Variant report

Variant	rs7522283
Chromosome Location	chr1:113254267-113254268
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:1)
CpG islands
(count:0)
Chromatin interactive
region (count:6)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

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

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr1:113254130-113255451	K562	blood:	n/a	n/a

No data

(count:6 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr1:113160602..113163896-chr1:113252357..113259247,7	K562	blood:
2	chr1:113215712..113221627-chr1:113253708..113259381,5	MCF-7	breast:
3	chr1:113239573..113244483-chr1:113252369..113259292,10	K562	blood:
4	chr1:113254236..113255978-chr1:113257610..113260572,2	MCF-7	breast:
5	chr1:113166528..113169223-chr1:113253776..113256616,2	MCF-7	breast:
6	chr1:113253460..113256284-chr1:113256871..113259194,3	MCF-7	breast:

No data

Variant related genes	Relation type
ENSG00000261595	TF binding region
RHOC	TF binding region
ENSG00000271810	TF binding region
ENSG00000155363	Chromatin interaction
ENSG00000007341	Chromatin interaction
ENSG00000235299	Chromatin interaction
ENSG00000116489	Chromatin interaction
ENSG00000261595	Chromatin interaction
ENSG00000155367	Chromatin interaction

Extended variants
information (count: 25 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:12)

rs_ID	r²[population]
rs11102513	0.95[JPT][hapmap]
rs11102514	0.95[JPT][hapmap]
rs11102522	1.00[CEU][hapmap];0.84[GIH][hapmap];0.91[JPT][hapmap];0.91[MEX][hapmap];0.96[TSI][hapmap];0.83[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs12040903	0.92[ASN][1000 genomes]
rs12040988	0.95[JPT][hapmap]
rs12049572	0.82[JPT][hapmap]
rs12120956	0.95[JPT][hapmap]
rs12122980	0.95[JPT][hapmap]
rs12130243	0.95[JPT][hapmap]
rs12756815	0.95[JPT][hapmap]
rs17030613	0.95[JPT][hapmap]
rs2273368	0.82[JPT][hapmap]

Variant overlapped rSNPs/rCNVs (count:13 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1002971	chr1:112924725-113740584	Weak transcription Enhancers Active TSS Flanking Bivalent TSS/Enh Flanking Active TSS Strong transcription Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	166 gene(s)	inside rSNPs	diseases
2	nsv535059	chr1:112924725-113740584	Enhancers Weak transcription Strong transcription Flanking Active TSS Bivalent/Poised TSS Active TSS Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	166 gene(s)	inside rSNPs	diseases
3	nsv1010276	chr1:113123932-113740584	Weak transcription Enhancers Strong transcription Active TSS Flanking Active TSS Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	158 gene(s)	inside rSNPs	diseases
4	nsv533295	chr1:113167645-113589588	Flanking Active TSS Active TSS Strong transcription Weak transcription Enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	93 gene(s)	inside rSNPs	diseases
5	nsv1012119	chr1:113214869-113759081	Enhancers Weak transcription Genic enhancers Bivalent Enhancer Strong transcription Flanking Active TSS Flanking Bivalent TSS/Enh Active TSS ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	103 gene(s)	inside rSNPs	diseases
6	nsv535060	chr1:113214869-113759081	Enhancers Flanking Active TSS Weak transcription Transcr. at gene 5' and 3' Genic enhancers Active TSS Bivalent Enhancer Strong transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	103 gene(s)	inside rSNPs	diseases
7	nsv529238	chr1:113229946-113759080	Weak transcription Enhancers Strong transcription Genic enhancers Active TSS Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	100 gene(s)	inside rSNPs	diseases
8	esv18511	chr1:113246318-113350775	Enhancers Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent/Poised TSS Strong transcription Weak transcription Transcr. at gene 5' and 3' ZNF genes & repeats Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	36 gene(s)	inside rSNPs	diseases
9	nsv998794	chr1:113246630-113310418	Active TSS Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Weak transcription Bivalent/Poised TSS Enhancers Genic enhancers Strong transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	36 gene(s)	inside rSNPs	diseases
10	nsv872157	chr1:113247467-113265819	Flanking Active TSS Flanking Bivalent TSS/Enh Weak transcription Bivalent Enhancer Active TSS Transcr. at gene 5' and 3' Enhancers Genic enhancers Bivalent/Poised TSS Strong transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	35 gene(s)	inside rSNPs	diseases
11	nsv547566	chr1:113248365-113301657	Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS Enhancers Active TSS Weak transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3' Strong transcription Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	27 gene(s)	inside rSNPs	diseases
12	nsv872158	chr1:113250888-113265819	Active TSS Weak transcription Bivalent/Poised TSS Enhancers Bivalent Enhancer Flanking Active TSS Strong transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	18 gene(s)	inside rSNPs	diseases
13	nsv872159	chr1:113252091-113265819	Flanking Active TSS Bivalent Enhancer Weak transcription Flanking Bivalent TSS/Enh Active TSS Enhancers Bivalent/Poised TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs7522283	CHIA	cis	cerebellum	SCAN
rs7522283	PPM1J	cis	cerebellum	SCAN
rs7522283	CTTNBP2NL	cis	parietal	SCAN
rs7522283	KCND3	cis	cerebellum	SCAN

Chromatin state (count:66 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:113249000-113256400	Weak transcription	Fetal Heart	heart
2	chr1:113250400-113256000	Weak transcription	Brain Substantia Nigra	brain
3	chr1:113250400-113256000	Weak transcription	Right Ventricle	heart
4	chr1:113250400-113256200	Weak transcription	Esophagus	oesophagus
5	chr1:113250400-113256200	Weak transcription	Gastric	stomach
6	chr1:113250400-113256400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
7	chr1:113250400-113256600	Weak transcription	Brain Angular Gyrus	brain
8	chr1:113250400-113256600	Weak transcription	Brain Cingulate Gyrus	brain
9	chr1:113250400-113256600	Weak transcription	Psoas Muscle	Psoas
10	chr1:113250400-113256800	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
11	chr1:113250400-113256800	Weak transcription	Aorta	Aorta
12	chr1:113250600-113255200	Weak transcription	Brain Hippocampus Middle	brain
13	chr1:113250600-113255800	Weak transcription	Liver	Liver
14	chr1:113250600-113256000	Weak transcription	Adipose Nuclei	Adipose
15	chr1:113250600-113256000	Weak transcription	Brain Anterior Caudate	brain
16	chr1:113250600-113256000	Weak transcription	Left Ventricle	heart
17	chr1:113250600-113256000	Weak transcription	Stomach Mucosa	stomach
18	chr1:113250600-113256200	Weak transcription	Pancreas	Pancrea
19	chr1:113250600-113256200	Weak transcription	Spleen	Spleen
20	chr1:113250600-113256600	Weak transcription	Brain Inferior Temporal Lobe	brain
21	chr1:113250600-113256800	Weak transcription	Colon Smooth Muscle	Colon
22	chr1:113250600-113257000	Weak transcription	HUVEC	blood vessel
23	chr1:113250800-113255600	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
24	chr1:113250800-113256000	Weak transcription	Primary B cells from peripheral blood	blood
25	chr1:113250800-113256200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
26	chr1:113250800-113256200	Weak transcription	Primary B cells from cord blood	blood
27	chr1:113250800-113256600	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
28	chr1:113250800-113256600	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
29	chr1:113250800-113256600	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
30	chr1:113250800-113256600	Weak transcription	Osteobl	bone
31	chr1:113251000-113256200	Weak transcription	HMEC	breast
32	chr1:113251000-113256400	Weak transcription	NHEK	skin
33	chr1:113251000-113257200	Weak transcription	Hela-S3	cervix
34	chr1:113251400-113256200	Weak transcription	K562	blood
35	chr1:113251400-113256800	Weak transcription	Placenta Amnion	Placenta Amnion
36	chr1:113252000-113255600	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
37	chr1:113252400-113254400	Strong transcription	Breast Myoepithelial Primary Cells	Breast
38	chr1:113252400-113255600	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
39	chr1:113253000-113256000	Weak transcription	GM12878-XiMat	blood
40	chr1:113253400-113254400	Bivalent Enhancer	iPS-15b Cell Line	embryonic stem cell
41	chr1:113253400-113256000	Weak transcription	H9 Cell Line	embryonic stem cell
42	chr1:113253400-113256200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
43	chr1:113253400-113256400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
44	chr1:113253800-113254400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
45	chr1:113253800-113254400	Bivalent Enhancer	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
46	chr1:113253800-113254400	Bivalent Enhancer	Fetal Thymus	thymus
47	chr1:113253800-113254800	Enhancers	iPS-18 Cell Line	embryonic stem cell
48	chr1:113253800-113255000	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
49	chr1:113253800-113255400	Genic enhancers	Skeletal Muscle Male	skeletal muscle
50	chr1:113253800-113255800	Enhancers	H1 Cell Line	embryonic stem cell

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