Variant report

Variant	rs62260663
Chromosome Location	chr3:49814949-49814950
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 56 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:50)

rs_ID	r²[population]
rs11130217	0.93[AFR][1000 genomes];0.91[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs11709734	0.89[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs11720705	0.93[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs12715437	0.95[AFR][1000 genomes];0.95[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs13091525	1.00[ASN][1000 genomes]
rs13097720	1.00[ASN][1000 genomes]
rs1491985	0.89[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs17304079	1.00[ASN][1000 genomes]
rs1799844	0.82[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1996663	0.87[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs1996664	0.87[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs28535523	0.93[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs3020779	0.81[EUR][1000 genomes]
rs35012435	1.00[ASN][1000 genomes]
rs35129566	0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35375092	1.00[ASN][1000 genomes]
rs35491931	1.00[ASN][1000 genomes]
rs35849525	1.00[ASN][1000 genomes]
rs55997059	0.89[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs58339610	0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs59357103	0.80[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs59684465	0.91[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs61557789	0.91[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs62260720	0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62260723	0.91[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs62260755	1.00[ASN][1000 genomes]
rs62262061	1.00[ASN][1000 genomes]
rs62262106	1.00[ASN][1000 genomes]
rs62262118	1.00[ASN][1000 genomes]
rs62262722	0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62262730	0.87[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6787892	1.00[ASN][1000 genomes]
rs6790568	0.95[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs6804970	0.91[AFR][1000 genomes];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6809879	0.83[AFR][1000 genomes];0.93[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs71326904	1.00[ASN][1000 genomes]
rs7613603	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7615318	1.00[ASN][1000 genomes]
rs7620848	0.91[AFR][1000 genomes];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7621797	0.92[AFR][1000 genomes];0.98[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7628207	0.89[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs7635601	1.00[ASN][1000 genomes]
rs7637711	0.91[AFR][1000 genomes];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7649428	0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9829155	0.96[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9835157	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9836756	0.90[AFR][1000 genomes];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9851651	0.93[AFR][1000 genomes];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9870755	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9870858	0.98[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv1796352	chr3:49687101-49949959	Genic enhancers Weak transcription Enhancers Active TSS Flanking Active TSS Bivalent Enhancer Strong transcription Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	90 gene(s)	inside rSNPs	diseases
2	nsv834688	chr3:49811115-50019299	Weak transcription Active TSS Flanking Active TSS Strong transcription Enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer Genic enhancers Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	60 gene(s)	inside rSNPs	diseases
3	nsv237797	chr3:49811452-49817742	Weak transcription Strong transcription Enhancers Genic enhancers Flanking Active TSS	TF binding region Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
4	nsv237675	chr3:49811454-49817742	Enhancers Weak transcription Genic enhancers Strong transcription Flanking Active TSS	TF binding region Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
5	nsv965165	chr3:49811992-49817515	Weak transcription Strong transcription Enhancers Genic enhancers Flanking Active TSS	TF binding region Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
6	esv1809827	chr3:49812331-49934179	Weak transcription Active TSS Enhancers Flanking Active TSS Genic enhancers Strong transcription Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	30 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs62260663	RNF123	cis	Artery Tibial	GTEx
rs62260663	AMT	cis	Thyroid	GTEx
rs62260663	AMT	cis	lung	GTEx

Chromatin state (count:122 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:49775600-49817000	Weak transcription	Primary T killer memory cells from peripheral blood	blood
2	chr3:49775800-49823000	Weak transcription	Placenta Amnion	Placenta Amnion
3	chr3:49776400-49818000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
4	chr3:49776400-49818000	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
5	chr3:49776400-49818200	Weak transcription	Fetal Kidney	kidney
6	chr3:49785600-49822400	Weak transcription	HSMMtube	muscle
7	chr3:49785600-49822600	Weak transcription	Esophagus	oesophagus
8	chr3:49785800-49818000	Weak transcription	Rectal Mucosa Donor 31	rectum
9	chr3:49786000-49823000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
10	chr3:49786200-49822400	Weak transcription	HMEC	breast
11	chr3:49786400-49817800	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
12	chr3:49786600-49817800	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
13	chr3:49793800-49817600	Weak transcription	Spleen	Spleen
14	chr3:49795000-49818000	Weak transcription	Psoas Muscle	Psoas
15	chr3:49795000-49819000	Weak transcription	Right Ventricle	heart
16	chr3:49795000-49821000	Weak transcription	K562	blood
17	chr3:49795400-49822400	Weak transcription	Stomach Mucosa	stomach
18	chr3:49802400-49818000	Weak transcription	Right Atrium	heart
19	chr3:49804000-49822600	Weak transcription	H1 Cell Line	embryonic stem cell
20	chr3:49804200-49816000	Weak transcription	Cortex derived primary cultured neurospheres	brain
21	chr3:49806200-49818800	Weak transcription	HUES6 Cell Line	embryonic stem cell
22	chr3:49806600-49819000	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
23	chr3:49807600-49817800	Weak transcription	Small Intestine	intestine
24	chr3:49807800-49817800	Weak transcription	NH-A	brain
25	chr3:49807800-49822600	Weak transcription	Pancreatic Islets	Pancreatic Islet
26	chr3:49808000-49816600	Weak transcription	HUES64 Cell Line	embryonic stem cell
27	chr3:49808200-49816200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
28	chr3:49808200-49818000	Weak transcription	Aorta	Aorta
29	chr3:49808400-49818000	Weak transcription	NHLF	lung
30	chr3:49809200-49817800	Strong transcription	Fetal Thymus	thymus
31	chr3:49809200-49818000	Weak transcription	Primary hematopoietic stem cells	blood
32	chr3:49809400-49817800	Weak transcription	GM12878-XiMat	blood
33	chr3:49809400-49822800	Weak transcription	A549	lung
34	chr3:49809600-49816800	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
35	chr3:49809600-49822400	Weak transcription	NHDF-Ad	bronchial
36	chr3:49810400-49816800	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
37	chr3:49810400-49822400	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
38	chr3:49811200-49815800	Strong transcription	Monocytes-CD14+_RO01746	blood
39	chr3:49812000-49822800	Weak transcription	iPS-15b Cell Line	embryonic stem cell
40	chr3:49812200-49822800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
41	chr3:49812400-49815000	Strong transcription	Primary T cells from cord blood	blood
42	chr3:49812400-49815400	Strong transcription	Primary neutrophils fromperipheralblood	blood
43	chr3:49812400-49817800	Strong transcription	Primary B cells from peripheral blood	blood
44	chr3:49812400-49818000	Strong transcription	Primary hematopoietic stem cells short term culture	blood
45	chr3:49812600-49815000	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
46	chr3:49812600-49815000	Strong transcription	Lung	lung
47	chr3:49812600-49815200	Strong transcription	Placenta	Placenta
48	chr3:49812600-49815400	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
49	chr3:49812600-49817800	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
50	chr3:49812600-49817800	Strong transcription	Fetal Intestine Small	intestine

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