Variant report

Variant	rs1138690
Chromosome Location	chr4:3291401-3291402
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr4:3291362-3291470	HUVEC	blood vessel:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr4:3245063..3247633-chr4:3289230..3291965,2	MCF-7	breast:
2	chr4:3289451..3291897-chr4:3292555..3295827,4	K562	blood:

Variant related genes	Relation type
RGS12	TF binding region
ENSG00000159788	Chromatin interaction
ENSG00000188981	Chromatin interaction

Extended variants
information (count: 32 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:18)

rs_ID	r²[population]
rs12500459	0.86[JPT][hapmap];0.89[ASN][1000 genomes]
rs12504986	0.84[ASN][1000 genomes]
rs12505018	0.89[ASN][1000 genomes]
rs12506821	0.90[CHB][hapmap];0.82[CHD][hapmap];0.94[JPT][hapmap];0.89[ASN][1000 genomes]
rs12508004	0.90[CHB][hapmap];0.82[CHD][hapmap];0.94[JPT][hapmap];0.89[ASN][1000 genomes]
rs12510489	0.90[CHB][hapmap];0.82[CHD][hapmap];0.94[JPT][hapmap];0.89[ASN][1000 genomes]
rs2051559	1.00[CHB][hapmap];0.84[CHD][hapmap];1.00[JPT][hapmap];0.97[ASN][1000 genomes]
rs3129317	0.93[AMR][1000 genomes];0.92[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs3135062	0.96[ASN][1000 genomes]
rs3135063	0.87[CEU][hapmap];0.93[JPT][hapmap];0.83[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs57010886	0.88[ASN][1000 genomes]
rs73193339	0.86[ASN][1000 genomes]
rs73193340	0.88[ASN][1000 genomes]
rs73193341	0.88[ASN][1000 genomes]
rs73193343	0.89[ASN][1000 genomes]
rs73193346	0.89[ASN][1000 genomes]
rs7658412	0.89[ASN][1000 genomes]
rs7658462	0.90[CHB][hapmap];0.82[CHD][hapmap];0.93[JPT][hapmap];0.86[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:14 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv3418626	chr4:2741174-3461492	Genic enhancers Weak transcription Active TSS Strong transcription Enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	63 gene(s)	inside rSNPs	diseases
2	esv3397632	chr4:2741239-3460583	Enhancers Flanking Active TSS Weak transcription Genic enhancers Active TSS Strong transcription Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	63 gene(s)	inside rSNPs	diseases
3	nsv998290	chr4:3176454-3355758	Strong transcription Enhancers Weak transcription ZNF genes & repeats Active TSS Bivalent/Poised TSS Genic enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	11 gene(s)	inside rSNPs	diseases
4	nsv878454	chr4:3215835-3305739	Active TSS Flanking Active TSS Bivalent Enhancer Enhancers Weak transcription Strong transcription Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region miRNA target site	6 gene(s)	inside rSNPs	diseases
5	nsv878455	chr4:3215835-3344891	Strong transcription Enhancers Weak transcription Bivalent Enhancer ZNF genes & repeats Flanking Active TSS Genic enhancers Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	10 gene(s)	inside rSNPs	diseases
6	nsv878456	chr4:3215835-3467519	Enhancers Weak transcription Strong transcription Flanking Active TSS Genic enhancers Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	13 gene(s)	inside rSNPs	diseases
7	nsv428106	chr4:3226182-3752322	Enhancers ZNF genes & repeats Weak transcription Strong transcription Active TSS Bivalent Enhancer Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	33 gene(s)	inside rSNPs	diseases
8	nsv878458	chr4:3235518-3303976	Active TSS Flanking Active TSS Enhancers Weak transcription Strong transcription Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region miRNA target site	6 gene(s)	inside rSNPs	diseases
9	nsv878459	chr4:3235518-3310831	Enhancers Active TSS Weak transcription Strong transcription Flanking Active TSS Genic enhancers Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region miRNA target site	7 gene(s)	inside rSNPs	diseases
10	nsv878460	chr4:3260154-3303976	Strong transcription Active TSS Transcr. at gene 5' and 3' Weak transcription Bivalent Enhancer Flanking Active TSS Enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Genic enhancers	TF binding region CpG island Chromatin interactive region	6 gene(s)	inside rSNPs	diseases
11	nsv878461	chr4:3270488-3339038	Weak transcription Enhancers Bivalent Enhancer Flanking Active TSS Active TSS Genic enhancers Strong transcription ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	9 gene(s)	inside rSNPs	diseases
12	nsv593440	chr4:3283422-3339038	Enhancers Weak transcription Bivalent Enhancer Genic enhancers Flanking Active TSS Strong transcription 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	9 gene(s)	inside rSNPs	diseases
13	nsv461165	chr4:3283422-3342137	Weak transcription Enhancers Strong transcription Active TSS Flanking Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	10 gene(s)	inside rSNPs	diseases
14	nsv593441	chr4:3283422-3342137	Enhancers Bivalent Enhancer Flanking Active TSS Weak transcription Active TSS Strong transcription Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	10 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs1138690	HGFAC	cis	cerebellum	SCAN
rs1138690	RGS12	cis	cerebellum	SCAN

Chromatin state (count:37 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:3286200-3292200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
2	chr4:3288000-3293200	Weak transcription	Brain Substantia Nigra	brain
3	chr4:3288200-3293200	Weak transcription	Primary T helper naive cells from peripheral blood	blood
4	chr4:3288400-3292400	Weak transcription	Pancreas	Pancrea
5	chr4:3288400-3293000	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
6	chr4:3288600-3292200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
7	chr4:3288600-3292600	Weak transcription	Placenta Amnion	Placenta Amnion
8	chr4:3288600-3293200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
9	chr4:3288600-3293200	Weak transcription	Brain Anterior Caudate	brain
10	chr4:3288800-3292600	Weak transcription	HMEC	breast
11	chr4:3289200-3292400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
12	chr4:3289200-3292600	Enhancers	Skeletal Muscle Female	skeletal muscle
13	chr4:3289400-3293000	Weak transcription	Brain Angular Gyrus	brain
14	chr4:3289600-3293200	Weak transcription	Brain Hippocampus Middle	brain
15	chr4:3289600-3293200	Weak transcription	Fetal Lung	lung
16	chr4:3289800-3292400	Weak transcription	Ovary	ovary
17	chr4:3289800-3292600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
18	chr4:3290000-3292600	Weak transcription	Cortex derived primary cultured neurospheres	brain
19	chr4:3290200-3292000	Weak transcription	Breast Myoepithelial Primary Cells	Breast
20	chr4:3290200-3292200	Weak transcription	Fetal Brain Female	brain
21	chr4:3290200-3292800	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
22	chr4:3290200-3293000	Enhancers	HepG2	liver
23	chr4:3290400-3292400	Enhancers	Fetal Muscle Leg	muscle
24	chr4:3290400-3292800	Weak transcription	Brain Cingulate Gyrus	brain
25	chr4:3290400-3293000	Weak transcription	Brain Inferior Temporal Lobe	brain
26	chr4:3290400-3293200	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
27	chr4:3290600-3292400	Weak transcription	Right Ventricle	heart
28	chr4:3290600-3292800	Weak transcription	Primary monocytes fromperipheralblood	blood
29	chr4:3290600-3292800	Weak transcription	Fetal Brain Male	brain
30	chr4:3290800-3292200	Weak transcription	Left Ventricle	heart
31	chr4:3290800-3292800	Weak transcription	Small Intestine	intestine
32	chr4:3290800-3293200	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
33	chr4:3291000-3292200	Weak transcription	Brain Germinal Matrix	brain
34	chr4:3291000-3293200	Weak transcription	Adipose Nuclei	Adipose
35	chr4:3291200-3292200	Weak transcription	Lung	lung
36	chr4:3291200-3292600	Weak transcription	Spleen	Spleen
37	chr4:3291400-3292600	Enhancers	Skeletal Muscle Male	skeletal muscle

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