Variant report

Variant	rs4683649
Chromosome Location	chr3:141644097-141644098
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 64 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:62)

rs_ID	r²[population]
rs10755098	0.84[ASN][1000 genomes]
rs10935439	0.83[AFR][1000 genomes];0.84[ASN][1000 genomes]
rs10935440	0.83[AFR][1000 genomes];0.84[ASN][1000 genomes]
rs10935441	0.83[AFR][1000 genomes];0.84[ASN][1000 genomes]
rs10935442	0.84[ASN][1000 genomes]
rs10935443	0.84[ASN][1000 genomes]
rs10935446	1.00[AFR][1000 genomes];0.90[EUR][1000 genomes]
rs10935447	1.00[AFR][1000 genomes];0.90[EUR][1000 genomes]
rs11539489	0.81[ASN][1000 genomes]
rs11569259	0.82[EUR][1000 genomes]
rs11569262	0.82[EUR][1000 genomes]
rs11569278	0.82[EUR][1000 genomes]
rs11569281	0.85[EUR][1000 genomes]
rs11569291	0.85[EUR][1000 genomes]
rs11706195	0.84[ASN][1000 genomes]
rs11707100	1.00[AFR][1000 genomes];0.88[EUR][1000 genomes]
rs11707427	0.83[AFR][1000 genomes];0.84[ASN][1000 genomes]
rs11710245	0.86[ASN][1000 genomes]
rs11711748	1.00[AFR][1000 genomes];0.90[EUR][1000 genomes]
rs11713023	1.00[AFR][1000 genomes];0.90[EUR][1000 genomes]
rs11721024	0.84[ASN][1000 genomes]
rs11844	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12486398	0.84[ASN][1000 genomes]
rs12487977	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12487983	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12490893	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12494971	1.00[AFR][1000 genomes];0.90[EUR][1000 genomes]
rs12497112	0.90[EUR][1000 genomes]
rs12497443	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1560411	0.81[ASN][1000 genomes]
rs16851892	0.84[ASN][1000 genomes]
rs2115935	0.84[ASN][1000 genomes]
rs2288634	1.00[AFR][1000 genomes];0.88[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2288635	1.00[AFR][1000 genomes];0.88[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2288636	1.00[AFR][1000 genomes];0.88[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2861382	0.82[ASN][1000 genomes]
rs34071952	0.83[AFR][1000 genomes];0.91[AMR][1000 genomes];0.87[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs36038301	0.84[ASN][1000 genomes]
rs3762726	0.90[EUR][1000 genomes]
rs3792410	0.86[ASN][1000 genomes]
rs3792411	0.86[ASN][1000 genomes]
rs3804772	1.00[AFR][1000 genomes];0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs3804773	0.86[ASN][1000 genomes]
rs3828398	1.00[AFR][1000 genomes];0.88[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4683412	1.00[AFR][1000 genomes];0.82[AMR][1000 genomes];0.93[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs4683413	0.82[EUR][1000 genomes]
rs4683414	0.82[EUR][1000 genomes]
rs4683638	0.83[AFR][1000 genomes];0.84[ASN][1000 genomes]
rs4683639	0.84[ASN][1000 genomes]
rs4683640	0.84[ASN][1000 genomes]
rs4683641	0.84[ASN][1000 genomes]
rs4683642	0.84[ASN][1000 genomes]
rs4683643	0.84[ASN][1000 genomes]
rs4683644	0.84[ASN][1000 genomes]
rs4683646	0.86[ASN][1000 genomes]
rs4683647	0.84[ASN][1000 genomes]
rs4683651	1.00[AFR][1000 genomes];0.94[AMR][1000 genomes];0.92[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4683652	0.97[EUR][1000 genomes]
rs55945175	0.84[ASN][1000 genomes]
rs59122181	0.83[AFR][1000 genomes];0.84[ASN][1000 genomes]
rs745966	1.00[AFR][1000 genomes];0.82[AMR][1000 genomes];0.92[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs7616903	0.84[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	nsv949709	chr3:141295050-142178144	Weak transcription Strong transcription Flanking Active TSS Enhancers Genic enhancers Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	61 gene(s)	inside rSNPs	diseases
2	nsv1013352	chr3:141541105-141870293	Weak transcription Enhancers Strong transcription Genic enhancers Flanking Active TSS ZNF genes & repeats 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	27 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs4683649	TFDP2	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:120 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:141597000-141646400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
2	chr3:141616200-141646600	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
3	chr3:141616200-141648600	Weak transcription	Pancreatic Islets	Pancreatic Islet
4	chr3:141620800-141646800	Weak transcription	Gastric	stomach
5	chr3:141621000-141646600	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
6	chr3:141621000-141670800	Weak transcription	Small Intestine	intestine
7	chr3:141622000-141645000	Strong transcription	Dnd41	blood
8	chr3:141622000-141647600	Strong transcription	Primary hematopoietic stem cells short term culture	blood
9	chr3:141622400-141647000	Strong transcription	HUES48 Cell Line	embryonic stem cell
10	chr3:141622600-141644800	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
11	chr3:141623600-141652400	Strong transcription	Fetal Thymus	thymus
12	chr3:141624600-141649200	Weak transcription	Brain Substantia Nigra	brain
13	chr3:141625600-141647200	Weak transcription	Liver	Liver
14	chr3:141625600-141668400	Weak transcription	Primary neutrophils fromperipheralblood	blood
15	chr3:141626600-141659000	Weak transcription	Pancreas	Pancrea
16	chr3:141627400-141646600	Weak transcription	Skeletal Muscle Female	skeletal muscle
17	chr3:141627600-141646400	Weak transcription	Brain Inferior Temporal Lobe	brain
18	chr3:141627600-141649200	Weak transcription	Primary B cells from peripheral blood	blood
19	chr3:141627800-141652600	Weak transcription	Brain Anterior Caudate	brain
20	chr3:141628200-141673600	Weak transcription	Colon Smooth Muscle	Colon
21	chr3:141628600-141646400	Weak transcription	Brain Cingulate Gyrus	brain
22	chr3:141628600-141658800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
23	chr3:141628600-141669000	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
24	chr3:141628800-141646000	Weak transcription	Stomach Smooth Muscle	stomach
25	chr3:141628800-141669800	Weak transcription	Fetal Lung	lung
26	chr3:141628800-141674000	Weak transcription	Brain Hippocampus Middle	brain
27	chr3:141629000-141739200	Weak transcription	Psoas Muscle	Psoas
28	chr3:141630000-141647000	Strong transcription	Primary monocytes fromperipheralblood	blood
29	chr3:141630600-141647400	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
30	chr3:141630600-141647400	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
31	chr3:141631200-141647600	Strong transcription	Monocytes-CD14+_RO01746	blood
32	chr3:141632000-141644200	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
33	chr3:141632000-141647400	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
34	chr3:141632000-141648800	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
35	chr3:141632200-141645000	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
36	chr3:141632200-141647800	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
37	chr3:141632200-141648000	Strong transcription	HUES6 Cell Line	embryonic stem cell
38	chr3:141632400-141654000	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
39	chr3:141633000-141659000	Weak transcription	NHLF	lung
40	chr3:141633600-141648000	Strong transcription	HUES64 Cell Line	embryonic stem cell
41	chr3:141633800-141646000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
42	chr3:141634200-141648600	Weak transcription	Aorta	Aorta
43	chr3:141634200-141682000	Weak transcription	Brain Angular Gyrus	brain
44	chr3:141634400-141648600	Weak transcription	Fetal Kidney	kidney
45	chr3:141634400-141656600	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
46	chr3:141635400-141646400	Weak transcription	Primary B cells from cord blood	blood
47	chr3:141635400-141648200	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
48	chr3:141635400-141648600	Strong transcription	Fetal Intestine Large	intestine
49	chr3:141635600-141644600	Strong transcription	Fetal Intestine Small	intestine
50	chr3:141635600-141645000	Strong transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived

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