Variant report

Variant	rs16844846
Chromosome Location	chr1:225592927-225592928
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr1:225592461-225603516	K562	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr1:225590339..225593004-chr1:225614495..225616348,2	MCF-7	breast:
2	chr1:225592721..225593555-chr12:51520651..51521367,2	Hela-S3	cervix:

Variant related genes	Relation type
LBR	TF binding region
ENSG00000143815	Chromatin interaction

Extended variants
information (count: 22 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:20)

rs_ID	r²[population]
rs12061268	1.00[CHB][hapmap]
rs12081774	1.00[CHB][hapmap]
rs12083979	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12085130	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12087159	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12088235	1.00[CHB][hapmap]
rs12089582	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12097737	1.00[CHB][hapmap]
rs1537877	1.00[JPT][hapmap]
rs16844841	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs16844847	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs16844850	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs16844853	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs17558869	1.00[JPT][hapmap]
rs41267357	1.00[AMR][1000 genomes]
rs41268715	0.90[AMR][1000 genomes]
rs41304014	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs41304141	1.00[AMR][1000 genomes]
rs61738690	1.00[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs6679318	1.00[CEU][hapmap];1.00[JPT][hapmap];0.88[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv3442497	chr1:225588829-225592927	Weak transcription Strong transcription ZNF genes & repeats Genic enhancers	TF binding region CpG island Chromatin interactive region miRNA target site	1 gene(s)	inside rSNPs	n/a
2	nsv832714	chr1:225592333-225805396	Enhancers Flanking Active TSS Weak transcription ZNF genes & repeats Strong transcription Genic enhancers Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	20 gene(s)	inside rSNPs	diseases

Variant related diseases (count:1)

Disease	PMID	Source
IgG glycosylation	23382691	GWAS catalog

Chromatin state (count:125 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:225568200-225595800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
2	chr1:225570800-225600000	Weak transcription	HSMMtube	muscle
3	chr1:225576200-225594400	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
4	chr1:225578000-225597800	Weak transcription	Brain Cingulate Gyrus	brain
5	chr1:225578000-225599200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
6	chr1:225580800-225599200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
7	chr1:225581600-225596200	Weak transcription	iPS-15b Cell Line	embryonic stem cell
8	chr1:225582000-225597800	Weak transcription	Brain Anterior Caudate	brain
9	chr1:225582200-225610400	Strong transcription	Fetal Thymus	thymus
10	chr1:225582600-225597800	Weak transcription	Fetal Brain Male	brain
11	chr1:225583200-225594000	Strong transcription	Duodenum Smooth Muscle	Duodenum
12	chr1:225583200-225597800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
13	chr1:225583400-225595400	Strong transcription	Fetal Brain Female	brain
14	chr1:225583400-225598000	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
15	chr1:225583400-225601600	Strong transcription	Primary monocytes fromperipheralblood	blood
16	chr1:225583400-225601600	Strong transcription	Monocytes-CD14+_RO01746	blood
17	chr1:225583400-225601800	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
18	chr1:225583600-225597800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
19	chr1:225583600-225602200	Weak transcription	Placenta Amnion	Placenta Amnion
20	chr1:225583800-225597800	Weak transcription	Brain Inferior Temporal Lobe	brain
21	chr1:225583800-225601600	Strong transcription	Primary B cells from cord blood	blood
22	chr1:225584000-225603800	Weak transcription	Psoas Muscle	Psoas
23	chr1:225584200-225610600	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
24	chr1:225584400-225600600	Weak transcription	Stomach Mucosa	stomach
25	chr1:225584800-225595000	Strong transcription	Fetal Intestine Large	intestine
26	chr1:225584800-225609800	Strong transcription	Dnd41	blood
27	chr1:225584800-225610400	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
28	chr1:225585000-225593000	Strong transcription	NHEK	skin
29	chr1:225585000-225595600	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
30	chr1:225585000-225595600	Strong transcription	Adipose Nuclei	Adipose
31	chr1:225585000-225609800	Strong transcription	Primary hematopoietic stem cells short term culture	blood
32	chr1:225585000-225609800	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
33	chr1:225585000-225609800	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
34	chr1:225585000-225610400	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
35	chr1:225585200-225595000	Strong transcription	HMEC	breast
36	chr1:225585200-225596000	Strong transcription	Liver	Liver
37	chr1:225585200-225609800	Strong transcription	Primary T helper cells fromperipheralblood	blood
38	chr1:225585400-225594400	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
39	chr1:225585600-225593000	Weak transcription	Pancreas	Pancrea
40	chr1:225585800-225610000	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
41	chr1:225585800-225610000	Strong transcription	K562	blood
42	chr1:225585800-225610400	Strong transcription	Primary T cells fromperipheralblood	blood
43	chr1:225586000-225601400	Strong transcription	Primary B cells from peripheral blood	blood
44	chr1:225586000-225607000	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
45	chr1:225587000-225601000	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
46	chr1:225587200-225593400	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
47	chr1:225587400-225595400	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
48	chr1:225587400-225598200	Weak transcription	Fetal Heart	heart
49	chr1:225587600-225596000	Strong transcription	Duodenum Mucosa	Duodenum
50	chr1:225587600-225596200	Strong transcription	HUES6 Cell Line	embryonic stem cell

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