Variant report

Variant	rs4942739
Chromosome Location	chr13:48606794-48606795
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr13:48605353..48607010-chr13:48845473..48847893,2	K562	blood:
2	chr13:48600867..48607443-chr13:48607705..48615093,10	MCF-7	breast:

Variant related genes	Relation type
ENSG00000136159	Chromatin interaction
ENSG00000136143	Chromatin interaction

Extended variants
information (count: 83 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:81)

rs_ID	r²[population]
rs1098354	0.83[ASN][1000 genomes]
rs11148100	0.84[AFR][1000 genomes];0.83[AMR][1000 genomes];0.82[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs1185727	0.92[AMR][1000 genomes];0.88[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1326135	0.81[ASN][1000 genomes]
rs1544078	0.81[AMR][1000 genomes]
rs17071168	0.85[ASN][1000 genomes]
rs1886975	0.81[AMR][1000 genomes];0.82[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2031590	0.87[AFR][1000 genomes];0.85[AMR][1000 genomes];0.85[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2148244	0.82[AFR][1000 genomes];0.81[AMR][1000 genomes];0.82[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2182376	0.81[AFR][1000 genomes];0.82[ASN][1000 genomes]
rs2296574	0.81[ASN][1000 genomes]
rs2406693	0.81[AMR][1000 genomes];0.82[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2406697	0.81[AFR][1000 genomes];0.82[ASN][1000 genomes]
rs4245347	0.82[AFR][1000 genomes];0.81[AMR][1000 genomes];0.82[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs4447314	0.82[ASN][1000 genomes]
rs4522322	0.90[AFR][1000 genomes];0.88[AMR][1000 genomes];0.86[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs4941621	0.92[AFR][1000 genomes];0.88[AMR][1000 genomes];0.86[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs4942726	0.83[ASN][1000 genomes]
rs4942728	0.85[AFR][1000 genomes];0.83[AMR][1000 genomes];0.82[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs4942730	0.81[AFR][1000 genomes];0.85[ASN][1000 genomes]
rs4942735	0.81[ASN][1000 genomes]
rs61973260	0.81[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs6561424	0.81[ASN][1000 genomes]
rs6561430	0.81[ASN][1000 genomes]
rs6561431	0.81[AFR][1000 genomes];0.83[ASN][1000 genomes]
rs6561432	0.82[AFR][1000 genomes];0.83[ASN][1000 genomes]
rs7318770	0.92[AFR][1000 genomes];0.88[AMR][1000 genomes];0.86[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7319245	0.92[AFR][1000 genomes];0.88[AMR][1000 genomes];0.86[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7325189	0.92[AFR][1000 genomes];0.90[AMR][1000 genomes];0.86[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7325437	0.82[AFR][1000 genomes];0.83[ASN][1000 genomes]
rs7326889	0.82[AFR][1000 genomes];0.81[AMR][1000 genomes];0.82[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs7327730	0.81[AFR][1000 genomes];0.82[ASN][1000 genomes]
rs7328525	0.90[AFR][1000 genomes];0.88[AMR][1000 genomes];0.86[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7328537	0.90[AFR][1000 genomes];0.88[AMR][1000 genomes];0.86[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7330130	0.82[AFR][1000 genomes];0.83[ASN][1000 genomes]
rs7330913	0.81[ASN][1000 genomes]
rs7331285	0.82[AFR][1000 genomes];0.83[ASN][1000 genomes]
rs7332304	0.81[AFR][1000 genomes];0.83[ASN][1000 genomes]
rs7337004	0.81[AFR][1000 genomes];0.83[ASN][1000 genomes]
rs7337744	0.81[ASN][1000 genomes]
rs7338373	0.82[AFR][1000 genomes];0.83[ASN][1000 genomes]
rs7990244	0.85[AFR][1000 genomes];0.86[AMR][1000 genomes];0.86[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7990266	0.85[AFR][1000 genomes];0.86[AMR][1000 genomes];0.86[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7994359	0.80[AMR][1000 genomes]
rs7996580	0.90[AFR][1000 genomes];0.92[AMR][1000 genomes];0.87[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7997802	0.86[AFR][1000 genomes];0.85[AMR][1000 genomes];0.85[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7998116	0.82[ASN][1000 genomes]
rs7998260	0.87[AFR][1000 genomes];0.85[AMR][1000 genomes];0.85[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7998497	0.86[AFR][1000 genomes];0.85[AMR][1000 genomes];0.83[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7998998	0.82[ASN][1000 genomes]
rs8000164	0.87[AFR][1000 genomes];0.85[AMR][1000 genomes];0.85[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs8001432	0.89[AFR][1000 genomes];0.85[AMR][1000 genomes];0.85[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs9316343	0.92[AFR][1000 genomes];0.88[AMR][1000 genomes];0.86[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs9316344	0.81[AFR][1000 genomes];0.82[ASN][1000 genomes]
rs9526422	0.82[AFR][1000 genomes];0.83[AMR][1000 genomes];0.82[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs9526429	0.81[ASN][1000 genomes]
rs9526430	0.81[AFR][1000 genomes];0.82[ASN][1000 genomes]
rs9526433	0.93[AFR][1000 genomes];0.88[AMR][1000 genomes];0.86[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs9534876	0.81[AMR][1000 genomes]
rs9534898	0.81[ASN][1000 genomes]
rs9534901	0.81[ASN][1000 genomes]
rs9534903	0.90[AFR][1000 genomes];0.88[AMR][1000 genomes];0.86[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs9534904	0.81[AFR][1000 genomes];0.82[ASN][1000 genomes]
rs9534905	0.81[AFR][1000 genomes];0.82[ASN][1000 genomes]
rs9534906	0.82[ASN][1000 genomes]
rs9534907	0.92[AFR][1000 genomes];0.88[AMR][1000 genomes];0.86[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs9534908	0.81[AFR][1000 genomes];0.82[ASN][1000 genomes]
rs9534912	0.81[AFR][1000 genomes];0.82[ASN][1000 genomes]
rs9534913	0.92[AFR][1000 genomes];0.88[AMR][1000 genomes];0.86[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs9534918	0.82[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs9534919	0.87[AFR][1000 genomes];0.82[AMR][1000 genomes];0.83[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs9534923	0.93[AFR][1000 genomes];0.88[AMR][1000 genomes];0.86[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs9534926	0.81[AFR][1000 genomes];0.82[ASN][1000 genomes]
rs9534929	0.83[AFR][1000 genomes];0.85[ASN][1000 genomes]
rs9567958	0.81[AMR][1000 genomes];0.82[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs9567964	0.82[AFR][1000 genomes];0.81[AMR][1000 genomes];0.82[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs9567972	0.81[ASN][1000 genomes]
rs9567976	0.81[AFR][1000 genomes];0.82[ASN][1000 genomes]
rs9567979	0.84[AFR][1000 genomes]
rs9567980	0.97[AFR][1000 genomes];0.94[AMR][1000 genomes];0.87[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs9567986	0.89[AMR][1000 genomes];0.87[EUR][1000 genomes];0.90[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv430556	chr13:48516799-48679099	ZNF genes & repeats Enhancers Weak transcription Strong transcription Flanking Active TSS Genic enhancers Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	40 gene(s)	inside rSNPs	diseases
2	nsv832601	chr13:48569952-48735939	Strong transcription Enhancers Weak transcription Flanking Active TSS Active TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	42 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs4942739	SUCLA2	Cis_1M	lymphoblastoid	RTeQTL
rs4942739	SUCLA2	cis	Muscle Skeletal	GTEx

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr13:48576000-48610800	Weak transcription	Primary T cells fromperipheralblood	blood
2	chr13:48576000-48611400	Weak transcription	Left Ventricle	heart
3	chr13:48576600-48610200	Weak transcription	Breast Myoepithelial Primary Cells	Breast
4	chr13:48584000-48610800	Weak transcription	Rectal Mucosa Donor 31	rectum
5	chr13:48584200-48611200	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
6	chr13:48599600-48610200	Weak transcription	HepG2	liver
7	chr13:48602000-48611200	Weak transcription	Brain Anterior Caudate	brain
8	chr13:48602400-48611000	Weak transcription	Primary T helper naive cells from peripheral blood	blood
9	chr13:48602600-48610800	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
10	chr13:48602800-48611400	Weak transcription	Aorta	Aorta
11	chr13:48603000-48610400	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
12	chr13:48603000-48611000	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
13	chr13:48603200-48610800	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
14	chr13:48603400-48610200	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
15	chr13:48603400-48610800	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
16	chr13:48603800-48610800	Weak transcription	Rectal Smooth Muscle	rectum
17	chr13:48603800-48611400	Weak transcription	Ovary	ovary
18	chr13:48604000-48608200	ZNF genes & repeats	Primary hematopoietic stem cells	blood
19	chr13:48604600-48609000	ZNF genes & repeats	Primary hematopoietic stem cells G-CSF-mobilized Male	--
20	chr13:48604800-48607000	ZNF genes & repeats	Fetal Intestine Small	intestine
21	chr13:48604800-48607400	ZNF genes & repeats	Monocytes-CD14+_RO01746	blood
22	chr13:48604800-48608200	ZNF genes & repeats	Fetal Lung	lung
23	chr13:48604800-48609200	ZNF genes & repeats	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
24	chr13:48605000-48607000	ZNF genes & repeats	Primary B cells from cord blood	blood
25	chr13:48605000-48607200	ZNF genes & repeats	Primary monocytes fromperipheralblood	blood
26	chr13:48605000-48607200	ZNF genes & repeats	Fetal Muscle Leg	muscle
27	chr13:48605000-48608400	ZNF genes & repeats	HUES64 Cell Line	embryonic stem cell
28	chr13:48605000-48611000	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
29	chr13:48605200-48607000	ZNF genes & repeats	Primary hematopoietic stem cells short term culture	blood
30	chr13:48605200-48609200	ZNF genes & repeats	Dnd41	blood
31	chr13:48605400-48607000	ZNF genes & repeats	Fetal Stomach	stomach
32	chr13:48605400-48607200	Strong transcription	Fetal Kidney	kidney
33	chr13:48605400-48610800	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
34	chr13:48605400-48610800	Weak transcription	Liver	Liver
35	chr13:48605400-48610800	Weak transcription	NHLF	lung
36	chr13:48605600-48608600	Weak transcription	Primary T cells from cord blood	blood
37	chr13:48605600-48609000	Weak transcription	Rectal Mucosa Donor 29	rectum
38	chr13:48605600-48610200	Weak transcription	Primary T helper cells PMA-I stimulated	--
39	chr13:48605800-48607200	ZNF genes & repeats	Foreskin Keratinocyte Primary Cells skin03	Skin
40	chr13:48606000-48607000	ZNF genes & repeats	Foreskin Keratinocyte Primary Cells skin02	Skin
41	chr13:48606000-48607000	ZNF genes & repeats	Fetal Thymus	thymus
42	chr13:48606000-48607200	ZNF genes & repeats	H1 Derived Mesenchymal Stem Cells	ES cell derived
43	chr13:48606200-48607000	ZNF genes & repeats	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
44	chr13:48606200-48607000	ZNF genes & repeats	ES-UCSF4 Cell Line	embryonic stem cell
45	chr13:48606200-48611000	Weak transcription	Primary T helper cells fromperipheralblood	blood
46	chr13:48606400-48610800	Weak transcription	Primary B cells from peripheral blood	blood
47	chr13:48606600-48610800	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
48	chr13:48606600-48610800	Weak transcription	Duodenum Mucosa	Duodenum
49	chr13:48606600-48611000	Weak transcription	Thymus	Thymus
50	chr13:48606600-48611400	Weak transcription	Sigmoid Colon	Sigmoid Colon

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links