Variant report

Variant	rs2838684
Chromosome Location	chr21:46204511-46204512
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr21:46197791..46202676-chr21:46204066..46207240,6	MCF-7	breast:
2	chr21:46202815..46206353-chr21:46211210..46215151,6	K562	blood:
3	chr21:46204105..46208556-chr21:46233916..46237563,3	K562	blood:
4	chr21:46184622..46186979-chr21:46203808..46205316,2	MCF-7	breast:
5	chr21:46191384..46193561-chr21:46204245..46206400,3	MCF-7	breast:

Extended variants
information (count: 25 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:21)

rs_ID	r²[population]
rs12626275	0.85[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	0.81[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs2008604	0.85[AMR][1000 genomes];0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs235340	0.82[JPT][hapmap]
rs235341	0.82[JPT][hapmap]
rs235351	1.00[JPT][hapmap];0.94[ASN][1000 genomes]
rs235362	0.95[GIH][hapmap];1.00[JPT][hapmap];0.94[ASN][1000 genomes]
rs235363	0.94[ASN][1000 genomes]
rs2838672	0.84[ASN][1000 genomes]
rs2838682	0.93[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2838685	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.97[LWK][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2838694	1.00[CEU][hapmap];0.86[CHB][hapmap];0.81[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.81[AMR][1000 genomes];0.88[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs2838696	1.00[CEU][hapmap];0.86[CHB][hapmap];1.00[JPT][hapmap];0.81[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs35627976	0.81[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs56357729	0.81[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7283211	0.81[AMR][1000 genomes];0.83[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs7283639	0.81[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs73232962	0.81[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs73232966	0.81[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
rs2838684	PTTG1IP	cis	lung	GTEx

Chromatin state (count:126 , 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	chr21:46188000-46208000	Strong transcription	Primary hematopoietic stem cells short term culture	blood
4	chr21:46188600-46208000	Strong transcription	Monocytes-CD14+_RO01746	blood
5	chr21:46189000-46221000	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
6	chr21:46189600-46207800	Strong transcription	Dnd41	blood
7	chr21:46190800-46209600	Weak transcription	Fetal Brain Male	brain
8	chr21:46193400-46212600	Weak transcription	Primary T killer memory cells from peripheral blood	blood
9	chr21:46193800-46206000	Weak transcription	Brain Hippocampus Middle	brain
10	chr21:46193800-46212800	Weak transcription	Psoas Muscle	Psoas
11	chr21:46195000-46211200	Weak transcription	Brain Inferior Temporal Lobe	brain
12	chr21:46195000-46212600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
13	chr21:46195000-46219800	Weak transcription	Small Intestine	intestine
14	chr21:46195200-46204600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
15	chr21:46195400-46220400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
16	chr21:46195600-46211400	Weak transcription	iPS-15b Cell Line	embryonic stem cell
17	chr21:46196000-46205600	Weak transcription	Brain Anterior Caudate	brain
18	chr21:46196000-46211800	Weak transcription	NHLF	lung
19	chr21:46197200-46213000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
20	chr21:46197200-46220400	Weak transcription	Primary neutrophils fromperipheralblood	blood
21	chr21:46197400-46204800	Weak transcription	Brain Substantia Nigra	brain
22	chr21:46197400-46212800	Weak transcription	Brain Cingulate Gyrus	brain
23	chr21:46198000-46207200	Weak transcription	NH-A	brain
24	chr21:46198200-46204800	Weak transcription	Placenta	Placenta
25	chr21:46198400-46207200	Weak transcription	Rectal Mucosa Donor 31	rectum
26	chr21:46198600-46204600	Weak transcription	Fetal Intestine Large	intestine
27	chr21:46198600-46212000	Weak transcription	Primary T helper naive cells from peripheral blood	blood
28	chr21:46198800-46208000	Strong transcription	K562	blood
29	chr21:46198800-46211400	Weak transcription	HUVEC	blood vessel
30	chr21:46198800-46213000	Weak transcription	Brain Angular Gyrus	brain
31	chr21:46198800-46219600	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
32	chr21:46198800-46220000	Weak transcription	H9 Cell Line	embryonic stem cell
33	chr21:46198800-46220000	Weak transcription	Fetal Kidney	kidney
34	chr21:46199200-46207000	Weak transcription	Osteobl	bone
35	chr21:46199800-46204600	Weak transcription	Skeletal Muscle Male	skeletal muscle
36	chr21:46199800-46209400	Weak transcription	NHDF-Ad	bronchial
37	chr21:46200000-46204800	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
38	chr21:46200000-46220400	Weak transcription	Placenta Amnion	Placenta Amnion
39	chr21:46200400-46204600	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
40	chr21:46200400-46204600	Weak transcription	Muscle Satellite Cultured Cells	--
41	chr21:46200400-46205200	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
42	chr21:46200400-46212800	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
43	chr21:46200400-46218200	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
44	chr21:46200600-46205200	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
45	chr21:46200600-46212800	Weak transcription	Colon Smooth Muscle	Colon
46	chr21:46200800-46207800	Strong transcription	Primary T cells from cord blood	blood
47	chr21:46201000-46204800	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
48	chr21:46201000-46205600	Weak transcription	Fetal Heart	heart
49	chr21:46201200-46204600	Weak transcription	Stomach Smooth Muscle	stomach
50	chr21:46201200-46220400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell

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