Variant report

Variant	rs12513260
Chromosome Location	chr4:99978495-99978496
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: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	chr4:99915938..99917899-chr4:99977078..99979167,2	K562	blood:
2	chr4:99180664..99184251-chr4:99975282..99978632,3	MCF-7	breast:
3	chr4:99970407..99973729-chr4:99975886..99978831,3	K562	blood:
4	chr4:99977327..99979910-chr4:99986082..99988500,2	K562	blood:
5	chr4:99968920..99970832-chr4:99976861..99978967,2	MCF-7	breast:
6	chr4:99843188..99846109-chr4:99975647..99978634,2	K562	blood:
7	chr4:99968894..99970769-chr4:99978380..99981030,2	MCF-7	breast:
8	chr4:99914957..99918006-chr4:99977078..99979167,5	K562	blood:

No data

Variant related genes	Relation type
ENSG00000138698	Chromatin interaction
ENSG00000164024	Chromatin interaction
ENSG00000214559	Chromatin interaction

Extended variants
information (count: 15 )
Associated
traits (count: 0)

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

rs_ID	r²[population]
rs10489131	1.00[CEU][hapmap];0.89[CHB][hapmap];0.83[JPT][hapmap];0.93[AFR][1000 genomes];0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10489132	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11097642	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[AFR][1000 genomes];0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11726503	0.87[CHB][hapmap]
rs11737022	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12508113	0.93[AFR][1000 genomes];0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs55985943	0.87[AFR][1000 genomes];0.84[ASN][1000 genomes]
rs60067299	0.90[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7661773	0.93[AFR][1000 genomes];0.84[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7683532	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[AFR][1000 genomes];0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7687617	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7694657	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1009017	chr4:99669441-100406394	Active TSS Enhancers Flanking Active TSS Weak transcription Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	57 gene(s)	inside rSNPs	diseases
2	nsv1002927	chr4:99952472-100148690	Enhancers Weak transcription Flanking Active TSS Strong transcription Active TSS 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	28 gene(s)	inside rSNPs	diseases
3	nsv879656	chr4:99976646-100533722	Weak transcription Enhancers Strong transcription Flanking Active TSS Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	36 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:125 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:99944200-99979000	Weak transcription	Colonic Mucosa	Colon
2	chr4:99944200-99979200	Weak transcription	Right Ventricle	heart
3	chr4:99944400-99979200	Weak transcription	Brain Hippocampus Middle	brain
4	chr4:99946400-99979000	Weak transcription	Esophagus	oesophagus
5	chr4:99947000-99979000	Weak transcription	Gastric	stomach
6	chr4:99947000-99979200	Weak transcription	Pancreas	Pancrea
7	chr4:99947400-99982600	Weak transcription	Psoas Muscle	Psoas
8	chr4:99949000-99979000	Weak transcription	Small Intestine	intestine
9	chr4:99954000-99999200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
10	chr4:99955400-99980800	Weak transcription	HSMMtube	muscle
11	chr4:99956200-99995000	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
12	chr4:99959800-100000200	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
13	chr4:99964200-99979000	Weak transcription	Brain Germinal Matrix	brain
14	chr4:99965000-99982000	Weak transcription	Placenta Amnion	Placenta Amnion
15	chr4:99965000-99982200	Weak transcription	Brain Inferior Temporal Lobe	brain
16	chr4:99969200-99979200	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
17	chr4:99971000-99988800	Weak transcription	Fetal Brain Male	brain
18	chr4:99971800-99991600	Weak transcription	Brain Anterior Caudate	brain
19	chr4:99971800-99997600	Weak transcription	Spleen	Spleen
20	chr4:99972000-99979200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
21	chr4:99972000-99982400	Weak transcription	Lung	lung
22	chr4:99972400-99978600	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
23	chr4:99972400-99979200	Weak transcription	Ovary	ovary
24	chr4:99973800-99979000	Weak transcription	H9 Cell Line	embryonic stem cell
25	chr4:99973800-99979000	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
26	chr4:99973800-99979000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
27	chr4:99973800-99981200	Weak transcription	Skeletal Muscle Male	skeletal muscle
28	chr4:99974000-99979000	Weak transcription	Fetal Lung	lung
29	chr4:99974000-99979000	Weak transcription	Sigmoid Colon	Sigmoid Colon
30	chr4:99974000-99993000	Weak transcription	iPS-15b Cell Line	embryonic stem cell
31	chr4:99974200-99978600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
32	chr4:99974200-99978800	Weak transcription	Skeletal Muscle Female	skeletal muscle
33	chr4:99974400-99978600	Weak transcription	Primary hematopoietic stem cells	blood
34	chr4:99974400-99978800	Weak transcription	Adipose Nuclei	Adipose
35	chr4:99974400-99979000	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
36	chr4:99974400-99979000	Weak transcription	Thymus	Thymus
37	chr4:99974400-99982400	Weak transcription	Brain Cingulate Gyrus	brain
38	chr4:99974600-99978600	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
39	chr4:99974600-99979000	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
40	chr4:99974800-99978800	Weak transcription	Primary B cells from cord blood	blood
41	chr4:99974800-99979200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
42	chr4:99975200-99979000	Weak transcription	Fetal Muscle Leg	muscle
43	chr4:99975400-99979000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
44	chr4:99975600-99978800	Weak transcription	Fetal Stomach	stomach
45	chr4:99975800-99979000	Weak transcription	Rectal Mucosa Donor 29	rectum
46	chr4:99976000-99979000	Weak transcription	Fetal Muscle Trunk	muscle
47	chr4:99976000-99979200	Weak transcription	Left Ventricle	heart
48	chr4:99976000-99989800	Weak transcription	Fetal Brain Female	brain
49	chr4:99976200-99978600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
50	chr4:99976200-99979200	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin

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