Variant report

Variant	rs62396459
Chromosome Location	chr6:38538677-38538678
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	chr6:38538560..38540420-chr6:38542934..38544675,2	MCF-7	breast:
2	chr6:38537441..38539090-chr6:38669827..38671558,2	K562	blood:

Variant related genes	Relation type
ENSG00000124767	Chromatin interaction

Extended variants
information (count: 12 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:9)

rs_ID	r²[population]
rs12525759	0.95[AFR][1000 genomes];0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs16890826	0.92[AFR][1000 genomes];0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs16890840	0.84[AMR][1000 genomes]
rs2748168	0.84[ASN][1000 genomes]
rs2748169	0.85[AMR][1000 genomes];0.87[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2814891	0.85[AMR][1000 genomes];0.81[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2814893	0.82[ASN][1000 genomes]
rs60227349	0.84[AMR][1000 genomes]
rs62399160	1.00[AFR][1000 genomes];1.00[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	nsv1021991	chr6:37893949-38738720	Weak transcription Enhancers Strong transcription Flanking Active TSS Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Active TSS Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	20 gene(s)	inside rSNPs	diseases
2	nsv885817	chr6:38036420-39019503	Enhancers Weak transcription Flanking Active TSS Bivalent/Poised TSS Strong transcription Active TSS Genic enhancers ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	26 gene(s)	inside rSNPs	diseases
3	nsv534620	chr6:38049585-38602064	Enhancers Strong transcription Weak transcription Flanking Active TSS Genic enhancers ZNF genes & repeats Bivalent Enhancer Active 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

No data

Chromatin state (count:71 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:38496600-38539600	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
2	chr6:38497000-38538800	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
3	chr6:38497000-38539400	Weak transcription	Primary T cells fromperipheralblood	blood
4	chr6:38510600-38546800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
5	chr6:38513000-38539200	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
6	chr6:38514200-38539400	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
7	chr6:38516000-38538800	Weak transcription	Primary T helper cells PMA-I stimulated	--
8	chr6:38519200-38538800	Weak transcription	Primary T cells from cord blood	blood
9	chr6:38519200-38539400	Weak transcription	Left Ventricle	heart
10	chr6:38519600-38554800	Weak transcription	Sigmoid Colon	Sigmoid Colon
11	chr6:38523000-38571600	Weak transcription	HSMMtube	muscle
12	chr6:38524000-38539200	Weak transcription	Pancreatic Islets	Pancreatic Islet
13	chr6:38532200-38539600	Weak transcription	Primary hematopoietic stem cells	blood
14	chr6:38532400-38547800	Weak transcription	Fetal Kidney	kidney
15	chr6:38533000-38544000	Weak transcription	Monocytes-CD14+_RO01746	blood
16	chr6:38533200-38547000	Weak transcription	Aorta	Aorta
17	chr6:38534000-38539200	Weak transcription	Primary T helper cells fromperipheralblood	blood
18	chr6:38534200-38539600	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
19	chr6:38534200-38544800	Weak transcription	Fetal Intestine Large	intestine
20	chr6:38534400-38544400	Weak transcription	Primary monocytes fromperipheralblood	blood
21	chr6:38534400-38561600	Weak transcription	Primary neutrophils fromperipheralblood	blood
22	chr6:38534800-38547000	Weak transcription	Rectal Mucosa Donor 29	rectum
23	chr6:38535400-38554600	Weak transcription	Fetal Stomach	stomach
24	chr6:38535600-38539000	Weak transcription	HUVEC	blood vessel
25	chr6:38535600-38539200	Weak transcription	GM12878-XiMat	blood
26	chr6:38535600-38543600	Weak transcription	Ovary	ovary
27	chr6:38535600-38543600	Weak transcription	Skeletal Muscle Female	skeletal muscle
28	chr6:38535600-38544800	Weak transcription	Brain Cingulate Gyrus	brain
29	chr6:38535600-38547000	Weak transcription	Brain Substantia Nigra	brain
30	chr6:38535600-38547000	Weak transcription	Fetal Muscle Leg	muscle
31	chr6:38535600-38555400	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
32	chr6:38535600-38555800	Weak transcription	Brain Inferior Temporal Lobe	brain
33	chr6:38535600-38556000	Weak transcription	Brain Hippocampus Middle	brain
34	chr6:38535600-38556000	Weak transcription	NHLF	lung
35	chr6:38535600-38557600	Weak transcription	HSMM	muscle
36	chr6:38535800-38539400	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
37	chr6:38535800-38539400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
38	chr6:38535800-38543800	Weak transcription	Adipose Nuclei	Adipose
39	chr6:38535800-38544200	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
40	chr6:38535800-38547800	Weak transcription	Osteobl	bone
41	chr6:38535800-38548000	Weak transcription	Fetal Heart	heart
42	chr6:38535800-38559800	Weak transcription	Fetal Lung	lung
43	chr6:38535800-38560200	Weak transcription	NH-A	brain
44	chr6:38535800-38564000	Weak transcription	Duodenum Smooth Muscle	Duodenum
45	chr6:38535800-38578200	Weak transcription	Colon Smooth Muscle	Colon
46	chr6:38536000-38546800	Weak transcription	Muscle Satellite Cultured Cells	--
47	chr6:38536200-38539400	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
48	chr6:38536200-38556000	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
49	chr6:38536200-38559200	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
50	chr6:38536400-38544000	Weak transcription	Psoas Muscle	Psoas

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