Variant report

Variant	rs13422681
Chromosome Location	chr2:47460212-47460213
allele	A/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	chr2:47457584..47460333-chr2:47462013..47466109,5	K562	blood:
2	chr2:47457105..47460333-chr2:47461555..47466109,6	K562	blood:
3	chr2:47399058..47406701-chr2:47458639..47471254,30	K562	blood:
4	chr2:47402299..47404755-chr2:47459494..47461483,3	K562	blood:
5	chr2:47419054..47421254-chr2:47460035..47461567,2	MCF-7	breast:
6	chr2:47402441..47405401-chr2:47458332..47462423,3	MCF-7	breast:
7	chr2:47450260..47451975-chr2:47459520..47461671,2	MCF-7	breast:
8	chr2:47452155..47456845-chr2:47457854..47461355,4	K562	blood:

No data

Variant related genes	Relation type
ENSG00000143933	Chromatin interaction
ENSG00000226087	Chromatin interaction

Extended variants
information (count: 19 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:15)

rs_ID	r²[population]
rs10169873	0.83[JPT][hapmap];0.80[ASN][1000 genomes]
rs1021609	0.82[ASN][1000 genomes]
rs1021610	0.82[ASN][1000 genomes]
rs1039162	0.83[CHB][hapmap]
rs11899830	0.81[ASN][1000 genomes]
rs11899833	0.81[ASN][1000 genomes]
rs12612040	0.85[JPT][hapmap]
rs13391158	0.83[CHB][hapmap];0.82[CHD][hapmap];0.84[ASN][1000 genomes]
rs17485833	0.85[ASW][hapmap];0.90[GIH][hapmap];0.82[JPT][hapmap]
rs17557422	0.81[ASN][1000 genomes]
rs4952877	0.83[CHB][hapmap];0.82[JPT][hapmap];0.83[ASN][1000 genomes]
rs4953479	0.82[CHB][hapmap];0.80[JPT][hapmap];0.83[ASN][1000 genomes]
rs6544972	0.85[ASW][hapmap];0.90[GIH][hapmap];0.88[MKK][hapmap]
rs904166	0.82[CHD][hapmap];0.83[ASN][1000 genomes]
rs904167	0.81[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	nsv817517	chr2:46819371-47715140	Enhancers Weak transcription Genic enhancers Bivalent Enhancer Flanking Active TSS Strong transcription Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	152 gene(s)	inside rSNPs	diseases
2	nsv1004828	chr2:47056849-47814482	Weak transcription Enhancers Strong transcription Genic enhancers Flanking Active TSS Transcr. at gene 5' and 3' Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	144 gene(s)	inside rSNPs	diseases
3	esv10649	chr2:47429316-47472670	Enhancers Weak transcription Flanking Active TSS Bivalent Enhancer Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
4	nsv531348	chr2:47433147-47827310	Flanking Bivalent TSS/Enh Weak transcription Strong transcription Enhancers Flanking Active TSS Genic enhancers Active TSS Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	50 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs13422681	CALM2	cis	parietal	SCAN
rs13422681	THADA	cis	cerebellum	SCAN
rs13422681	CALM2	cis	cerebellum	SCAN

Chromatin state (count:32 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:47453800-47463600	Weak transcription	Right Atrium	heart
2	chr2:47453800-47463800	Weak transcription	Spleen	Spleen
3	chr2:47454000-47461000	Weak transcription	iPS-20b Cell Line	embryonic stem cell
4	chr2:47454800-47461000	Weak transcription	Stomach Smooth Muscle	stomach
5	chr2:47455400-47463600	Weak transcription	HUES6 Cell Line	embryonic stem cell
6	chr2:47455400-47463600	Weak transcription	HSMMtube	muscle
7	chr2:47455600-47461000	Weak transcription	Fetal Intestine Small	intestine
8	chr2:47455600-47463600	Weak transcription	Brain Anterior Caudate	brain
9	chr2:47455600-47464600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
10	chr2:47455800-47460800	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
11	chr2:47455800-47461400	Weak transcription	K562	blood
12	chr2:47456000-47463600	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
13	chr2:47457800-47460400	Weak transcription	Fetal Muscle Trunk	muscle
14	chr2:47458000-47460400	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
15	chr2:47458000-47461000	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
16	chr2:47458000-47463600	Weak transcription	HSMM	muscle
17	chr2:47458200-47463800	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
18	chr2:47458600-47464000	Weak transcription	Breast Myoepithelial Primary Cells	Breast
19	chr2:47458800-47461200	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
20	chr2:47459000-47460400	Weak transcription	Cortex derived primary cultured neurospheres	brain
21	chr2:47459000-47464600	Weak transcription	Ovary	ovary
22	chr2:47459600-47460400	Enhancers	Adipose Nuclei	Adipose
23	chr2:47459600-47460600	Enhancers	NHLF	lung
24	chr2:47459600-47461200	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
25	chr2:47459600-47462400	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
26	chr2:47459800-47461000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
27	chr2:47460000-47460400	Enhancers	HepG2	liver
28	chr2:47460000-47460600	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
29	chr2:47460000-47461800	Enhancers	Fetal Adrenal Gland	Adrenal Gland
30	chr2:47460000-47465400	Enhancers	Fetal Intestine Large	intestine
31	chr2:47460200-47460600	Enhancers	Rectal Smooth Muscle	rectum
32	chr2:47460200-47464000	Weak transcription	Colon Smooth Muscle	Colon

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