Variant report

Variant	rs1209954
Chromosome Location	chr21:40181766-40181767
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr21:40181085..40183143-chr21:40216302..40218892,2	K562	blood:
2	chr21:40181532..40184339-chr21:40284437..40287872,3	K562	blood:
3	chr21:40110884..40114912-chr21:40179006..40181984,4	MCF-7	breast:

Variant related genes	Relation type
ENSG00000223806	Chromatin interaction
ENSG00000229986	Chromatin interaction
ENSG00000234035	Chromatin interaction

Extended variants
information (count: 14 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:11)

rs_ID	r²[population]
rs1209930	0.82[ASN][1000 genomes]
rs1209944	0.83[CHD][hapmap]
rs1209949	0.88[AFR][1000 genomes];0.87[AMR][1000 genomes];0.80[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1209951	0.88[AFR][1000 genomes];0.87[AMR][1000 genomes];0.80[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1209952	0.85[ASW][hapmap];0.93[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];0.98[LWK][hapmap];0.90[MEX][hapmap];0.85[MKK][hapmap];0.80[TSI][hapmap];0.96[YRI][hapmap];0.96[AFR][1000 genomes];0.96[AMR][1000 genomes];0.91[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1209955	0.84[AMR][1000 genomes];0.91[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2070529	0.87[CEU][hapmap];0.85[TSI][hapmap]
rs2070530	0.87[CEU][hapmap];0.85[TSI][hapmap]
rs457705	0.87[CEU][hapmap];0.85[TSI][hapmap]
rs460982	0.87[CEU][hapmap];0.85[TSI][hapmap]
rs461155	0.87[CEU][hapmap];0.85[TSI][hapmap]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1058591	chr21:40114130-40190594	Flanking Bivalent TSS/Enh Weak transcription Flanking Active TSS Enhancers Active TSS Genic enhancers Strong transcription Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	28 gene(s)	inside rSNPs	diseases
2	nsv1062425	chr21:40172471-40380976	Enhancers Flanking Active TSS Weak transcription Genic enhancers Flanking Bivalent TSS/Enh Strong transcription Active TSS Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	47 gene(s)	inside rSNPs	diseases
3	nsv544442	chr21:40172471-40380976	Enhancers Genic enhancers Active TSS Weak transcription Strong transcription Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats Flanking Active TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	47 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs1209954	KCNJ6	cis	parietal	SCAN

Chromatin state (count:123 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr21:40176600-40182000	Active TSS	Brain Anterior Caudate	brain
2	chr21:40176800-40182800	Active TSS	Brain Cingulate Gyrus	brain
3	chr21:40176800-40182800	Active TSS	Brain Hippocampus Middle	brain
4	chr21:40177200-40182400	Active TSS	Lung	lung
5	chr21:40177600-40182200	Active TSS	Brain Inferior Temporal Lobe	brain
6	chr21:40178600-40182800	Transcr. at gene 5' and 3'	NHEK	skin
7	chr21:40179000-40182800	Transcr. at gene 5' and 3'	Primary hematopoietic stem cells short term culture	blood
8	chr21:40179000-40184000	Transcr. at gene 5' and 3'	Dnd41	blood
9	chr21:40179000-40184800	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
10	chr21:40179200-40181800	Weak transcription	HSMM	muscle
11	chr21:40179200-40184600	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
12	chr21:40179400-40182000	Transcr. at gene 5' and 3'	Primary hematopoietic stem cells G-CSF-mobilized Male	--
13	chr21:40179600-40181800	Transcr. at gene 5' and 3'	IMR90 fetal lung fibroblasts Cell Line	lung
14	chr21:40179600-40181800	Transcr. at gene 5' and 3'	HepG2	liver
15	chr21:40179600-40182200	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
16	chr21:40179600-40182400	Transcr. at gene 5' and 3'	Primary hematopoietic stem cells G-CSF-mobilized Female	--
17	chr21:40179600-40182600	Transcr. at gene 5' and 3'	Fetal Intestine Large	intestine
18	chr21:40179600-40182600	Weak transcription	Osteobl	bone
19	chr21:40179600-40183000	Transcr. at gene 5' and 3'	Foreskin Keratinocyte Primary Cells skin03	Skin
20	chr21:40179600-40183600	Transcr. at gene 5' and 3'	A549	lung
21	chr21:40179600-40184800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
22	chr21:40179600-40184800	Weak transcription	HSMMtube	muscle
23	chr21:40179800-40181800	Transcr. at gene 5' and 3'	Fetal Lung	lung
24	chr21:40179800-40182800	Transcr. at gene 5' and 3'	Hela-S3	cervix
25	chr21:40179800-40183000	Weak transcription	Primary T cells fromperipheralblood	blood
26	chr21:40179800-40183400	Transcr. at gene 5' and 3'	Liver	Liver
27	chr21:40179800-40185200	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
28	chr21:40180000-40181800	Enhancers	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
29	chr21:40180000-40181800	Genic enhancers	ES-UCSF4 Cell Line	embryonic stem cell
30	chr21:40180000-40182200	Transcr. at gene 5' and 3'	Breast Myoepithelial Primary Cells	Breast
31	chr21:40180000-40182800	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
32	chr21:40180000-40183000	Genic enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
33	chr21:40180000-40183000	Transcr. at gene 5' and 3'	Fetal Intestine Small	intestine
34	chr21:40180000-40183000	Transcr. at gene 5' and 3'	NHLF	lung
35	chr21:40180000-40184800	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
36	chr21:40180000-40185000	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
37	chr21:40180000-40186200	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
38	chr21:40180200-40181800	Active TSS	Esophagus	oesophagus
39	chr21:40180200-40181800	Enhancers	Placenta Amnion	Placenta Amnion
40	chr21:40180200-40182000	Enhancers	H9 Cell Line	embryonic stem cell
41	chr21:40180200-40183400	Active TSS	Right Atrium	heart
42	chr21:40180200-40183600	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
43	chr21:40180200-40183800	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
44	chr21:40180200-40185800	Enhancers	iPS-15b Cell Line	embryonic stem cell
45	chr21:40180200-40186200	Weak transcription	Primary T killer memory cells from peripheral blood	blood
46	chr21:40180200-40198400	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
47	chr21:40180400-40181800	Flanking Active TSS	Primary neutrophils fromperipheralblood	blood
48	chr21:40180400-40181800	Genic enhancers	Fetal Thymus	thymus
49	chr21:40180400-40182000	Enhancers	ES-I3 Cell Line	embryonic stem cell
50	chr21:40180400-40182000	Weak transcription	Primary T helper cells fromperipheralblood	blood

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