Variant report

Variant	rs1086893
Chromosome Location	chr1:212563114-212563115
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr1:212561364..212563303-chr1:212611566..212613873,2	K562	blood:
2	chr1:212554525..212557472-chr1:212560250..212563380,3	K562	blood:

Extended variants
information (count: 11 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:5)

rs_ID	r²[population]
rs3099112	0.84[AFR][1000 genomes]
rs518793	0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs612414	0.80[ASN][1000 genomes]
rs701905	0.94[AFR][1000 genomes];0.81[AMR][1000 genomes];0.88[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs792448	0.97[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[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	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
2	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
3	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
4	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
5	nsv1013110	chr1:212555764-212948092	Flanking Active TSS Bivalent/Poised TSS Strong transcription Enhancers Bivalent Enhancer Weak transcription ZNF genes & repeats Active TSS Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	81 gene(s)	inside rSNPs	diseases
6	nsv535287	chr1:212555764-212948092	Weak transcription Bivalent Enhancer Flanking Active TSS Enhancers Strong transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Active TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	81 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs1086893	NENF	cis	Esophagus Mucosa	GTEx
rs1086893	C1orf75	Cis_1M	lymphoblastoid	RTeQTL
rs1086893	TMEM206	cis	Esophagus Mucosa	GTEx

Chromatin state (count:90 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:212502600-212563400	Strong transcription	Primary monocytes fromperipheralblood	blood
2	chr1:212502600-212564600	Strong transcription	Monocytes-CD14+_RO01746	blood
3	chr1:212526800-212582800	Weak transcription	Fetal Brain Male	brain
4	chr1:212528400-212583000	Weak transcription	Fetal Kidney	kidney
5	chr1:212529800-212563200	Strong transcription	Primary hematopoietic stem cells short term culture	blood
6	chr1:212534000-212570200	Weak transcription	HSMM	muscle
7	chr1:212534400-212570600	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
8	chr1:212538000-212571000	Weak transcription	NH-A	brain
9	chr1:212540400-212575400	Weak transcription	HUVEC	blood vessel
10	chr1:212540600-212564000	Weak transcription	Stomach Mucosa	stomach
11	chr1:212543600-212565200	Weak transcription	Fetal Lung	lung
12	chr1:212547000-212563400	Strong transcription	Fetal Thymus	thymus
13	chr1:212548600-212563800	Strong transcription	Primary T cells from cord blood	blood
14	chr1:212553200-212569400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
15	chr1:212553200-212578400	Weak transcription	K562	blood
16	chr1:212555400-212563200	Weak transcription	Psoas Muscle	Psoas
17	chr1:212556800-212587600	Weak transcription	Small Intestine	intestine
18	chr1:212558600-212578800	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
19	chr1:212558600-212580000	Weak transcription	Left Ventricle	heart
20	chr1:212559200-212564800	Weak transcription	HMEC	breast
21	chr1:212559400-212563600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
22	chr1:212560200-212563200	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
23	chr1:212560200-212578400	Weak transcription	Primary T helper naive cells from peripheral blood	blood
24	chr1:212560400-212563200	Weak transcription	Brain Cingulate Gyrus	brain
25	chr1:212560400-212570600	Weak transcription	NHLF	lung
26	chr1:212560400-212580200	Weak transcription	Rectal Mucosa Donor 29	rectum
27	chr1:212560600-212563200	Weak transcription	Skeletal Muscle Female	skeletal muscle
28	chr1:212560600-212563600	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
29	chr1:212560600-212563600	Weak transcription	Brain Inferior Temporal Lobe	brain
30	chr1:212560600-212563800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
31	chr1:212560600-212563800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
32	chr1:212560600-212563800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
33	chr1:212560600-212563800	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
34	chr1:212560600-212563800	Weak transcription	Ovary	ovary
35	chr1:212560600-212563800	Weak transcription	Spleen	Spleen
36	chr1:212560600-212566000	Weak transcription	Duodenum Smooth Muscle	Duodenum
37	chr1:212560600-212567000	Weak transcription	Right Ventricle	heart
38	chr1:212560600-212568000	Weak transcription	Rectal Smooth Muscle	rectum
39	chr1:212560600-212570000	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
40	chr1:212560600-212570200	Weak transcription	Brain Substantia Nigra	brain
41	chr1:212560600-212578200	Weak transcription	Sigmoid Colon	Sigmoid Colon
42	chr1:212560600-212578800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
43	chr1:212560600-212580200	Weak transcription	HSMMtube	muscle
44	chr1:212560600-212582000	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
45	chr1:212560600-212582000	Weak transcription	Gastric	stomach
46	chr1:212561000-212563400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
47	chr1:212561000-212563600	Weak transcription	Pancreas	Pancrea
48	chr1:212561000-212563800	Weak transcription	Duodenum Mucosa	Duodenum
49	chr1:212561000-212575400	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
50	chr1:212561000-212578000	Weak transcription	Primary T killer naive cells fromperipheralblood	blood

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links