Variant report

Variant	rs12636246
Chromosome Location	chr3:138346586-138346587
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr3:138324541..138329357-chr3:138346474..138351112,6	MCF-7	breast:

Variant related genes	Relation type
ENSG00000158234	Chromatin interaction

Extended variants
information (count: 60 )
Associated
traits (count: 5 )

rSNPs within LD-proxies of this variant (count:52)

rs_ID	r²[population]
rs1082034	0.81[ASN][1000 genomes]
rs10935282	0.92[CEU][hapmap];0.81[CHB][hapmap];0.88[CHD][hapmap];0.89[GIH][hapmap];0.86[JPT][hapmap];0.96[MKK][hapmap];0.91[TSI][hapmap]
rs10935287	0.82[ASN][1000 genomes]
rs11709290	0.90[CHB][hapmap];0.86[CHD][hapmap];0.86[JPT][hapmap]
rs11717771	0.80[ASN][1000 genomes]
rs12487652	0.84[ASN][1000 genomes]
rs12487694	0.81[ASN][1000 genomes]
rs12490633	0.81[CEU][hapmap];0.86[CHB][hapmap];0.89[CHD][hapmap];0.86[JPT][hapmap];0.82[ASN][1000 genomes]
rs12497070	0.84[ASN][1000 genomes]
rs12632793	0.80[CHB][hapmap]
rs12636910	0.81[CEU][hapmap];0.80[CHB][hapmap];0.86[CHD][hapmap];0.82[JPT][hapmap];0.84[ASN][1000 genomes]
rs13098789	0.83[ASN][1000 genomes]
rs1672927	0.81[CEU][hapmap];0.90[CHB][hapmap];0.89[CHD][hapmap];0.86[JPT][hapmap];0.80[ASN][1000 genomes]
rs1672928	0.90[CHB][hapmap];0.95[JPT][hapmap];0.80[ASN][1000 genomes]
rs1672932	0.81[CEU][hapmap];0.90[CHB][hapmap];0.85[CHD][hapmap];0.86[JPT][hapmap];0.82[ASN][1000 genomes]
rs1672963	0.81[ASN][1000 genomes]
rs1673608	0.81[CEU][hapmap];0.86[CHB][hapmap];0.89[CHD][hapmap];0.86[JPT][hapmap];0.81[ASN][1000 genomes]
rs1673622	0.80[CEU][hapmap];0.90[CHB][hapmap];0.86[JPT][hapmap];0.84[ASN][1000 genomes]
rs2607790	0.81[ASN][1000 genomes]
rs28719641	0.82[ASN][1000 genomes]
rs35500947	0.83[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs35932955	0.90[EUR][1000 genomes]
rs3773748	0.82[JPT][hapmap]
rs3813264	0.90[CHB][hapmap];0.86[CHD][hapmap];0.86[JPT][hapmap]
rs3884240	0.81[CEU][hapmap];0.86[CHB][hapmap];0.86[CHD][hapmap];0.86[JPT][hapmap]
rs3884241	0.81[CEU][hapmap];0.86[CHB][hapmap];0.86[JPT][hapmap]
rs4894389	0.81[ASN][1000 genomes]
rs497334	0.81[CEU][hapmap];0.86[CHB][hapmap];0.86[JPT][hapmap];0.82[ASN][1000 genomes]
rs503922	0.81[CEU][hapmap];0.90[CHB][hapmap];0.89[CHD][hapmap];0.86[JPT][hapmap];0.84[ASN][1000 genomes]
rs529615	0.81[CEU][hapmap];0.86[CHB][hapmap];0.89[CHD][hapmap];0.86[JPT][hapmap];0.84[ASN][1000 genomes]
rs537210	0.80[ASN][1000 genomes]
rs542010	0.86[CHB][hapmap];0.88[CHD][hapmap];0.82[JPT][hapmap];0.81[ASN][1000 genomes]
rs56394118	0.82[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs564800	0.85[CHB][hapmap];0.88[CHD][hapmap];0.82[JPT][hapmap];0.81[ASN][1000 genomes]
rs582386	0.81[ASN][1000 genomes]
rs609797	0.81[CEU][hapmap];0.86[CHB][hapmap];0.89[CHD][hapmap];0.86[JPT][hapmap]
rs612471	0.80[ASN][1000 genomes]
rs620035	0.81[ASN][1000 genomes]
rs6439809	0.81[CEU][hapmap];0.85[CHB][hapmap];0.86[JPT][hapmap]
rs6439810	0.81[CEU][hapmap];0.86[CHB][hapmap];0.86[CHD][hapmap];0.86[JPT][hapmap];0.82[ASN][1000 genomes]
rs6762114	0.83[ASN][1000 genomes]
rs6771237	0.82[ASN][1000 genomes]
rs73229526	0.82[ASN][1000 genomes]
rs7645920	0.81[CEU][hapmap];0.86[CHB][hapmap];0.86[JPT][hapmap]
rs773443	0.85[ASN][1000 genomes]
rs773450	0.81[CEU][hapmap];0.90[CHB][hapmap];0.89[CHD][hapmap];0.86[JPT][hapmap];0.82[ASN][1000 genomes]
rs774012	0.86[CHB][hapmap];0.89[CHD][hapmap];0.86[JPT][hapmap]
rs814022	0.81[CEU][hapmap];0.86[CHB][hapmap];0.89[CHD][hapmap];0.86[JPT][hapmap];0.81[ASN][1000 genomes]
rs936316	0.81[CEU][hapmap];0.86[CHB][hapmap];0.89[CHD][hapmap];0.86[JPT][hapmap];0.81[ASN][1000 genomes]
rs9823182	0.82[ASN][1000 genomes]
rs9848938	0.89[CHB][hapmap];0.85[JPT][hapmap]
rs9855306	0.86[CHB][hapmap];0.89[CHD][hapmap];0.86[JPT][hapmap]

Variant overlapped rSNPs/rCNVs (count:8 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv530057	chr3:138014877-138734390	Weak transcription Strong transcription Enhancers Active TSS ZNF genes & repeats Flanking Active TSS Genic enhancers Bivalent Enhancer 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	38 gene(s)	inside rSNPs	diseases
2	nsv999041	chr3:138148812-138347988	Flanking Active TSS Weak transcription Strong transcription Active TSS Bivalent Enhancer ZNF genes & repeats Enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	15 gene(s)	inside rSNPs	diseases
3	nsv1013074	chr3:138213166-138737688	Strong transcription Enhancers Weak transcription ZNF genes & repeats Bivalent/Poised TSS Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Active TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	32 gene(s)	inside rSNPs	diseases
4	nsv1002612	chr3:138213274-138831792	Weak transcription Strong transcription Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Flanking Active TSS Enhancers Genic enhancers Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	38 gene(s)	inside rSNPs	diseases
5	nsv536726	chr3:138213274-138831792	Enhancers Flanking Active TSS Strong transcription Weak transcription ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Active TSS Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	38 gene(s)	inside rSNPs	diseases
6	nsv1009726	chr3:138219923-138737688	Weak transcription Enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Active TSS Strong transcription ZNF genes & repeats Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	32 gene(s)	inside rSNPs	diseases
7	nsv869205	chr3:138248190-138775288	Enhancers Weak transcription Flanking Bivalent TSS/Enh Active TSS Bivalent/Poised TSS Flanking Active TSS Bivalent Enhancer Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	33 gene(s)	inside rSNPs	diseases
8	nsv868955	chr3:138248190-138848947	Bivalent Enhancer Bivalent/Poised TSS Strong transcription Flanking Active TSS Enhancers Weak transcription ZNF genes & repeats Flanking Bivalent TSS/Enh Active TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	37 gene(s)	inside rSNPs	diseases

mRNA abundance (count:5)

SNP	Gene	Cis/trans	Tissue	Source
rs12636246	FAIM	cis	parietal	SCAN
rs12636246	FAIM	cis	cerebellum	SCAN
rs12636246	ESYT3	cis	cerebellum	SCAN
rs12636246	ENSG00000158234	cis	multi-tissue	Pritchard
rs12636246	MSL2	cis	cerebellum	SCAN

Chromatin state (count:78 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:138328400-138350200	Weak transcription	Lung	lung
2	chr3:138328400-138353200	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
3	chr3:138328400-138355000	Weak transcription	Esophagus	oesophagus
4	chr3:138328600-138349400	Weak transcription	Ovary	ovary
5	chr3:138328600-138358000	Weak transcription	Psoas Muscle	Psoas
6	chr3:138328800-138358000	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
7	chr3:138329000-138346800	Weak transcription	Fetal Muscle Leg	muscle
8	chr3:138329000-138347600	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
9	chr3:138329000-138348000	Weak transcription	Fetal Intestine Large	intestine
10	chr3:138329000-138348200	Weak transcription	Left Ventricle	heart
11	chr3:138329000-138348400	Weak transcription	Aorta	Aorta
12	chr3:138329000-138348400	Weak transcription	Sigmoid Colon	Sigmoid Colon
13	chr3:138329000-138348600	Weak transcription	Fetal Intestine Small	intestine
14	chr3:138329000-138350000	Weak transcription	Primary hematopoietic stem cells short term culture	blood
15	chr3:138329000-138354200	Weak transcription	Fetal Lung	lung
16	chr3:138329200-138348200	Weak transcription	Skeletal Muscle Female	skeletal muscle
17	chr3:138333200-138347000	Weak transcription	Fetal Thymus	thymus
18	chr3:138334200-138348600	Weak transcription	Thymus	Thymus
19	chr3:138335400-138348200	Weak transcription	Adipose Nuclei	Adipose
20	chr3:138335400-138368000	Weak transcription	Right Ventricle	heart
21	chr3:138337000-138360400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
22	chr3:138337800-138353600	Weak transcription	Colonic Mucosa	Colon
23	chr3:138338000-138353400	Weak transcription	Colon Smooth Muscle	Colon
24	chr3:138338200-138348200	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
25	chr3:138338200-138350000	Weak transcription	Rectal Smooth Muscle	rectum
26	chr3:138338600-138348000	Weak transcription	Hela-S3	cervix
27	chr3:138338600-138350400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
28	chr3:138339000-138348600	Weak transcription	Fetal Brain Female	brain
29	chr3:138339000-138351600	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
30	chr3:138339400-138348000	Weak transcription	Skeletal Muscle Male	skeletal muscle
31	chr3:138340400-138393800	Weak transcription	Fetal Brain Male	brain
32	chr3:138341000-138350600	Weak transcription	HepG2	liver
33	chr3:138341200-138348000	Weak transcription	Duodenum Smooth Muscle	Duodenum
34	chr3:138341200-138351600	Weak transcription	Fetal Kidney	kidney
35	chr3:138341200-138355800	Weak transcription	Dnd41	blood
36	chr3:138341400-138349600	Weak transcription	Stomach Smooth Muscle	stomach
37	chr3:138341400-138354600	Weak transcription	Brain Angular Gyrus	brain
38	chr3:138341600-138348600	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
39	chr3:138341800-138355200	Weak transcription	Primary B cells from cord blood	blood
40	chr3:138342400-138362200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
41	chr3:138342600-138348200	Weak transcription	Pancreas	Pancrea
42	chr3:138342600-138356400	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
43	chr3:138342800-138348400	Weak transcription	Gastric	stomach
44	chr3:138343200-138352200	Weak transcription	Primary T cells from cord blood	blood
45	chr3:138343600-138352200	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
46	chr3:138344000-138348600	Weak transcription	Fetal Stomach	stomach
47	chr3:138344800-138348000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
48	chr3:138344800-138354000	Weak transcription	Duodenum Mucosa	Duodenum
49	chr3:138345000-138346600	Strong transcription	Primary hematopoietic stem cells	blood
50	chr3:138345000-138354800	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung

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