Variant report

Variant	rs2838682
Chromosome Location	chr21:46200628-46200629
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:0)
CpG islands
(count:0)
Chromatin interactive
region (count:8)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:8 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr21:46171813..46174336-chr21:46199513..46201823,2	K562	blood:
2	chr21:46185007..46187777-chr21:46197158..46201208,5	MCF-7	breast:
3	chr21:46199620..46201400-chr21:46208147..46210925,2	MCF-7	breast:
4	chr21:46197899..46200792-chr21:46212721..46215023,2	MCF-7	breast:
5	chr21:46191363..46195338-chr21:46195868..46201575,8	MCF-7	breast:
6	chr21:46177180..46179450-chr21:46200338..46203449,3	MCF-7	breast:
7	chr21:46181840..46185418-chr21:46198665..46202269,4	MCF-7	breast:
8	chr21:46197791..46202676-chr21:46204066..46207240,6	MCF-7	breast:

No data

Extended variants
information (count: 23 )
Associated
traits (count: 1 )

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

rs_ID	r²[population]
rs12626275	0.82[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs17004701	0.91[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs17526563	0.85[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs2008604	0.82[AMR][1000 genomes];0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs235351	0.94[ASN][1000 genomes]
rs235362	0.94[ASN][1000 genomes]
rs235363	0.94[ASN][1000 genomes]
rs2838672	0.84[ASN][1000 genomes]
rs2838684	0.93[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2838685	0.94[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2838694	0.85[AMR][1000 genomes];0.88[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs2838696	0.85[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs35627976	0.85[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs56357729	0.85[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7283211	0.85[AMR][1000 genomes];0.83[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs7283639	0.85[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs73232962	0.85[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs73232966	0.85[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs9647228	0.82[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv916258	chr21:45995986-46624705	Weak transcription Enhancers Flanking Active TSS Strong transcription Genic enhancers Bivalent/Poised TSS Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	102 gene(s)	inside rSNPs	diseases
2	nsv913956	chr21:46096964-46279505	Enhancers Bivalent Enhancer Active TSS Weak transcription Strong transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Flanking Active TSS Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	44 gene(s)	inside rSNPs	diseases
3	nsv1062245	chr21:46096964-46332587	Active TSS Bivalent Enhancer Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Strong transcription Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	51 gene(s)	inside rSNPs	diseases
4	nsv544478	chr21:46096964-46332587	Enhancers Flanking Active TSS Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Weak transcription Bivalent/Poised TSS Genic enhancers Strong transcription Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	51 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs2838682	PTTG1IP	cis	lung	GTEx

Chromatin state (count:127 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr21:46187000-46213000	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
2	chr21:46187800-46206200	Strong transcription	Fetal Thymus	thymus
3	chr21:46188000-46201600	Strong transcription	Duodenum Mucosa	Duodenum
4	chr21:46188000-46203000	Weak transcription	Pancreatic Islets	Pancreatic Islet
5	chr21:46188000-46203200	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
6	chr21:46188000-46208000	Strong transcription	Primary hematopoietic stem cells short term culture	blood
7	chr21:46188200-46201600	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
8	chr21:46188600-46201600	Strong transcription	Fetal Stomach	stomach
9	chr21:46188600-46208000	Strong transcription	Monocytes-CD14+_RO01746	blood
10	chr21:46189000-46201400	Strong transcription	Primary monocytes fromperipheralblood	blood
11	chr21:46189000-46221000	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
12	chr21:46189200-46203000	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
13	chr21:46189600-46201800	Strong transcription	Primary B cells from peripheral blood	blood
14	chr21:46189600-46203600	Strong transcription	HUES48 Cell Line	embryonic stem cell
15	chr21:46189600-46207800	Strong transcription	Dnd41	blood
16	chr21:46190800-46209600	Weak transcription	Fetal Brain Male	brain
17	chr21:46193400-46212600	Weak transcription	Primary T killer memory cells from peripheral blood	blood
18	chr21:46193800-46206000	Weak transcription	Brain Hippocampus Middle	brain
19	chr21:46193800-46212800	Weak transcription	Psoas Muscle	Psoas
20	chr21:46194800-46203200	Weak transcription	Rectal Smooth Muscle	rectum
21	chr21:46195000-46211200	Weak transcription	Brain Inferior Temporal Lobe	brain
22	chr21:46195000-46212600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
23	chr21:46195000-46219800	Weak transcription	Small Intestine	intestine
24	chr21:46195200-46204600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
25	chr21:46195400-46220400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
26	chr21:46195600-46211400	Weak transcription	iPS-15b Cell Line	embryonic stem cell
27	chr21:46195800-46203200	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
28	chr21:46196000-46205600	Weak transcription	Brain Anterior Caudate	brain
29	chr21:46196000-46211800	Weak transcription	NHLF	lung
30	chr21:46196800-46203400	Weak transcription	Brain Germinal Matrix	brain
31	chr21:46197000-46203200	Weak transcription	Fetal Brain Female	brain
32	chr21:46197200-46213000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
33	chr21:46197200-46220400	Weak transcription	Primary neutrophils fromperipheralblood	blood
34	chr21:46197400-46203000	Weak transcription	H1 Cell Line	embryonic stem cell
35	chr21:46197400-46204800	Weak transcription	Brain Substantia Nigra	brain
36	chr21:46197400-46212800	Weak transcription	Brain Cingulate Gyrus	brain
37	chr21:46197600-46201400	Strong transcription	Primary B cells from cord blood	blood
38	chr21:46198000-46201400	Strong transcription	Foreskin Fibroblast Primary Cells skin02	Skin
39	chr21:46198000-46207200	Weak transcription	NH-A	brain
40	chr21:46198200-46201400	Enhancers	HSMMtube	muscle
41	chr21:46198200-46204800	Weak transcription	Placenta	Placenta
42	chr21:46198400-46200800	Weak transcription	Colonic Mucosa	Colon
43	chr21:46198400-46207200	Weak transcription	Rectal Mucosa Donor 31	rectum
44	chr21:46198600-46203200	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
45	chr21:46198600-46204600	Weak transcription	Fetal Intestine Large	intestine
46	chr21:46198600-46212000	Weak transcription	Primary T helper naive cells from peripheral blood	blood
47	chr21:46198800-46200800	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
48	chr21:46198800-46201600	Enhancers	Pancreas	Pancrea
49	chr21:46198800-46202800	Weak transcription	iPS-18 Cell Line	embryonic stem cell
50	chr21:46198800-46204200	Weak transcription	iPS-20b Cell Line	embryonic stem cell

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