Variant report

Variant	rs61829243
Chromosome Location	chr1:212959475-212959476
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr1:212958137..212960134-chr1:212960164..212962206,2	K562	blood:
2	chr1:212955485..212957431-chr1:212958159..212961189,3	K562	blood:
3	chr1:212958789..212962181-chr1:212964353..212966610,4	K562	blood:

Variant related genes	Relation type
ENSG00000203705	Chromatin interaction
ENSG00000117697	Chromatin interaction

Extended variants
information (count: 35 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:30)

rs_ID	r²[population]
rs10494955	0.86[ASN][1000 genomes]
rs10863993	0.82[ASN][1000 genomes]
rs10863998	0.84[ASN][1000 genomes]
rs10863999	0.85[ASN][1000 genomes]
rs11120012	0.80[ASN][1000 genomes]
rs11120013	0.81[ASN][1000 genomes]
rs11120024	0.83[ASN][1000 genomes]
rs11120025	0.82[ASN][1000 genomes]
rs11120026	0.88[ASN][1000 genomes]
rs11120027	0.91[AFR][1000 genomes];0.88[ASN][1000 genomes]
rs12064985	0.87[ASN][1000 genomes]
rs12088916	0.83[ASN][1000 genomes]
rs12097897	0.85[ASN][1000 genomes]
rs12126017	0.85[ASN][1000 genomes]
rs12132316	0.81[ASN][1000 genomes]
rs12136046	0.82[ASN][1000 genomes]
rs12136834	0.82[ASN][1000 genomes]
rs12722742	0.83[ASN][1000 genomes]
rs12741704	0.88[ASN][1000 genomes]
rs3820679	0.88[ASN][1000 genomes]
rs4951463	0.88[ASN][1000 genomes]
rs4951638	0.81[ASN][1000 genomes]
rs6540763	0.81[ASN][1000 genomes]
rs6661720	0.82[ASN][1000 genomes]
rs6679350	0.88[ASN][1000 genomes]
rs6679549	0.88[ASN][1000 genomes]
rs6690689	0.82[ASN][1000 genomes]
rs6693311	0.83[ASN][1000 genomes]
rs6702611	0.85[ASN][1000 genomes]
rs7556272	0.82[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv549148	chr1:212876902-212962207	Enhancers ZNF genes & repeats Weak transcription Strong transcription Flanking Active TSS Genic enhancers Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region	7 gene(s)	inside rSNPs	diseases
2	nsv1001637	chr1:212907611-213034606	Active TSS Enhancers Weak transcription ZNF genes & repeats Strong transcription Genic enhancers Flanking Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	33 gene(s)	inside rSNPs	diseases
3	esv2756884	chr1:212925429-213006397	Strong transcription Weak transcription Flanking Active TSS Active TSS Enhancers ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	22 gene(s)	inside rSNPs	diseases
4	esv2758997	chr1:212925429-213006397	Weak transcription Enhancers Strong transcription Flanking Active TSS Genic enhancers ZNF genes & repeats Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	22 gene(s)	inside rSNPs	diseases
5	nsv1010003	chr1:212944240-212986996	Strong transcription Enhancers Weak transcription Flanking Active TSS Active TSS ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	18 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs61829243	FLVCR1-AS1	cis	Esophagus Muscularis	GTEx
rs61829243	FLVCR1-AS1	cis	Artery Aorta	GTEx
rs61829243	LQK1	Cis_1M	lymphoblastoid	RTeQTL
rs61829243	FLVCR1-AS1	cis	Adipose Subcutaneous	GTEx

Chromatin state (count:124 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:212895400-212964600	Weak transcription	Pancreas	Pancrea
2	chr1:212895600-212964600	Weak transcription	Gastric	stomach
3	chr1:212923600-212963800	Weak transcription	Brain Angular Gyrus	brain
4	chr1:212923600-212964400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
5	chr1:212923800-212964200	Weak transcription	HMEC	breast
6	chr1:212926600-212963400	Weak transcription	Rectal Smooth Muscle	rectum
7	chr1:212927400-212963400	Weak transcription	Small Intestine	intestine
8	chr1:212927400-212964200	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
9	chr1:212936600-212959800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
10	chr1:212936600-212960200	Weak transcription	Lung	lung
11	chr1:212936600-212964400	Weak transcription	Esophagus	oesophagus
12	chr1:212941200-212964200	Weak transcription	Right Ventricle	heart
13	chr1:212942400-212964200	Weak transcription	Aorta	Aorta
14	chr1:212942600-212964400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
15	chr1:212942800-212964200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
16	chr1:212943200-212964200	Weak transcription	Brain Inferior Temporal Lobe	brain
17	chr1:212944200-212964400	Weak transcription	Fetal Heart	heart
18	chr1:212945800-212959800	Weak transcription	Ovary	ovary
19	chr1:212948400-212960000	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
20	chr1:212950400-212964200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
21	chr1:212950800-212959800	Weak transcription	Fetal Intestine Small	intestine
22	chr1:212951800-212964400	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
23	chr1:212952400-212963000	Weak transcription	Brain Cingulate Gyrus	brain
24	chr1:212952600-212963600	Weak transcription	Colonic Mucosa	Colon
25	chr1:212953000-212959800	Weak transcription	NHEK	skin
26	chr1:212953000-212964400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
27	chr1:212953200-212964400	Weak transcription	Placenta Amnion	Placenta Amnion
28	chr1:212953800-212960200	Strong transcription	Primary T helper cells PMA-I stimulated	--
29	chr1:212953800-212960200	Strong transcription	HSMM	muscle
30	chr1:212953800-212961000	Strong transcription	Primary hematopoietic stem cells short term culture	blood
31	chr1:212954000-212960600	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
32	chr1:212954000-212960600	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
33	chr1:212954000-212960600	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
34	chr1:212954000-212960800	Strong transcription	Placenta	Placenta
35	chr1:212954000-212961000	Strong transcription	iPS-18 Cell Line	embryonic stem cell
36	chr1:212954000-212961000	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
37	chr1:212954000-212961000	Strong transcription	Liver	Liver
38	chr1:212954000-212961000	Strong transcription	Fetal Thymus	thymus
39	chr1:212954000-212961200	Strong transcription	HUES6 Cell Line	embryonic stem cell
40	chr1:212954000-212961200	Strong transcription	Primary T helper cells fromperipheralblood	blood
41	chr1:212954200-212960400	Strong transcription	Primary T cells fromperipheralblood	blood
42	chr1:212954200-212960600	Strong transcription	Primary B cells from cord blood	blood
43	chr1:212954200-212960600	Strong transcription	Skeletal Muscle Female	skeletal muscle
44	chr1:212954200-212960600	Strong transcription	K562	blood
45	chr1:212954200-212960800	Strong transcription	Primary B cells from peripheral blood	blood
46	chr1:212954200-212960800	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
47	chr1:212954200-212961000	Strong transcription	Dnd41	blood
48	chr1:212954200-212961600	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
49	chr1:212954400-212964400	Weak transcription	Spleen	Spleen
50	chr1:212954600-212960400	Strong transcription	Fetal Intestine Large	intestine

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