Variant report

Variant	rs1199346
Chromosome Location	chr3:138072809-138072810
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr3:138065032..138067985-chr3:138070541..138072955,3	MCF-7	breast:
2	chr3:138071826..138074930-chr3:138082332..138084280,3	K562	blood:
3	chr3:138066416..138068564-chr3:138071079..138073147,2	K562	blood:

Variant related genes	Relation type
ENSG00000158186	Chromatin interaction

Extended variants
information (count: 33 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:27)

rs_ID	r²[population]
rs1199333	0.86[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs1199334	1.00[ASN][1000 genomes]
rs1199335	0.89[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs1199336	0.89[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs1199347	0.89[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs1201763	1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1209710	0.91[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs1212469	0.95[ASN][1000 genomes]
rs1308362	0.80[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs1624314	0.89[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs166195	1.00[ASN][1000 genomes]
rs166196	1.00[ASN][1000 genomes]
rs1679149	0.86[ASN][1000 genomes]
rs1720825	0.80[AMR][1000 genomes]
rs183151	0.90[ASN][1000 genomes]
rs194146	0.86[ASN][1000 genomes]
rs253662	0.80[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs253666	0.91[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs40005	0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs40412	0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs42761	1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4346503	0.80[AMR][1000 genomes]
rs4437085	1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6809480	0.80[AMR][1000 genomes]
rs774373	0.89[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs799328	0.89[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs811332	0.89[AMR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv530056	chr3:137312356-138161861	Weak transcription Active TSS Enhancers Genic enhancers Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Flanking Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	26 gene(s)	inside rSNPs	diseases
2	nsv877537	chr3:137979007-138215114	Weak transcription Flanking Bivalent TSS/Enh Strong transcription Enhancers Active TSS Bivalent/Poised TSS Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	11 gene(s)	inside rSNPs	diseases
3	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
4	nsv528349	chr3:138025396-138132393	Flanking Bivalent TSS/Enh Flanking Active TSS Enhancers Weak transcription Strong transcription Genic enhancers Active TSS Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
5	esv1796956	chr3:138051423-138122781	Strong transcription Enhancers Flanking Active TSS Weak transcription Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
6	esv1848610	chr3:138051423-138133412	Bivalent Enhancer Genic enhancers Enhancers Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh Weak transcription Strong transcription Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:68 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:138068400-138083000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
2	chr3:138068600-138084600	Weak transcription	Gastric	stomach
3	chr3:138068800-138075800	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
4	chr3:138068800-138076000	Weak transcription	HUES48 Cell Line	embryonic stem cell
5	chr3:138068800-138093200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
6	chr3:138069000-138073600	Weak transcription	Fetal Stomach	stomach
7	chr3:138069000-138076000	Weak transcription	H9 Cell Line	embryonic stem cell
8	chr3:138069000-138077800	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
9	chr3:138069200-138074000	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
10	chr3:138069200-138075600	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
11	chr3:138069200-138088200	Weak transcription	Fetal Lung	lung
12	chr3:138069400-138073600	Enhancers	Psoas Muscle	Psoas
13	chr3:138069400-138074000	Weak transcription	Fetal Brain Female	brain
14	chr3:138069400-138075600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
15	chr3:138069400-138078000	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
16	chr3:138069400-138080600	Weak transcription	NHLF	lung
17	chr3:138070000-138075400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
18	chr3:138070000-138096600	Weak transcription	Fetal Brain Male	brain
19	chr3:138070200-138073400	Enhancers	Adipose Nuclei	Adipose
20	chr3:138070200-138073400	Enhancers	Skeletal Muscle Male	skeletal muscle
21	chr3:138070200-138074000	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
22	chr3:138070200-138086400	Weak transcription	Duodenum Smooth Muscle	Duodenum
23	chr3:138070600-138073400	Enhancers	Right Ventricle	heart
24	chr3:138070800-138075000	Weak transcription	Brain Angular Gyrus	brain
25	chr3:138070800-138075400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
26	chr3:138070800-138076800	Weak transcription	Colon Smooth Muscle	Colon
27	chr3:138071000-138074000	Weak transcription	Stomach Smooth Muscle	stomach
28	chr3:138071000-138074200	Weak transcription	Brain Cingulate Gyrus	brain
29	chr3:138071000-138074200	Weak transcription	Brain Inferior Temporal Lobe	brain
30	chr3:138071000-138074400	Genic enhancers	Breast Myoepithelial Primary Cells	Breast
31	chr3:138071000-138075600	Weak transcription	Brain Hippocampus Middle	brain
32	chr3:138071000-138085600	Weak transcription	Brain Germinal Matrix	brain
33	chr3:138071200-138073200	Enhancers	Fetal Heart	heart
34	chr3:138071200-138073600	Genic enhancers	HSMM	muscle
35	chr3:138071200-138074000	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
36	chr3:138071200-138074000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
37	chr3:138071200-138074200	Weak transcription	Brain Substantia Nigra	brain
38	chr3:138071200-138075000	Weak transcription	Brain Anterior Caudate	brain
39	chr3:138071200-138075200	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
40	chr3:138071200-138075400	Weak transcription	HUES6 Cell Line	embryonic stem cell
41	chr3:138071200-138075400	Weak transcription	Muscle Satellite Cultured Cells	--
42	chr3:138071200-138075400	Weak transcription	Lung	lung
43	chr3:138071200-138075600	Weak transcription	H1 Cell Line	embryonic stem cell
44	chr3:138071200-138075600	Weak transcription	Cortex derived primary cultured neurospheres	brain
45	chr3:138071200-138075600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
46	chr3:138071200-138075600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
47	chr3:138071200-138075600	Weak transcription	Fetal Muscle Trunk	muscle
48	chr3:138071200-138075600	Weak transcription	Ovary	ovary
49	chr3:138071200-138075600	Weak transcription	Pancreas	Pancrea
50	chr3:138071200-138080800	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin

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