Variant report

Variant	rs1128250
Chromosome Location	chr7:21956405-21956406
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 25 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:22)

rs_ID	r²[population]
rs10950883	0.87[AMR][1000 genomes];0.91[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12055905	0.86[AMR][1000 genomes];0.90[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12055908	0.88[AMR][1000 genomes];0.86[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs12539984	0.87[AMR][1000 genomes];0.90[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12673256	0.87[AMR][1000 genomes];0.91[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1919906	0.89[AMR][1000 genomes];0.87[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs4398800	0.83[AFR][1000 genomes]
rs55658106	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs57033293	0.91[AFR][1000 genomes];0.92[AMR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs57082026	0.88[AMR][1000 genomes];0.92[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs59258063	0.89[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs62445924	0.89[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs62445926	0.88[AMR][1000 genomes];0.92[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs62445928	0.87[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs62445933	0.85[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs62445935	0.87[ASN][1000 genomes]
rs6959493	0.89[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs6959806	0.91[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs6963571	0.88[AMR][1000 genomes];0.88[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs6978094	1.00[CEU][hapmap];0.95[GIH][hapmap];0.92[MEX][hapmap];0.96[TSI][hapmap];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs7798564	1.00[CEU][hapmap];1.00[CHB][hapmap];0.91[CHD][hapmap];0.95[GIH][hapmap];0.90[JPT][hapmap];0.87[MEX][hapmap];0.89[TSI][hapmap];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7807924	0.85[CEU][hapmap];1.00[CHB][hapmap];0.91[CHD][hapmap];0.95[GIH][hapmap];0.90[JPT][hapmap];0.83[MEX][hapmap];0.88[TSI][hapmap];0.87[AMR][1000 genomes];0.90[EUR][1000 genomes];0.93[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1018133	chr7:21740118-22055283	Active TSS Enhancers Strong transcription Weak transcription Flanking Active TSS Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	22 gene(s)	inside rSNPs	diseases
2	nsv830922	chr7:21793386-21964675	Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Strong transcription Genic enhancers Bivalent Enhancer Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region miRNA target site	3 gene(s)	inside rSNPs	diseases
3	nsv1027453	chr7:21918474-21982448	Enhancers Flanking Active TSS Genic enhancers Strong transcription Weak transcription Active TSS ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region miRNA target site	2 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs1128250	IL6	cis	cerebellum	SCAN
rs1128250	CDCA7L	Cis_1M	lymphoblastoid	RTeQTL
rs1128250	C7orf46	cis	parietal	SCAN
rs1128250	CDCA7L	cis	multi-tissue	Pritchard

Chromatin state (count:91 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:21933000-21963200	Weak transcription	A549	lung
2	chr7:21936600-21956600	Strong transcription	iPS-20b Cell Line	embryonic stem cell
3	chr7:21937200-21956600	Strong transcription	iPS-18 Cell Line	embryonic stem cell
4	chr7:21938600-21984000	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
5	chr7:21938800-21956600	Strong transcription	Primary T cells from cord blood	blood
6	chr7:21942400-21957200	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
7	chr7:21944000-21957400	Weak transcription	Colonic Mucosa	Colon
8	chr7:21944400-21956600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
9	chr7:21946200-21957600	Weak transcription	Placenta Amnion	Placenta Amnion
10	chr7:21946200-21963400	Weak transcription	Brain Hippocampus Middle	brain
11	chr7:21947800-21958000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
12	chr7:21948400-21960400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
13	chr7:21948800-21981000	Weak transcription	Sigmoid Colon	Sigmoid Colon
14	chr7:21950400-21960400	Weak transcription	Fetal Brain Female	brain
15	chr7:21950800-21956600	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
16	chr7:21951600-21982600	Weak transcription	HSMM	muscle
17	chr7:21952400-21963200	Weak transcription	Psoas Muscle	Psoas
18	chr7:21952600-21958400	Weak transcription	Skeletal Muscle Male	skeletal muscle
19	chr7:21952600-21977400	Weak transcription	NHDF-Ad	bronchial
20	chr7:21952800-21960000	Weak transcription	Skeletal Muscle Female	skeletal muscle
21	chr7:21952800-21963200	Weak transcription	Muscle Satellite Cultured Cells	--
22	chr7:21953400-21960200	Weak transcription	Brain Germinal Matrix	brain
23	chr7:21953600-21956600	Strong transcription	Primary hematopoietic stem cells short term culture	blood
24	chr7:21953600-21956600	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
25	chr7:21953600-21956600	Strong transcription	Fetal Thymus	thymus
26	chr7:21953600-21956800	Strong transcription	Primary hematopoietic stem cells	blood
27	chr7:21953600-21957000	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
28	chr7:21953800-21958200	Weak transcription	Left Ventricle	heart
29	chr7:21954000-21956600	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
30	chr7:21954000-21956600	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
31	chr7:21954200-21959000	Weak transcription	Right Atrium	heart
32	chr7:21954400-21958200	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
33	chr7:21954400-21958200	Weak transcription	Primary T helper cells PMA-I stimulated	--
34	chr7:21954400-21960400	Weak transcription	Brain Anterior Caudate	brain
35	chr7:21954400-21963200	Weak transcription	Hela-S3	cervix
36	chr7:21954600-21958400	Weak transcription	Colon Smooth Muscle	Colon
37	chr7:21954800-21956600	Strong transcription	Primary B cells from cord blood	blood
38	chr7:21954800-21956600	Weak transcription	NHLF	lung
39	chr7:21954800-21957200	Weak transcription	Primary T helper cells fromperipheralblood	blood
40	chr7:21954800-21957200	Weak transcription	Duodenum Mucosa	Duodenum
41	chr7:21954800-21957800	Weak transcription	Primary monocytes fromperipheralblood	blood
42	chr7:21954800-21961800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
43	chr7:21954800-21962800	Weak transcription	Pancreas	Pancrea
44	chr7:21954800-21966200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
45	chr7:21954800-21970400	Weak transcription	Liver	Liver
46	chr7:21954800-21971800	Weak transcription	Gastric	stomach
47	chr7:21955000-21956800	Weak transcription	Primary T cells fromperipheralblood	blood
48	chr7:21955000-21957000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
49	chr7:21955000-21957400	Strong transcription	Primary B cells from peripheral blood	blood
50	chr7:21955000-21958200	Weak transcription	Primary neutrophils fromperipheralblood	blood

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