Variant report

Variant	rs13430277
Chromosome Location	chr2:47455238-47455239
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr2:47401787..47404343-chr2:47454142..47456763,3	MCF-7	breast:
2	chr2:47399756..47406251-chr2:47447036..47455846,12	MCF-7	breast:
3	chr2:47399705..47406684-chr2:47448496..47456698,16	K562	blood:
4	chr2:47419286..47421209-chr2:47454882..47457693,2	MCF-7	breast:
5	chr2:47451335..47453658-chr2:47453697..47456326,2	MCF-7	breast:
6	chr2:47399705..47405092-chr2:47450546..47458227,19	K562	blood:
7	chr2:47452345..47454121-chr2:47454262..47455774,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000143933	Chromatin interaction
ENSG00000226087	Chromatin interaction

Extended variants
information (count: 18 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:14)

rs_ID	r²[population]
rs10221560	1.00[CHB][hapmap];1.00[JPT][hapmap];0.80[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs13384441	0.98[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13390912	0.90[AMR][1000 genomes];0.81[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs13391158	0.85[GIH][hapmap]
rs1723482	0.80[CEU][hapmap];0.80[CHB][hapmap]
rs1723484	0.80[CEU][hapmap];0.80[CHB][hapmap]
rs1723493	0.81[CEU][hapmap]
rs72879030	0.89[ASN][1000 genomes]
rs72879063	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs815802	0.80[CHB][hapmap]
rs815815	0.81[CEU][hapmap];0.80[CHB][hapmap]
rs815816	0.80[CHB][hapmap]
rs904166	0.85[GIH][hapmap]
rs998587	0.87[CEU][hapmap];0.90[CHB][hapmap];1.00[JPT][hapmap];0.92[YRI][hapmap];0.91[AFR][1000 genomes];0.96[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[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:4)

SNP	Gene	Cis/trans	Tissue	Source
rs13430277	TTC7A	cis	cerebellum	SCAN
rs13430277	C2orf61	cis	cerebellum	SCAN
rs13430277	CALM2	cis	cerebellum	SCAN
rs13430277	CALM2	cis	parietal	SCAN

Chromatin state (count:51 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:47447200-47455400	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
2	chr2:47448000-47455400	Enhancers	Fetal Muscle Leg	muscle
3	chr2:47450000-47455600	Enhancers	Fetal Intestine Small	intestine
4	chr2:47450000-47455800	Enhancers	K562	blood
5	chr2:47450000-47456000	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
6	chr2:47450200-47455600	Enhancers	Fetal Intestine Large	intestine
7	chr2:47451000-47455600	Enhancers	Placenta	Placenta
8	chr2:47452200-47455400	Enhancers	Brain Hippocampus Middle	brain
9	chr2:47452200-47455800	Enhancers	Fetal Adrenal Gland	Adrenal Gland
10	chr2:47452400-47455400	Enhancers	Cortex derived primary cultured neurospheres	brain
11	chr2:47452600-47455600	Enhancers	Brain Dorsolateral Prefrontal Cortex	brain
12	chr2:47452600-47455800	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
13	chr2:47452800-47455400	Enhancers	Fetal Brain Male	brain
14	chr2:47453000-47455400	Enhancers	Brain Cingulate Gyrus	brain
15	chr2:47453200-47455400	Enhancers	HSMMtube	muscle
16	chr2:47453200-47457600	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
17	chr2:47453200-47457800	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
18	chr2:47453200-47459600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
19	chr2:47453600-47455400	Enhancers	HSMM	muscle
20	chr2:47453600-47457400	Weak transcription	Rectal Smooth Muscle	rectum
21	chr2:47453600-47457600	Weak transcription	Breast Myoepithelial Primary Cells	Breast
22	chr2:47453800-47463600	Weak transcription	Right Atrium	heart
23	chr2:47453800-47463800	Weak transcription	Spleen	Spleen
24	chr2:47454000-47457600	Weak transcription	Adipose Nuclei	Adipose
25	chr2:47454000-47458800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
26	chr2:47454000-47461000	Weak transcription	iPS-20b Cell Line	embryonic stem cell
27	chr2:47454200-47457400	Weak transcription	Skeletal Muscle Male	skeletal muscle
28	chr2:47454200-47457400	Weak transcription	Skeletal Muscle Female	skeletal muscle
29	chr2:47454200-47457600	Weak transcription	Colon Smooth Muscle	Colon
30	chr2:47454400-47455400	Bivalent Enhancer	HepG2	liver
31	chr2:47454400-47455600	Enhancers	Brain Germinal Matrix	brain
32	chr2:47454400-47455800	Enhancers	Fetal Brain Female	brain
33	chr2:47454600-47455400	Flanking Active TSS	H9 Derived Neuron Cultured Cells	ES cell derived
34	chr2:47454600-47455400	Enhancers	Brain Angular Gyrus	brain
35	chr2:47454600-47455600	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
36	chr2:47454600-47455600	Flanking Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
37	chr2:47454600-47455800	Enhancers	Ovary	ovary
38	chr2:47454600-47457600	Weak transcription	Liver	Liver
39	chr2:47454800-47455400	Enhancers	HUES6 Cell Line	embryonic stem cell
40	chr2:47454800-47455400	Enhancers	HUES64 Cell Line	embryonic stem cell
41	chr2:47454800-47455400	Flanking Active TSS	Brain Inferior Temporal Lobe	brain
42	chr2:47454800-47455800	Enhancers	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
43	chr2:47454800-47456000	Enhancers	H9 Cell Line	embryonic stem cell
44	chr2:47454800-47461000	Weak transcription	Stomach Smooth Muscle	stomach
45	chr2:47455000-47455400	Enhancers	Fetal Muscle Trunk	muscle
46	chr2:47455000-47456000	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
47	chr2:47455000-47459600	Weak transcription	NHLF	lung
48	chr2:47455200-47455400	Enhancers	iPS-15b Cell Line	embryonic stem cell
49	chr2:47455200-47455400	Enhancers	Brain Substantia Nigra	brain
50	chr2:47455200-47455600	Enhancers	Brain Anterior Caudate	brain

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