Variant report

Variant	rs2838447
Chromosome Location	chr21:45370888-45370889
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr21:45370723..45373935-chr21:45374637..45377762,3	K562	blood:
2	chr21:45368958..45371465-chr21:45372849..45375980,3	K562	blood:
3	chr21:45365752..45369442-chr21:45370702..45375252,7	MCF-7	breast:

Variant related genes	Relation type
ENSG00000160216	Chromatin interaction

Extended variants
information (count: 26 )
Associated
traits (count: 2 )

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

rs_ID	r²[population]
rs14151	0.86[CHB][hapmap]
rs2000788	0.82[ASN][1000 genomes]
rs2254072	1.00[CEU][hapmap];0.91[CHB][hapmap];0.90[JPT][hapmap];0.86[ASN][1000 genomes]
rs2838449	0.87[ASN][1000 genomes]
rs2838450	1.00[CEU][hapmap]
rs2838455	0.91[CHB][hapmap];0.95[JPT][hapmap]
rs2838458	0.91[CHB][hapmap];0.95[JPT][hapmap]
rs3788092	0.88[ASN][1000 genomes]
rs3788096	0.91[CHB][hapmap];0.90[JPT][hapmap]
rs4818874	0.82[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs4818877	0.82[ASN][1000 genomes]
rs4819354	0.82[ASN][1000 genomes]
rs57524571	0.81[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs59443212	0.86[ASN][1000 genomes]
rs61033068	0.80[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs7282631	0.86[CHB][hapmap];0.85[JPT][hapmap]
rs915876	1.00[CEU][hapmap];0.91[CHB][hapmap];0.88[CHD][hapmap];0.91[GIH][hapmap];0.95[JPT][hapmap];0.96[MEX][hapmap];0.82[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs9974326	1.00[CEU][hapmap];1.00[MEX][hapmap]
rs9982600	1.00[CEU][hapmap]
rs9983354	0.85[CHB][hapmap];0.89[JPT][hapmap]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv531545	chr21:45095397-45395904	Enhancers Flanking Active TSS Weak transcription Flanking Bivalent TSS/Enh Genic enhancers 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	49 gene(s)	inside rSNPs	diseases
2	esv33817	chr21:45169412-46031810	Weak transcription Bivalent/Poised TSS Enhancers Flanking Active TSS Strong transcription Genic enhancers Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	121 gene(s)	inside rSNPs	diseases
3	nsv913887	chr21:45344799-45670770	Flanking Active TSS Enhancers Weak transcription Strong transcription Active TSS Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	57 gene(s)	inside rSNPs	diseases
4	nsv913888	chr21:45351206-45428278	Genic enhancers Enhancers Strong transcription Flanking Active TSS Weak transcription Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Active TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	15 gene(s)	inside rSNPs	diseases
5	nsv1055772	chr21:45353436-45373304	Weak transcription Enhancers Genic enhancers Strong transcription Flanking Active TSS Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
6	nsv913889	chr21:45361044-45414119	Weak transcription Genic enhancers Flanking Active TSS Enhancers Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	12 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs2838447	TRPM2	cis	cerebellum	SCAN
rs2838447	DNMT3L	cis	parietal	SCAN

Chromatin state (count:93 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr21:45343000-45372400	Weak transcription	Small Intestine	intestine
2	chr21:45343800-45379800	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
3	chr21:45359000-45371400	Weak transcription	HSMMtube	muscle
4	chr21:45359200-45376000	Weak transcription	HUVEC	blood vessel
5	chr21:45359200-45378800	Weak transcription	NHEK	skin
6	chr21:45359200-45379000	Weak transcription	Rectal Smooth Muscle	rectum
7	chr21:45359400-45371800	Weak transcription	Stomach Mucosa	stomach
8	chr21:45359400-45376000	Weak transcription	Muscle Satellite Cultured Cells	--
9	chr21:45359400-45389000	Weak transcription	Primary neutrophils fromperipheralblood	blood
10	chr21:45359800-45376400	Weak transcription	NHLF	lung
11	chr21:45360800-45371800	Weak transcription	Rectal Mucosa Donor 31	rectum
12	chr21:45361000-45379200	Weak transcription	Ovary	ovary
13	chr21:45363600-45377000	Strong transcription	Monocytes-CD14+_RO01746	blood
14	chr21:45364800-45378400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
15	chr21:45366600-45371000	Strong transcription	Fetal Intestine Large	intestine
16	chr21:45366800-45372200	Strong transcription	Foreskin Fibroblast Primary Cells skin02	Skin
17	chr21:45367200-45376600	Weak transcription	Pancreas	Pancrea
18	chr21:45367200-45379200	Weak transcription	Fetal Brain Female	brain
19	chr21:45368400-45379400	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
20	chr21:45368400-45379800	Weak transcription	Rectal Mucosa Donor 29	rectum
21	chr21:45368600-45372200	Weak transcription	Sigmoid Colon	Sigmoid Colon
22	chr21:45368600-45374000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
23	chr21:45368600-45374600	Weak transcription	Gastric	stomach
24	chr21:45369000-45376400	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
25	chr21:45369200-45379400	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
26	chr21:45369400-45371200	Strong transcription	Cortex derived primary cultured neurospheres	brain
27	chr21:45369400-45371400	Weak transcription	Colonic Mucosa	Colon
28	chr21:45369400-45372800	Weak transcription	Stomach Smooth Muscle	stomach
29	chr21:45369400-45375800	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
30	chr21:45369400-45378200	Weak transcription	K562	blood
31	chr21:45369400-45378600	Weak transcription	HepG2	liver
32	chr21:45369400-45379800	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
33	chr21:45369400-45388800	Weak transcription	Colon Smooth Muscle	Colon
34	chr21:45369600-45371000	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
35	chr21:45369600-45371000	Strong transcription	Lung	lung
36	chr21:45369600-45371200	Weak transcription	Skeletal Muscle Male	skeletal muscle
37	chr21:45369600-45371400	Strong transcription	Foreskin Fibroblast Primary Cells skin01	Skin
38	chr21:45369600-45371400	Weak transcription	Skeletal Muscle Female	skeletal muscle
39	chr21:45369600-45371600	Strong transcription	Fetal Intestine Small	intestine
40	chr21:45369600-45372000	Strong transcription	Primary monocytes fromperipheralblood	blood
41	chr21:45369600-45372600	Weak transcription	Fetal Muscle Leg	muscle
42	chr21:45369600-45373000	Weak transcription	HSMM	muscle
43	chr21:45369600-45374400	Weak transcription	Esophagus	oesophagus
44	chr21:45369600-45376000	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
45	chr21:45369600-45376000	Strong transcription	Fetal Stomach	stomach
46	chr21:45369600-45376200	Weak transcription	Brain Hippocampus Middle	brain
47	chr21:45369600-45376200	Weak transcription	Fetal Lung	lung
48	chr21:45369600-45376400	Weak transcription	Adipose Nuclei	Adipose
49	chr21:45369600-45376400	Weak transcription	Brain Anterior Caudate	brain
50	chr21:45369600-45376400	Weak transcription	Brain Substantia Nigra	brain

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