Variant report

Variant	rs351401
Chromosome Location	chr1:212463792-212463793
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr1:212348711..212350970-chr1:212462639..212464212,2	K562	blood:
2	chr1:212325528..212328341-chr1:212462025..212464406,2	K562	blood:
3	chr1:212206484..212209401-chr1:212463346..212466333,2	K562	blood:
4	chr1:212216853..212219063-chr1:212462611..212464754,2	K562	blood:

Variant related genes	Relation type
ENSG00000143493	Chromatin interaction
ENSG00000143476	Chromatin interaction

Extended variants
information (count: 48 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:38)

rs_ID	r²[population]
rs10019	0.81[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs11119904	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs12023488	0.85[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs12033246	0.84[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs12035647	0.98[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs12036130	0.93[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12410664	0.81[AMR][1000 genomes]
rs1389371	0.83[EUR][1000 genomes]
rs17042034	0.98[AMR][1000 genomes];0.94[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs1774249	0.83[EUR][1000 genomes]
rs1992643	0.90[AFR][1000 genomes];0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2252044	0.85[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs2516331	0.84[EUR][1000 genomes]
rs2589474	0.84[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs3099112	0.82[AFR][1000 genomes];0.85[EUR][1000 genomes]
rs351373	0.84[EUR][1000 genomes]
rs351377	0.80[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs351378	0.84[EUR][1000 genomes]
rs351379	0.83[EUR][1000 genomes]
rs351380	0.98[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs351386	0.83[EUR][1000 genomes]
rs351393	0.80[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs351398	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs351407	0.84[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs351408	0.84[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs351417	0.88[AFR][1000 genomes];0.98[AMR][1000 genomes];0.94[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs351419	0.85[AFR][1000 genomes];0.94[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs3767861	0.81[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs3767862	0.81[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs3767863	0.86[EUR][1000 genomes]
rs4951582	0.83[EUR][1000 genomes]
rs4951589	0.86[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs6659594	0.86[EUR][1000 genomes]
rs7415843	0.83[AFR][1000 genomes];0.86[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs7519959	0.86[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs7521853	0.80[EUR][1000 genomes]
rs7544225	0.83[EUR][1000 genomes]
rs792445	0.84[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:10 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv999738	chr1:212218618-212513690	Enhancers Weak transcription Strong transcription Active TSS ZNF genes & repeats Flanking Active TSS Bivalent/Poised TSS Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	36 gene(s)	inside rSNPs	diseases
2	nsv1009376	chr1:212292357-212680320	Weak transcription Strong transcription Enhancers Transcr. at gene 5' and 3' Active TSS ZNF genes & repeats Flanking Active TSS Bivalent Enhancer Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	48 gene(s)	inside rSNPs	diseases
3	nsv549139	chr1:212332294-212876902	Flanking Active TSS Weak transcription Bivalent Enhancer Strong transcription Enhancers Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	114 gene(s)	inside rSNPs	diseases
4	nsv997629	chr1:212404489-212658785	Strong transcription Weak transcription Enhancers Flanking Active TSS Active TSS Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	45 gene(s)	inside rSNPs	diseases
5	nsv535286	chr1:212404489-212658785	Strong transcription Weak transcription ZNF genes & repeats Enhancers Flanking Active TSS Bivalent Enhancer Active TSS Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	45 gene(s)	inside rSNPs	diseases
6	esv1799093	chr1:212447167-212468974	Enhancers Flanking Active TSS Weak transcription Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	27 gene(s)	inside rSNPs	diseases
7	esv1800932	chr1:212447167-212468974	Flanking Active TSS Enhancers Weak transcription Active TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	27 gene(s)	inside rSNPs	diseases
8	esv1839997	chr1:212447167-212468974	Flanking Active TSS Weak transcription Active TSS Enhancers Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	27 gene(s)	inside rSNPs	diseases
9	nsv873155	chr1:212449195-212502157	Enhancers Weak transcription Flanking Active TSS Active TSS Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	27 gene(s)	inside rSNPs	diseases
10	esv1839887	chr1:212457414-212478047	Enhancers Weak transcription Flanking Active TSS Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Genic enhancers Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	27 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs351401	NENF	cis	Esophagus Mucosa	GTEx
rs351401	TMEM206	cis	Esophagus Mucosa	GTEx
rs351401	C1orf75	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:113 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:212460000-212463800	Active TSS	Right Atrium	heart
2	chr1:212460200-212489200	Weak transcription	Spleen	Spleen
3	chr1:212460800-212464400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
4	chr1:212461000-212464400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
5	chr1:212461000-212464600	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
6	chr1:212461000-212464600	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
7	chr1:212461000-212464600	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
8	chr1:212461000-212464800	Weak transcription	Placenta	Placenta
9	chr1:212461000-212466000	Enhancers	Colon Smooth Muscle	Colon
10	chr1:212461000-212469000	Enhancers	Brain Substantia Nigra	brain
11	chr1:212461000-212476200	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
12	chr1:212461200-212466600	Enhancers	NHEK	skin
13	chr1:212461200-212467200	Enhancers	HMEC	breast
14	chr1:212461400-212464400	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
15	chr1:212461600-212463800	Enhancers	Small Intestine	intestine
16	chr1:212461600-212464400	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
17	chr1:212461600-212465400	Enhancers	iPS-15b Cell Line	embryonic stem cell
18	chr1:212461600-212465600	Flanking Active TSS	Primary T cells from cord blood	blood
19	chr1:212461600-212468800	Weak transcription	H1 Cell Line	embryonic stem cell
20	chr1:212461800-212463800	Enhancers	Cortex derived primary cultured neurospheres	brain
21	chr1:212461800-212464400	Weak transcription	Esophagus	oesophagus
22	chr1:212461800-212464400	Weak transcription	Fetal Muscle Trunk	muscle
23	chr1:212461800-212464400	Weak transcription	Fetal Muscle Leg	muscle
24	chr1:212461800-212464400	Weak transcription	Fetal Thymus	thymus
25	chr1:212461800-212464400	Weak transcription	Gastric	stomach
26	chr1:212461800-212464400	Weak transcription	Lung	lung
27	chr1:212461800-212464400	Weak transcription	Pancreas	Pancrea
28	chr1:212461800-212464600	Weak transcription	Colonic Mucosa	Colon
29	chr1:212461800-212464800	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
30	chr1:212461800-212465000	Enhancers	NHLF	lung
31	chr1:212461800-212470200	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
32	chr1:212462000-212464000	Enhancers	Stomach Mucosa	stomach
33	chr1:212462000-212465200	Enhancers	Hela-S3	cervix
34	chr1:212462000-212465400	Enhancers	HUES64 Cell Line	embryonic stem cell
35	chr1:212462000-212465400	Enhancers	iPS-18 Cell Line	embryonic stem cell
36	chr1:212462000-212471200	Enhancers	Primary T helper naive cells from peripheral blood	blood
37	chr1:212462200-212464400	Weak transcription	Primary T cells fromperipheralblood	blood
38	chr1:212462200-212464400	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
39	chr1:212462200-212464600	Enhancers	Brain Hippocampus Middle	brain
40	chr1:212462200-212465400	Enhancers	Fetal Lung	lung
41	chr1:212462200-212466000	Enhancers	HepG2	liver
42	chr1:212462200-212466600	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
43	chr1:212462200-212467200	Enhancers	Skeletal Muscle Male	skeletal muscle
44	chr1:212462200-212468800	Enhancers	Brain Anterior Caudate	brain
45	chr1:212462200-212471000	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
46	chr1:212462200-212471000	Enhancers	Primary T killer naive cells fromperipheralblood	blood
47	chr1:212462400-212463800	Weak transcription	HSMM	muscle
48	chr1:212462400-212464000	Weak transcription	Pancreatic Islets	Pancreatic Islet
49	chr1:212462400-212464000	Weak transcription	Osteobl	bone
50	chr1:212462400-212464200	Enhancers	Primary mononuclear cells fromperipheralblood	Blood

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