Variant report

Variant	rs10001956
Chromosome Location	chr4:190866555-190866556
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr4:190860013..190863665-chr4:190864707..190867481,3	K562	blood:
2	chr4:190860570..190863518-chr4:190865417..190868067,2	K562	blood:

Variant related genes	Relation type
ENSG00000109536	Chromatin interaction
ENSG00000245685	Chromatin interaction

Extended variants
information (count: 39 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:39)

rs_ID	r²[population]
rs11132770	0.86[AFR][1000 genomes];0.92[AMR][1000 genomes];0.92[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs11132771	0.93[AMR][1000 genomes];0.93[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs1138718	0.80[AFR][1000 genomes];0.82[EUR][1000 genomes]
rs11736363	0.81[AMR][1000 genomes]
rs11736387	0.83[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs11736960	0.85[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs12646565	0.99[AFR][1000 genomes];0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12646667	0.98[AFR][1000 genomes];0.96[AMR][1000 genomes];0.93[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs12646672	0.89[EUR][1000 genomes]
rs12649488	0.98[AFR][1000 genomes];0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12649515	0.89[EUR][1000 genomes]
rs13121836	1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs13121986	1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs13133725	0.98[AFR][1000 genomes];0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs13133958	0.99[AFR][1000 genomes];0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs13146111	0.84[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs13148101	0.97[AFR][1000 genomes];0.92[AMR][1000 genomes];0.90[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs1961818	0.87[AMR][1000 genomes];0.87[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2037947	0.98[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2037948	0.93[AMR][1000 genomes];0.93[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2078634	0.87[AMR][1000 genomes];0.88[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2411530	0.81[EUR][1000 genomes]
rs2411549	0.89[AFR][1000 genomes];0.92[AMR][1000 genomes];0.91[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2411550	0.81[ASN][1000 genomes]
rs3775989	0.85[EUR][1000 genomes]
rs4145515	0.96[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4145516	0.92[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs4145517	0.97[AMR][1000 genomes];0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6553396	0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6816856	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6820684	0.95[AMR][1000 genomes];0.91[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs6837422	0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7657916	0.96[EUR][1000 genomes]
rs7658339	0.95[EUR][1000 genomes]
rs7668489	0.88[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7675870	0.87[EUR][1000 genomes]
rs7691161	0.92[EUR][1000 genomes]
rs9992042	0.92[EUR][1000 genomes]
rs9996679	0.85[AFR][1000 genomes];0.99[AMR][1000 genomes];0.95[EUR][1000 genomes];0.89[ASN][1000 genomes]

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs10001956	AF146191.4	cis	Thyroid	GTEx
rs10001956	LOC728339	cis	brain	BrainEAC
rs10001956	AF146191.4	cis	Esophagus Muscularis	GTEx

Chromatin state (count:93 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:190862600-190868800	Weak transcription	Lung	lung
2	chr4:190862600-190868800	Weak transcription	Pancreas	Pancrea
3	chr4:190862600-190869800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
4	chr4:190862600-190881000	Weak transcription	Spleen	Spleen
5	chr4:190862800-190867000	ZNF genes & repeats	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
6	chr4:190863000-190866600	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
7	chr4:190863000-190880800	Weak transcription	Brain Angular Gyrus	brain
8	chr4:190863200-190866600	Weak transcription	Stomach Mucosa	stomach
9	chr4:190863200-190866600	Weak transcription	Hela-S3	cervix
10	chr4:190863200-190868800	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
11	chr4:190863200-190868800	Weak transcription	Rectal Mucosa Donor 31	rectum
12	chr4:190863200-190869800	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
13	chr4:190863200-190869800	Weak transcription	Left Ventricle	heart
14	chr4:190863200-190873800	Weak transcription	Placenta	Placenta
15	chr4:190863200-190874600	Weak transcription	Fetal Intestine Large	intestine
16	chr4:190863200-190875600	Weak transcription	Fetal Thymus	thymus
17	chr4:190863200-190876000	Weak transcription	Stomach Smooth Muscle	stomach
18	chr4:190863200-190876400	Weak transcription	Osteobl	bone
19	chr4:190863200-190879400	Weak transcription	Gastric	stomach
20	chr4:190863200-190880400	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
21	chr4:190863200-190880400	Weak transcription	Fetal Intestine Small	intestine
22	chr4:190863200-190880800	Weak transcription	HSMMtube	muscle
23	chr4:190863200-190882000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
24	chr4:190863400-190868800	Weak transcription	Right Atrium	heart
25	chr4:190863400-190875200	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
26	chr4:190863600-190868800	Weak transcription	Thymus	Thymus
27	chr4:190863600-190869000	Weak transcription	Primary T cells fromperipheralblood	blood
28	chr4:190863600-190877200	Weak transcription	Primary hematopoietic stem cells	blood
29	chr4:190863600-190877200	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
30	chr4:190863600-190878800	Weak transcription	Brain Germinal Matrix	brain
31	chr4:190863600-190882000	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
32	chr4:190863800-190866600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
33	chr4:190863800-190866600	Weak transcription	Primary B cells from peripheral blood	blood
34	chr4:190863800-190866600	Weak transcription	Muscle Satellite Cultured Cells	--
35	chr4:190863800-190866600	Weak transcription	Brain Hippocampus Middle	brain
36	chr4:190863800-190866600	Weak transcription	Duodenum Mucosa	Duodenum
37	chr4:190863800-190866600	Weak transcription	Fetal Brain Male	brain
38	chr4:190863800-190866800	Weak transcription	Fetal Kidney	kidney
39	chr4:190863800-190868000	Weak transcription	Fetal Stomach	stomach
40	chr4:190863800-190868800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
41	chr4:190863800-190868800	Weak transcription	Right Ventricle	heart
42	chr4:190863800-190868800	Weak transcription	Sigmoid Colon	Sigmoid Colon
43	chr4:190863800-190870200	Weak transcription	Colonic Mucosa	Colon
44	chr4:190863800-190876000	Weak transcription	Skeletal Muscle Female	skeletal muscle
45	chr4:190863800-190880200	Weak transcription	Skeletal Muscle Male	skeletal muscle
46	chr4:190863800-190881000	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
47	chr4:190864000-190866600	Weak transcription	Adipose Nuclei	Adipose
48	chr4:190864000-190875400	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
49	chr4:190864000-190878400	Weak transcription	A549	lung
50	chr4:190864200-190866600	Weak transcription	Breast Myoepithelial Primary Cells	Breast

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links