Variant report

Variant	rs1078368
Chromosome Location	chr5:58317865-58317866
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 9 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:5)

rs_ID	r²[population]
rs2036220	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2968003	1.00[CEU][hapmap];0.88[CHB][hapmap];0.94[JPT][hapmap];0.88[AMR][1000 genomes];0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2968005	0.81[LWK][hapmap];0.80[MKK][hapmap];0.89[YRI][hapmap]
rs2968016	0.90[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs7714708	0.94[CHB][hapmap];0.97[CHD][hapmap];1.00[JPT][hapmap];0.82[LWK][hapmap];0.83[YRI][hapmap];0.90[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv2830363	chr5:57893949-58555491	Weak transcription Active TSS Enhancers Flanking Active TSS Transcr. at gene 5' and 3' Strong transcription Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	8 gene(s)	inside rSNPs	diseases
2	nsv830312	chr5:58191579-58382226	Enhancers ZNF genes & repeats Active TSS Weak transcription Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS Strong transcription Flanking Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	3 gene(s)	inside rSNPs	diseases
3	nsv830313	chr5:58273724-58421098	Enhancers Weak transcription Active TSS Flanking Active TSS Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Strong transcription Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	3 gene(s)	inside rSNPs	diseases
4	nsv1032308	chr5:58312468-58371239	Enhancers Weak transcription Active TSS Flanking Active TSS Bivalent Enhancer ZNF genes & repeats Strong transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs1078368	RAB3C	cis	parietal	SCAN
rs1078368	IL6ST	cis	parietal	SCAN

Chromatin state (count:64 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:58279600-58330400	Weak transcription	Fetal Stomach	stomach
2	chr5:58281800-58321600	Weak transcription	Osteobl	bone
3	chr5:58286200-58330400	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
4	chr5:58286200-58330600	Weak transcription	Thymus	Thymus
5	chr5:58288800-58330600	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
6	chr5:58296000-58321600	Weak transcription	Aorta	Aorta
7	chr5:58299800-58318000	Weak transcription	Right Ventricle	heart
8	chr5:58302400-58321600	Weak transcription	Gastric	stomach
9	chr5:58307000-58322000	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
10	chr5:58310800-58323400	Weak transcription	Fetal Muscle Trunk	muscle
11	chr5:58313000-58333400	Weak transcription	Lung	lung
12	chr5:58313200-58325600	Weak transcription	Fetal Lung	lung
13	chr5:58313200-58330200	Weak transcription	Primary T helper naive cells from peripheral blood	blood
14	chr5:58314000-58318600	Strong transcription	Fetal Thymus	thymus
15	chr5:58314200-58318000	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
16	chr5:58314200-58318400	Enhancers	Fetal Heart	heart
17	chr5:58314400-58323200	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
18	chr5:58314600-58321600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
19	chr5:58314800-58318600	Enhancers	Skeletal Muscle Female	skeletal muscle
20	chr5:58314800-58323000	Weak transcription	Primary hematopoietic stem cells	blood
21	chr5:58315000-58325800	Weak transcription	Fetal Muscle Leg	muscle
22	chr5:58315200-58318600	Genic enhancers	Primary T cells from cord blood	blood
23	chr5:58315400-58318600	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
24	chr5:58315600-58318000	Weak transcription	Left Ventricle	heart
25	chr5:58316200-58318000	Enhancers	ES-WA7 Cell Line	embryonic stem cell
26	chr5:58316400-58318000	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
27	chr5:58316400-58318000	Enhancers	Skeletal Muscle Male	skeletal muscle
28	chr5:58316400-58318800	Enhancers	Colon Smooth Muscle	Colon
29	chr5:58316600-58318000	Enhancers	HUES6 Cell Line	embryonic stem cell
30	chr5:58316600-58318000	Enhancers	Duodenum Mucosa	Duodenum
31	chr5:58316600-58318200	Enhancers	Colonic Mucosa	Colon
32	chr5:58316600-58319200	Enhancers	Hela-S3	cervix
33	chr5:58316800-58318400	Enhancers	iPS-20b Cell Line	embryonic stem cell
34	chr5:58316800-58318400	Enhancers	Rectal Smooth Muscle	rectum
35	chr5:58316800-58318600	Strong transcription	Primary hematopoietic stem cells short term culture	blood
36	chr5:58316800-58318600	Enhancers	Pancreatic Islets	Pancreatic Islet
37	chr5:58316800-58318600	Enhancers	Rectal Mucosa Donor 29	rectum
38	chr5:58316800-58318600	Enhancers	Rectal Mucosa Donor 31	rectum
39	chr5:58316800-58318600	Transcr. at gene 5' and 3'	A549	lung
40	chr5:58317000-58318800	Genic enhancers	Primary T helper cells PMA-I stimulated	--
41	chr5:58317200-58318200	Genic enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
42	chr5:58317200-58318400	Genic enhancers	Primary T helper naive cells fromperipheralblood	blood
43	chr5:58317200-58322800	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
44	chr5:58317200-58323400	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
45	chr5:58317200-58331600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
46	chr5:58317400-58319800	Weak transcription	Fetal Kidney	kidney
47	chr5:58317400-58320600	Weak transcription	Fetal Intestine Large	intestine
48	chr5:58317400-58325200	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
49	chr5:58317600-58318000	Weak transcription	Primary T helper cells fromperipheralblood	blood
50	chr5:58317600-58318200	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived

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