Variant report

Variant	rs55854080
Chromosome Location	chr1:212811494-212811495
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	chr1:212731680..212733732-chr1:212810239..212812823,2	K562	blood:

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-BATF3-2	chr1:212810445-212811889	XLOC_001195

Extended variants
information (count: 25 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:19)

rs_ID	r²[population]
rs11571532	1.00[ASN][1000 genomes]
rs11571536	1.00[ASN][1000 genomes]
rs11571538	1.00[ASN][1000 genomes]
rs11571552	1.00[ASN][1000 genomes]
rs17019442	1.00[ASN][1000 genomes]
rs35777725	1.00[ASN][1000 genomes]
rs3890801	0.85[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs56023947	0.84[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs6540751	1.00[ASN][1000 genomes]
rs6656504	0.80[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6670396	1.00[ASN][1000 genomes]
rs6682816	0.80[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72756370	1.00[ASN][1000 genomes]
rs72756371	1.00[ASN][1000 genomes]
rs74138596	0.94[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs74138599	0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs74138600	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs74138601	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7551520	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[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	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
2	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
3	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
4	esv2757770	chr1:212648143-212843103	Flanking Active TSS Enhancers Bivalent Enhancer Weak transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS Active TSS Strong transcription Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	77 gene(s)	inside rSNPs	diseases
5	esv2758996	chr1:212648143-212843103	Enhancers Flanking Bivalent TSS/Enh Genic enhancers Active TSS Bivalent Enhancer Flanking Active TSS Weak transcription Strong transcription Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	77 gene(s)	inside rSNPs	diseases
6	nsv428588	chr1:212705588-212862875	Active TSS Enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer Weak transcription Strong transcription Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	78 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:66 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:212794400-212812200	Weak transcription	H9 Cell Line	embryonic stem cell
2	chr1:212802600-212822800	Weak transcription	Fetal Kidney	kidney
3	chr1:212807800-212812600	Enhancers	Primary monocytes fromperipheralblood	blood
4	chr1:212807800-212812800	Enhancers	Primary hematopoietic stem cells short term culture	blood
5	chr1:212808000-212812600	Enhancers	Cortex derived primary cultured neurospheres	brain
6	chr1:212808200-212812800	Enhancers	Fetal Stomach	stomach
7	chr1:212808200-212813000	Enhancers	Fetal Heart	heart
8	chr1:212808200-212813000	Enhancers	Fetal Thymus	thymus
9	chr1:212808400-212812600	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
10	chr1:212808600-212813000	Enhancers	Fetal Muscle Trunk	muscle
11	chr1:212808800-212811600	Weak transcription	HUES48 Cell Line	embryonic stem cell
12	chr1:212808800-212811800	Enhancers	HSMM	muscle
13	chr1:212808800-212812600	Enhancers	Right Ventricle	heart
14	chr1:212808800-212812800	Enhancers	Placenta	Placenta
15	chr1:212809400-212812600	Enhancers	Fetal Brain Male	brain
16	chr1:212810000-212811600	Enhancers	Muscle Satellite Cultured Cells	--
17	chr1:212810000-212811600	Weak transcription	Fetal Brain Female	brain
18	chr1:212810000-212811800	Enhancers	HUVEC	blood vessel
19	chr1:212810000-212811800	Flanking Active TSS	NHDF-Ad	bronchial
20	chr1:212810000-212812400	Enhancers	Fetal Lung	lung
21	chr1:212810200-212811600	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
22	chr1:212810200-212811600	Enhancers	GM12878-XiMat	blood
23	chr1:212810200-212812800	Flanking Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
24	chr1:212810200-212812800	Enhancers	Thymus	Thymus
25	chr1:212810400-212811800	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
26	chr1:212810400-212812600	Flanking Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
27	chr1:212810600-212811600	Weak transcription	Colon Smooth Muscle	Colon
28	chr1:212810600-212812400	Bivalent Enhancer	Foreskin Fibroblast Primary Cells skin01	Skin
29	chr1:212810600-212812400	Weak transcription	Brain Angular Gyrus	brain
30	chr1:212810600-212812400	Weak transcription	Duodenum Smooth Muscle	Duodenum
31	chr1:212810600-212812600	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
32	chr1:212810600-212813200	Enhancers	Primary hematopoietic stem cells	blood
33	chr1:212810800-212811600	Weak transcription	Fetal Intestine Small	intestine
34	chr1:212810800-212811600	Active TSS	NHLF	lung
35	chr1:212810800-212811800	Weak transcription	Brain Hippocampus Middle	brain
36	chr1:212810800-212811800	Weak transcription	HSMMtube	muscle
37	chr1:212810800-212812200	Enhancers	Dnd41	blood
38	chr1:212810800-212812400	Weak transcription	Duodenum Mucosa	Duodenum
39	chr1:212810800-212812400	Weak transcription	Lung	lung
40	chr1:212810800-212812400	Enhancers	Monocytes-CD14+_RO01746	blood
41	chr1:212810800-212813000	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
42	chr1:212810800-212813000	Enhancers	Brain Dorsolateral Prefrontal Cortex	brain
43	chr1:212810800-212813000	Enhancers	Skeletal Muscle Male	skeletal muscle
44	chr1:212810800-212813600	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
45	chr1:212810800-212813800	Weak transcription	Rectal Mucosa Donor 31	rectum
46	chr1:212811000-212816800	Weak transcription	Fetal Intestine Large	intestine
47	chr1:212811200-212811600	Weak transcription	Brain Germinal Matrix	brain
48	chr1:212811200-212811800	Flanking Active TSS	IMR90 fetal lung fibroblasts Cell Line	lung
49	chr1:212811200-212811800	Flanking Active TSS	Left Ventricle	heart
50	chr1:212811200-212812000	Enhancers	iPS-15b Cell Line	embryonic stem cell

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