Variant report

Variant	rs2979245
Chromosome Location	chr8:8939373-8939374
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr8:8931416..8936474-chr8:8938271..8941320,7	K562	blood:
2	chr8:8932762..8934557-chr8:8938134..8939929,2	MCF-7	breast:
3	chr8:8939297..8940892-chr8:9008509..9010684,2	K562	blood:
4	chr8:8935137..8938110-chr8:8938203..8940506,3	MCF-7	breast:
5	chr8:8938481..8944528-chr8:8944977..8948023,6	K562	blood:

Variant related genes	Relation type
ENSG00000173281	Chromatin interaction
ENSG00000253426	Chromatin interaction

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

rSNPs within LD-proxies of this variant (count:3)

rs_ID	r²[population]
rs2979244	0.87[AFR][1000 genomes];0.95[ASN][1000 genomes]
rs4841097	0.81[ASW][hapmap];0.81[CEU][hapmap];0.89[GIH][hapmap];0.82[MEX][hapmap];0.80[TSI][hapmap];0.80[YRI][hapmap];0.88[AMR][1000 genomes]
rs55911799	0.81[AMR][1000 genomes];0.86[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv890331	chr8:8093240-8971100	Weak transcription Enhancers Active TSS Strong transcription Flanking Active TSS ZNF genes & repeats Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	43 gene(s)	inside rSNPs	diseases
2	nsv917117	chr8:8621658-9313799	Active TSS Weak transcription Enhancers Flanking Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Strong transcription Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	43 gene(s)	inside rSNPs	diseases
3	nsv1022468	chr8:8857853-9209167	Enhancers Weak transcription Flanking Active TSS Strong transcription Active TSS Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	31 gene(s)	inside rSNPs	diseases
4	nsv539460	chr8:8857853-9209167	Enhancers Active TSS Weak transcription Strong transcription Flanking Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	31 gene(s)	inside rSNPs	diseases
5	nsv817373	chr8:8857854-9361049	Enhancers ZNF genes & repeats Weak transcription Active TSS Strong transcription Flanking Active TSS 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	36 gene(s)	inside rSNPs	diseases
6	nsv518456	chr8:8939125-8948469	Enhancers Weak transcription Flanking Active TSS Active TSS Bivalent Enhancer	Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	n/a

mRNA abundance (count:6)

SNP	Gene	Cis/trans	Tissue	Source
rs2979245	C8orf79	cis	cerebellum	SCAN
rs2979245	MFHAS1	cis	cerebellum	SCAN
rs2979245	PRSS55	cis	cerebellum	SCAN
rs2979245	FAM86B3P	cis	Esophagus Mucosa	GTEx
rs2979245	FLJ10661	cis	cerebellum	SCAN
rs2979245	PPP1R3B	cis	cerebellum	SCAN

Chromatin state (count:77 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr8:8924000-8939600	Weak transcription	Right Ventricle	heart
2	chr8:8929600-8940000	Weak transcription	Aorta	Aorta
3	chr8:8930200-8940400	Enhancers	Fetal Intestine Large	intestine
4	chr8:8931800-8940800	Enhancers	Fetal Intestine Small	intestine
5	chr8:8932600-8939600	Weak transcription	Ovary	ovary
6	chr8:8932600-8951800	Weak transcription	Pancreas	Pancrea
7	chr8:8932800-8945600	Weak transcription	Thymus	Thymus
8	chr8:8933000-8939400	Enhancers	K562	blood
9	chr8:8933200-8939400	Weak transcription	Fetal Lung	lung
10	chr8:8933200-8939600	Weak transcription	Rectal Smooth Muscle	rectum
11	chr8:8934200-8940000	Enhancers	Placenta Amnion	Placenta Amnion
12	chr8:8935000-8939600	Weak transcription	NHLF	lung
13	chr8:8935200-8939400	Weak transcription	HSMM	muscle
14	chr8:8935200-8939600	Weak transcription	Skeletal Muscle Female	skeletal muscle
15	chr8:8935400-8939400	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
16	chr8:8935400-8939400	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
17	chr8:8935400-8939400	Weak transcription	NH-A	brain
18	chr8:8935400-8939600	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
19	chr8:8935400-8939600	Weak transcription	HSMMtube	muscle
20	chr8:8935400-8959600	Weak transcription	HUES64 Cell Line	embryonic stem cell
21	chr8:8935600-8939400	Weak transcription	Skeletal Muscle Male	skeletal muscle
22	chr8:8935600-8939600	Weak transcription	Psoas Muscle	Psoas
23	chr8:8935600-8939600	Weak transcription	Right Atrium	heart
24	chr8:8935800-8940000	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
25	chr8:8936000-8940400	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
26	chr8:8936200-8940000	Enhancers	Primary T regulatory cells fromperipheralblood	blood
27	chr8:8936200-8940400	Enhancers	Primary T helper cells PMA-I stimulated	--
28	chr8:8936400-8940400	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
29	chr8:8936600-8939600	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
30	chr8:8936800-8939400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
31	chr8:8937000-8939600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
32	chr8:8937400-8940400	Enhancers	Primary T cells effector/memory enriched fromperipheralblood	blood
33	chr8:8937400-8940600	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
34	chr8:8937400-8943400	Enhancers	Hela-S3	cervix
35	chr8:8937600-8939400	Enhancers	HUVEC	blood vessel
36	chr8:8937800-8940400	Enhancers	Small Intestine	intestine
37	chr8:8937800-8940800	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
38	chr8:8937800-8940800	Enhancers	Primary hematopoietic stem cells short term culture	blood
39	chr8:8938000-8939400	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
40	chr8:8938000-8939400	Enhancers	Monocytes-CD14+_RO01746	blood
41	chr8:8938000-8939400	Weak transcription	NHDF-Ad	bronchial
42	chr8:8938000-8939600	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
43	chr8:8938000-8940400	Enhancers	Primary monocytes fromperipheralblood	blood
44	chr8:8938000-8940400	Enhancers	Sigmoid Colon	Sigmoid Colon
45	chr8:8938000-8945200	Weak transcription	Placenta	Placenta
46	chr8:8938000-8951800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
47	chr8:8938200-8939400	Enhancers	A549	lung
48	chr8:8938200-8939600	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
49	chr8:8938200-8939600	Enhancers	Rectal Mucosa Donor 31	rectum
50	chr8:8938200-8940400	Enhancers	Duodenum Mucosa	Duodenum

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