Variant report

Variant	rs2836822
Chromosome Location	chr21:40378632-40378633
allele	A/G
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	chr21:40376259-40379214	HUVEC	blood vessel:	n/a	n/a
2	STAT3	chr21:40378560-40379184	MCF10A-Er-Src	breast:	n/a	chr21:40378898-40378910
3	POLR2A	chr21:40378625-40379782	MCF10A-Er-Src	breast:	n/a	n/a
4	FOS	chr21:40378545-40378948	MCF10A-Er-Src	breast:	n/a	n/a
5	FOS	chr21:40378599-40379067	MCF10A-Er-Src	breast:	n/a	n/a
6	STAT3	chr21:40378584-40379066	MCF10A-Er-Src	breast:	n/a	chr21:40378898-40378910

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-PSMG1-6	chr21:40378574-40378710	ENSG00000237721

Variant related genes	Relation type
ENSG00000235888	TF binding region

Extended variants
information (count: 9 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:4)

rs_ID	r²[population]
rs2836815	0.82[JPT][hapmap]
rs2836823	0.82[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.81[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.96[MEX][hapmap];0.87[TSI][hapmap];0.82[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs3746882	1.00[LWK][hapmap]
rs9305658	0.91[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	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
2	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
3	nsv587477	chr21:40228920-40512004	Enhancers Flanking Active TSS Weak transcription Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Active TSS Genic enhancers Bivalent/Poised TSS Strong transcription Transcr. at gene 5' and 3'	TF binding region Chromatin interactive region lncRNA	35 gene(s)	inside rSNPs	diseases
4	nsv1061831	chr21:40376316-40583555	Enhancers Strong transcription Weak transcription Active TSS Flanking Active TSS Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	34 gene(s)	inside rSNPs	diseases
5	nsv544443	chr21:40376316-40583555	Enhancers Flanking Active TSS Weak transcription Active TSS Transcr. at gene 5' and 3' Strong transcription Bivalent Enhancer ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	34 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs2836822	RIPK4	cis	parietal	SCAN

Chromatin state (count:73 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr21:40366400-40381600	Weak transcription	Psoas Muscle	Psoas
2	chr21:40370800-40379200	Enhancers	NHDF-Ad	bronchial
3	chr21:40371200-40379800	Enhancers	Primary hematopoietic stem cells	blood
4	chr21:40371600-40379200	Bivalent Enhancer	Fetal Adrenal Gland	Adrenal Gland
5	chr21:40372000-40385000	Weak transcription	Pancreas	Pancrea
6	chr21:40373200-40379000	Weak transcription	Placenta Amnion	Placenta Amnion
7	chr21:40373400-40379000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
8	chr21:40374000-40380400	Enhancers	Adipose Nuclei	Adipose
9	chr21:40374600-40380400	Enhancers	Fetal Muscle Leg	muscle
10	chr21:40374800-40381000	Enhancers	Fetal Thymus	thymus
11	chr21:40375200-40379000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
12	chr21:40375400-40380000	Enhancers	Fetal Stomach	stomach
13	chr21:40375400-40380000	Enhancers	Sigmoid Colon	Sigmoid Colon
14	chr21:40375600-40379200	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
15	chr21:40375600-40379200	Enhancers	Osteobl	bone
16	chr21:40375800-40378800	Enhancers	Colon Smooth Muscle	Colon
17	chr21:40375800-40380400	Enhancers	Breast Myoepithelial Primary Cells	Breast
18	chr21:40376000-40379200	Enhancers	Brain Hippocampus Middle	brain
19	chr21:40376000-40379200	Enhancers	Spleen	Spleen
20	chr21:40376000-40379400	Enhancers	Primary B cells from cord blood	blood
21	chr21:40376000-40379600	Enhancers	Skeletal Muscle Female	skeletal muscle
22	chr21:40376000-40381200	Enhancers	Fetal Muscle Trunk	muscle
23	chr21:40376000-40381200	Enhancers	Placenta	Placenta
24	chr21:40376000-40384600	Enhancers	Lung	lung
25	chr21:40376200-40379200	Enhancers	Primary B cells from peripheral blood	blood
26	chr21:40376200-40379200	Enhancers	Stomach Mucosa	stomach
27	chr21:40376200-40379800	Enhancers	Right Atrium	heart
28	chr21:40376400-40379200	Flanking Active TSS	Primary hematopoietic stem cells short term culture	blood
29	chr21:40376400-40379200	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
30	chr21:40376600-40379200	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
31	chr21:40376600-40379400	Enhancers	HUES6 Cell Line	embryonic stem cell
32	chr21:40376600-40380200	Weak transcription	Fetal Kidney	kidney
33	chr21:40376600-40380400	Enhancers	Rectal Mucosa Donor 29	rectum
34	chr21:40376600-40383200	Enhancers	Fetal Lung	lung
35	chr21:40376800-40379600	Enhancers	H1 Cell Line	embryonic stem cell
36	chr21:40376800-40380400	Enhancers	Colonic Mucosa	Colon
37	chr21:40377000-40380000	Enhancers	iPS-15b Cell Line	embryonic stem cell
38	chr21:40377200-40379400	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
39	chr21:40377400-40380600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
40	chr21:40377400-40381600	Weak transcription	Aorta	Aorta
41	chr21:40377600-40378800	Enhancers	Dnd41	blood
42	chr21:40377600-40382400	Weak transcription	Fetal Intestine Large	intestine
43	chr21:40377600-40384200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
44	chr21:40377600-40384600	Weak transcription	H9 Cell Line	embryonic stem cell
45	chr21:40377800-40378800	Weak transcription	HMEC	breast
46	chr21:40377800-40380000	Enhancers	Brain Anterior Caudate	brain
47	chr21:40377800-40380000	Weak transcription	Stomach Smooth Muscle	stomach
48	chr21:40377800-40383000	Weak transcription	Thymus	Thymus
49	chr21:40378200-40378800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
50	chr21:40378200-40379200	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--

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