Variant report

Variant	rs13013607
Chromosome Location	chr2:47418041-47418042
allele	A/G
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:9)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:9 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr2:47196076..47198728-chr2:47417712..47420454,3	MCF-7	breast:
2	chr2:47412361..47428396-chr2:47486545..47501626,43	MCF-7	breast:
3	chr2:47417461..47419938-chr2:47504987..47507021,2	MCF-7	breast:
4	chr2:47416956..47422470-chr2:47490735..47503252,22	MCF-7	breast:
5	chr2:47193634..47195706-chr2:47417970..47421057,3	MCF-7	breast:
6	chr2:47417605..47420292-chr2:47545533..47548225,3	MCF-7	breast:
7	chr2:47416349..47419173-chr2:47571939..47573600,2	MCF-7	breast:
8	chr2:47257326..47259699-chr2:47417975..47420606,2	MCF-7	breast:
9	chr2:47302688..47305561-chr2:47417562..47420065,2	MCF-7	breast:

No data

Variant related genes	Relation type
ENSG00000234690	Chromatin interaction
ENSG00000119888	Chromatin interaction

Extended variants
information (count: 9 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:5)

rs_ID	r²[population]
rs13013543	1.00[CEU][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.94[TSI][hapmap];1.00[EUR][1000 genomes]
rs35701723	0.83[AFR][1000 genomes]
rs6715298	0.80[MKK][hapmap]
rs6750222	1.00[CHD][hapmap]
rs6757363	1.00[CHD][hapmap]

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	nsv457374	chr2:47313624-47448865	Enhancers Flanking Active TSS Weak transcription Genic enhancers Strong transcription Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	87 gene(s)	inside rSNPs	diseases
4	nsv581754	chr2:47313624-47448865	Weak transcription Strong transcription Genic enhancers Enhancers Flanking Active TSS Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	87 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs13013607	TTC7A	cis	cerebellum	SCAN
rs13013607	CALM2	cis	parietal	SCAN
rs13013607	CALM2	cis	cerebellum	SCAN
rs13013607	THADA	cis	cerebellum	SCAN

Chromatin state (count:62 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:47404400-47418600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
2	chr2:47414400-47418600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
3	chr2:47414400-47418600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
4	chr2:47414600-47418200	Weak transcription	iPS-18 Cell Line	embryonic stem cell
5	chr2:47414600-47418400	Weak transcription	iPS-15b Cell Line	embryonic stem cell
6	chr2:47414600-47418400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
7	chr2:47414800-47418600	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
8	chr2:47415200-47419600	Weak transcription	K562	blood
9	chr2:47416200-47419800	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
10	chr2:47416200-47421200	Enhancers	HUVEC	blood vessel
11	chr2:47416200-47421800	Enhancers	Fetal Stomach	stomach
12	chr2:47416200-47423800	Enhancers	HMEC	breast
13	chr2:47416400-47418600	Enhancers	Hela-S3	cervix
14	chr2:47416400-47421200	Flanking Active TSS	A549	lung
15	chr2:47416400-47421400	Enhancers	Rectal Smooth Muscle	rectum
16	chr2:47416400-47421400	Enhancers	HSMMtube	muscle
17	chr2:47416400-47423400	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
18	chr2:47416400-47423400	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
19	chr2:47416600-47419000	Enhancers	Fetal Lung	lung
20	chr2:47416600-47419400	Enhancers	Stomach Smooth Muscle	stomach
21	chr2:47416800-47418600	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
22	chr2:47416800-47419800	Enhancers	Cortex derived primary cultured neurospheres	brain
23	chr2:47416800-47421600	Enhancers	Colon Smooth Muscle	Colon
24	chr2:47416800-47424000	Enhancers	Fetal Intestine Small	intestine
25	chr2:47417000-47419400	Enhancers	Brain Germinal Matrix	brain
26	chr2:47417200-47418600	Enhancers	Brain Hippocampus Middle	brain
27	chr2:47417200-47419000	Weak transcription	Rectal Mucosa Donor 29	rectum
28	chr2:47417200-47419400	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
29	chr2:47417200-47421400	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
30	chr2:47417400-47418400	Weak transcription	Placenta Amnion	Placenta Amnion
31	chr2:47417400-47418600	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
32	chr2:47417400-47418600	Enhancers	Brain Anterior Caudate	brain
33	chr2:47417400-47418600	Bivalent Enhancer	HepG2	liver
34	chr2:47417400-47418800	Enhancers	HUES64 Cell Line	embryonic stem cell
35	chr2:47417400-47418800	Enhancers	Osteobl	bone
36	chr2:47417400-47421400	Enhancers	Duodenum Smooth Muscle	Duodenum
37	chr2:47417400-47422600	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
38	chr2:47417400-47423000	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
39	chr2:47417600-47418400	Weak transcription	Brain Substantia Nigra	brain
40	chr2:47417600-47418600	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
41	chr2:47417600-47418600	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
42	chr2:47417600-47418600	Weak transcription	Fetal Intestine Large	intestine
43	chr2:47417600-47418600	Weak transcription	Placenta	Placenta
44	chr2:47417600-47418600	Enhancers	NH-A	brain
45	chr2:47417600-47418800	Enhancers	Muscle Satellite Cultured Cells	--
46	chr2:47417600-47418800	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
47	chr2:47417600-47418800	Enhancers	HSMM	muscle
48	chr2:47417600-47419000	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
49	chr2:47417600-47419000	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
50	chr2:47417600-47419400	Enhancers	NHLF	lung

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