Variant report

Variant	rs9283939
Chromosome Location	chr8:104060202-104060203
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr8:103873846..103876788-chr8:104058991..104062713,4	MCF-7	breast:
2	chr8:103873603..103877584-chr8:104060030..104063017,4	K562	blood:
3	chr8:104059291..104063011-chr8:104063018..104066980,5	K562	blood:
4	chr8:104059266..104060791-chr8:104062781..104065186,2	K562	blood:

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-KB-1507C5.2.1-2	chr8:104058991-104060359	l_3662_chr8:104011570-104059274_thyroid

Variant related genes	Relation type
ENSG00000155097	Chromatin interaction
ENSG00000253320	Chromatin interaction
ENSG00000155096	Chromatin interaction

Extended variants
information (count: 18 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:17)

rs_ID	r²[population]
rs10099825	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs13271522	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.91[AFR][1000 genomes];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17200336	0.81[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.94[TSI][hapmap];0.90[YRI][hapmap];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2015790	0.87[AFR][1000 genomes];0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2047378	0.82[YRI][hapmap]
rs2048550	0.82[YRI][hapmap]
rs2270673	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];0.94[TSI][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2515194	0.82[YRI][hapmap]
rs2515198	0.88[CEU][hapmap];0.94[CHB][hapmap];0.84[ASN][1000 genomes]
rs28460720	0.89[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs35242416	0.85[AFR][1000 genomes];0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs3779909	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.94[TSI][hapmap];1.00[YRI][hapmap];0.91[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4147529	1.00[ASW][hapmap];0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];0.91[TSI][hapmap];1.00[YRI][hapmap];0.89[AFR][1000 genomes];0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4734068	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4734683	0.87[AFR][1000 genomes];0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4734684	1.00[ASW][hapmap];1.00[CEU][hapmap];0.89[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.89[MKK][hapmap];0.94[TSI][hapmap];1.00[YRI][hapmap];0.88[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs868936	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.89[AFR][1000 genomes];0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]

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	esv33118	chr8:103358567-104068172	Enhancers Weak transcription Flanking Active TSS Active TSS Strong transcription Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer Genic enhancers Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	145 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs9283939	CTHRC1	cis	cerebellum	SCAN
rs9283939	ATP6V1C1	cis	cerebellum	SCAN

Chromatin state (count:123 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr8:104034200-104068800	Weak transcription	Small Intestine	intestine
2	chr8:104034400-104069400	Weak transcription	Esophagus	oesophagus
3	chr8:104034600-104063600	Weak transcription	HSMMtube	muscle
4	chr8:104034600-104068400	Weak transcription	Right Ventricle	heart
5	chr8:104034800-104065600	Weak transcription	Fetal Kidney	kidney
6	chr8:104034800-104074600	Weak transcription	NHEK	skin
7	chr8:104035400-104061800	Weak transcription	Sigmoid Colon	Sigmoid Colon
8	chr8:104035400-104071200	Weak transcription	Brain Angular Gyrus	brain
9	chr8:104035800-104061800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
10	chr8:104036200-104065200	Weak transcription	Colon Smooth Muscle	Colon
11	chr8:104036800-104061200	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
12	chr8:104037200-104063400	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
13	chr8:104037200-104071400	Weak transcription	Fetal Brain Female	brain
14	chr8:104038000-104066800	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
15	chr8:104039000-104069400	Weak transcription	Spleen	Spleen
16	chr8:104039800-104061200	Weak transcription	GM12878-XiMat	blood
17	chr8:104040200-104071400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
18	chr8:104040600-104071400	Weak transcription	Pancreas	Pancrea
19	chr8:104043800-104068200	Weak transcription	H9 Cell Line	embryonic stem cell
20	chr8:104044000-104066400	Weak transcription	HMEC	breast
21	chr8:104046000-104068000	Weak transcription	NHLF	lung
22	chr8:104048400-104063800	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
23	chr8:104050400-104069200	Weak transcription	Aorta	Aorta
24	chr8:104050400-104086000	Weak transcription	Primary T killer memory cells from peripheral blood	blood
25	chr8:104050600-104066600	Weak transcription	Ovary	ovary
26	chr8:104050600-104089600	Weak transcription	Psoas Muscle	Psoas
27	chr8:104050800-104061400	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
28	chr8:104050800-104062400	Weak transcription	Brain Inferior Temporal Lobe	brain
29	chr8:104050800-104067800	Weak transcription	Brain Substantia Nigra	brain
30	chr8:104050800-104069800	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
31	chr8:104051600-104087400	Weak transcription	Pancreatic Islets	Pancreatic Islet
32	chr8:104052600-104065400	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
33	chr8:104052600-104066600	Strong transcription	Primary monocytes fromperipheralblood	blood
34	chr8:104052800-104082200	Weak transcription	Placenta Amnion	Placenta Amnion
35	chr8:104053000-104066800	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
36	chr8:104053000-104067000	Strong transcription	Monocytes-CD14+_RO01746	blood
37	chr8:104053000-104068600	Strong transcription	Duodenum Smooth Muscle	Duodenum
38	chr8:104053200-104064000	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
39	chr8:104053200-104073000	Weak transcription	Colonic Mucosa	Colon
40	chr8:104053200-104085600	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
41	chr8:104053600-104063400	Strong transcription	Liver	Liver
42	chr8:104053600-104083800	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
43	chr8:104053800-104067600	Strong transcription	Primary B cells from cord blood	blood
44	chr8:104054000-104084400	Strong transcription	Fetal Thymus	thymus
45	chr8:104054200-104083400	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
46	chr8:104054200-104083800	Strong transcription	Primary hematopoietic stem cells short term culture	blood
47	chr8:104054200-104084400	Strong transcription	Primary B cells from peripheral blood	blood
48	chr8:104055000-104061600	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
49	chr8:104055000-104065000	Weak transcription	Brain Cingulate Gyrus	brain
50	chr8:104055200-104087000	Weak transcription	K562	blood

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links