv883287	chr5:179526789-179584778	Flanking Bivalent TSS/Enh Weak transcription Flanking Active TSS Enhancers Bivalent Enhancer Genic enhancers ZNF genes & repeats Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' Strong transcription	TF binding region CpG island Chromatin interactive region	4 gene(s)	inside rSNPs	diseases
7	esv2758032	chr5:179534477-179729944	Strong transcription Weak transcription Flanking Bivalent TSS/Enh Enhancers Active TSS ZNF genes & repeats Bivalent Enhancer Flanking Active TSS Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	16 gene(s)	inside rSNPs	diseases
8	esv2759398	chr5:179534477-179729944	Weak transcription Strong transcription Enhancers ZNF genes & repeats Bivalent/Poised TSS Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	16 gene(s)	inside rSNPs	diseases
9	nsv883288	chr5:179537727-179608656	Weak transcription Enhancers Flanking Active TSS Bivalent Enhancer Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Strong transcription Genic enhancers Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region	4 gene(s)	inside rSNPs	diseases
10	nsv1030036	chr5:179543546-179610871	Weak transcription Flanking Active TSS Enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers Active TSS ZNF genes & repeats Strong transcription Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	4 gene(s)	inside rSNPs	diseases
11	nsv830562	chr5:179555313-179622441	Genic enhancers Enhancers Weak transcription Bivalent Enhancer Flanking Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Active TSS Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region	2 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:16 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:179555400-179571000	Weak transcription	Right Atrium	heart
2	chr5:179562600-179567000	Weak transcription	Brain Inferior Temporal Lobe	brain
3	chr5:179562800-179567000	Weak transcription	Brain Cingulate Gyrus	brain
4	chr5:179562800-179567400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
5	chr5:179564200-179567400	Weak transcription	Brain Germinal Matrix	brain
6	chr5:179565800-179567600	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
7	chr5:179566000-179570600	Enhancers	Cortex derived primary cultured neurospheres	brain
8	chr5:179566200-179567000	Bivalent Enhancer	Fetal Muscle Trunk	muscle
9	chr5:179566600-179567200	Bivalent Enhancer	Fetal Muscle Leg	muscle
10	chr5:179566600-179567600	Weak transcription	Fetal Brain Female	brain
11	chr5:179566600-179567800	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
12	chr5:179566600-179567800	Enhancers	Brain Angular Gyrus	brain
13	chr5:179566600-179568000	Enhancers	Brain Hippocampus Middle	brain
14	chr5:179566600-179570200	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
15	chr5:179566800-179567800	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
16	chr5:179566800-179568000	Enhancers	Brain Substantia Nigra	brain

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