Variant report

Variant	rs6438517
Chromosome Location	chr3:119019598-119019599
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr3:119016211..119028042-chr3:119037960..119043695,12	MCF-7	breast:

Variant related genes	Relation type
ENSG00000241155	Chromatin interaction

Extended variants
information (count: 19 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:16)

rs_ID	r²[population]
rs10934489	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11914541	0.91[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1542233	0.84[AFR][1000 genomes];0.89[AMR][1000 genomes]
rs2971544	0.81[ASN][1000 genomes]
rs4687993	0.96[AFR][1000 genomes];0.95[AMR][1000 genomes];0.90[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs56269733	0.81[AMR][1000 genomes];0.90[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs6775982	0.94[AFR][1000 genomes];0.92[AMR][1000 genomes];0.90[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs6800491	0.90[AFR][1000 genomes];0.92[AMR][1000 genomes];0.90[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs724653	0.81[ASN][1000 genomes]
rs7620780	0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7622994	0.91[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7623525	0.90[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs7625392	0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs7649480	0.86[AFR][1000 genomes]
rs7649558	0.93[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9834125	0.92[AFR][1000 genomes];0.90[AMR][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	nsv829694	chr3:119011488-119153579	Enhancers Strong transcription Weak transcription Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh Genic enhancers ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:94 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:119014200-119029800	Weak transcription	Gastric	stomach
2	chr3:119014200-119032800	Weak transcription	Pancreas	Pancrea
3	chr3:119014400-119019800	Weak transcription	NHEK	skin
4	chr3:119014400-119021600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
5	chr3:119014400-119021800	Weak transcription	Liver	Liver
6	chr3:119015000-119021800	Weak transcription	Fetal Intestine Large	intestine
7	chr3:119015000-119028600	Weak transcription	Brain Inferior Temporal Lobe	brain
8	chr3:119015000-119041200	Weak transcription	Aorta	Aorta
9	chr3:119015200-119020600	Weak transcription	Primary B cells from cord blood	blood
10	chr3:119015200-119021600	Weak transcription	H9 Cell Line	embryonic stem cell
11	chr3:119015200-119041000	Weak transcription	Fetal Kidney	kidney
12	chr3:119015400-119019800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
13	chr3:119015400-119019800	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
14	chr3:119015800-119020000	Weak transcription	Colonic Mucosa	Colon
15	chr3:119015800-119024400	Weak transcription	Rectal Smooth Muscle	rectum
16	chr3:119015800-119024400	Weak transcription	Sigmoid Colon	Sigmoid Colon
17	chr3:119016000-119021800	Weak transcription	HUES6 Cell Line	embryonic stem cell
18	chr3:119016000-119035400	Weak transcription	Fetal Brain Male	brain
19	chr3:119016000-119041000	Weak transcription	Rectal Mucosa Donor 31	rectum
20	chr3:119016400-119019600	Weak transcription	HMEC	breast
21	chr3:119016400-119024000	Weak transcription	Small Intestine	intestine
22	chr3:119016400-119040800	Weak transcription	Rectal Mucosa Donor 29	rectum
23	chr3:119016400-119041000	Weak transcription	Fetal Intestine Small	intestine
24	chr3:119016600-119019800	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
25	chr3:119016600-119020000	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
26	chr3:119016600-119021600	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
27	chr3:119016600-119021800	Weak transcription	NHLF	lung
28	chr3:119016600-119024400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
29	chr3:119016600-119025000	Genic enhancers	Cortex derived primary cultured neurospheres	brain
30	chr3:119016800-119024800	Enhancers	Fetal Heart	heart
31	chr3:119017000-119019800	Weak transcription	Esophagus	oesophagus
32	chr3:119017000-119019800	Weak transcription	NHDF-Ad	bronchial
33	chr3:119017200-119019800	Weak transcription	Primary B cells from peripheral blood	blood
34	chr3:119017200-119020200	Weak transcription	Placenta Amnion	Placenta Amnion
35	chr3:119017200-119021600	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
36	chr3:119017200-119021800	Weak transcription	Stomach Smooth Muscle	stomach
37	chr3:119017200-119023000	Weak transcription	Colon Smooth Muscle	Colon
38	chr3:119017200-119025000	Weak transcription	Primary T helper cells fromperipheralblood	blood
39	chr3:119017400-119020000	Weak transcription	Brain Substantia Nigra	brain
40	chr3:119017400-119021600	Weak transcription	Duodenum Smooth Muscle	Duodenum
41	chr3:119017400-119021600	Weak transcription	HSMM	muscle
42	chr3:119017400-119021800	Weak transcription	Ovary	ovary
43	chr3:119017400-119029800	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
44	chr3:119017400-119040600	Weak transcription	Primary T cells fromperipheralblood	blood
45	chr3:119017600-119020000	Weak transcription	Primary hematopoietic stem cells	blood
46	chr3:119017600-119020000	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
47	chr3:119017600-119020000	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
48	chr3:119017600-119020200	Weak transcription	Primary T cells from cord blood	blood
49	chr3:119017600-119020200	Weak transcription	Brain Anterior Caudate	brain
50	chr3:119017600-119020200	Weak transcription	Duodenum Mucosa	Duodenum

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