Variant report

Variant	rs6438509
Chromosome Location	chr3:118954931-118954932
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr3:118954516..118958209-chr3:118958247..118961418,8	MCF-7	breast:
2	chr3:118954843..118957176-chr3:119215915..119217953,2	MCF-7	breast:
3	chr3:118952753..118957545-chr3:118958102..118959880,7	K562	blood:

Variant related genes	Relation type
ENSG00000121578	Chromatin interaction
ENSG00000272662	Chromatin interaction
ENSG00000113845	Chromatin interaction

Extended variants
information (count: 8 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:5)

rs_ID	r²[population]
rs2084454	0.88[AFR][1000 genomes];0.96[AMR][1000 genomes];0.94[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4687841	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6438510	0.80[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6767078	0.88[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7625069	0.96[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[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	esv3487859	chr3:118570588-119419623	Weak transcription Active TSS Strong transcription Enhancers Flanking Active TSS ZNF genes & repeats Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	61 gene(s)	inside rSNPs	diseases
2	esv3487860	chr3:118570588-119419623	Strong transcription Enhancers Active TSS Weak transcription ZNF genes & repeats Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	61 gene(s)	inside rSNPs	diseases
3	esv18354	chr3:118855337-119000251	Enhancers Genic enhancers Strong transcription Flanking Active TSS Weak transcription Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	15 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:127 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:118924400-118959000	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
2	chr3:118927200-118955200	Strong transcription	Monocytes-CD14+_RO01746	blood
3	chr3:118927800-118956400	Strong transcription	iPS-20b Cell Line	embryonic stem cell
4	chr3:118928000-118955600	Strong transcription	Breast Myoepithelial Primary Cells	Breast
5	chr3:118929200-118956200	Strong transcription	HUES48 Cell Line	embryonic stem cell
6	chr3:118929200-118956200	Strong transcription	HUES64 Cell Line	embryonic stem cell
7	chr3:118929200-118956400	Strong transcription	H1 Cell Line	embryonic stem cell
8	chr3:118929200-118956600	Strong transcription	iPS-18 Cell Line	embryonic stem cell
9	chr3:118930000-118955400	Strong transcription	Primary B cells from peripheral blood	blood
10	chr3:118930200-118955800	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
11	chr3:118930200-118958400	Weak transcription	Hela-S3	cervix
12	chr3:118931600-118957400	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
13	chr3:118932600-118955800	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
14	chr3:118944400-118955800	Strong transcription	Placenta	Placenta
15	chr3:118944400-118956200	Strong transcription	HUES6 Cell Line	embryonic stem cell
16	chr3:118944800-118955000	Strong transcription	Primary B cells from cord blood	blood
17	chr3:118944800-118955000	Strong transcription	Fetal Lung	lung
18	chr3:118944800-118955600	Strong transcription	Primary hematopoietic stem cells short term culture	blood
19	chr3:118945000-118956000	Strong transcription	H9 Cell Line	embryonic stem cell
20	chr3:118945000-118956000	Strong transcription	Liver	Liver
21	chr3:118945800-118958600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
22	chr3:118946600-118957800	Weak transcription	Colon Smooth Muscle	Colon
23	chr3:118946800-118957200	Weak transcription	Pancreatic Islets	Pancreatic Islet
24	chr3:118947200-118955200	Strong transcription	Rectal Mucosa Donor 29	rectum
25	chr3:118947400-118955800	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
26	chr3:118948200-118955600	Weak transcription	Psoas Muscle	Psoas
27	chr3:118948200-118956200	Strong transcription	Rectal Mucosa Donor 31	rectum
28	chr3:118948400-118958600	Weak transcription	Colonic Mucosa	Colon
29	chr3:118949000-118958000	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
30	chr3:118949000-118958400	Weak transcription	Fetal Brain Male	brain
31	chr3:118949200-118957600	Weak transcription	Fetal Heart	heart
32	chr3:118949400-118957600	Weak transcription	Right Ventricle	heart
33	chr3:118949400-118958800	Weak transcription	Lung	lung
34	chr3:118949600-118955800	Genic enhancers	Primary T helper cells PMA-I stimulated	--
35	chr3:118949600-118957600	Weak transcription	Ovary	ovary
36	chr3:118949600-118958400	Weak transcription	Brain Substantia Nigra	brain
37	chr3:118949600-118958600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
38	chr3:118949600-118958600	Weak transcription	Brain Germinal Matrix	brain
39	chr3:118949600-118958800	Weak transcription	Gastric	stomach
40	chr3:118949800-118958800	Weak transcription	Spleen	Spleen
41	chr3:118950000-118958400	Weak transcription	Fetal Brain Female	brain
42	chr3:118950800-118956200	Strong transcription	Dnd41	blood
43	chr3:118951400-118955200	Strong transcription	Fetal Thymus	thymus
44	chr3:118951400-118955800	Strong transcription	Fetal Intestine Large	intestine
45	chr3:118951400-118957800	Weak transcription	Skeletal Muscle Male	skeletal muscle
46	chr3:118951600-118955200	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
47	chr3:118951600-118955600	Strong transcription	Sigmoid Colon	Sigmoid Colon
48	chr3:118951600-118958800	Weak transcription	Esophagus	oesophagus
49	chr3:118952000-118955600	Weak transcription	Pancreas	Pancrea
50	chr3:118952000-118958800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived

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