Variant report

Variant	rs6534686
Chromosome Location	chr4:129440172-129440173
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:0)
CpG islands
(count:0)
Chromatin interactive
region (count:4)
LncRNA
region (count:3)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:4 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr4:129439076..129440625-chr4:129477758..129479357,2	MCF-7	breast:
2	chr4:129434600..129436972-chr4:129437723..129440318,3	MCF-7	breast:
3	chr4:129438574..129440652-chr4:129732822..129734434,2	K562	blood:
4	chr4:129207853..129210265-chr4:129438502..129440309,2	MCF-7	breast:

(count:3 , 50 per page) page: 1

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-LARP1B-1	chr4:129439911-129440549	ENSG00000251432
2	lnc-LARP1B-1	chr4:129439911-129440554	NONHSAT098267
3	lnc-LARP1B-1	chr4:129439911-129440471	NONHSAT098273

No data

Variant related genes	Relation type
ENSG00000077684	Chromatin interaction
ENSG00000164040	Chromatin interaction

Extended variants
information (count: 16 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:15)

rs_ID	r²[population]
rs11733387	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11937124	0.87[AFR][1000 genomes];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs13108573	0.84[AMR][1000 genomes]
rs13115644	1.00[CHB][hapmap];1.00[AFR][1000 genomes];0.80[AMR][1000 genomes];0.91[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs1603886	0.95[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs1603887	0.95[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs2062456	0.87[CEU][hapmap];0.82[CHB][hapmap];0.82[JPT][hapmap];0.85[AMR][1000 genomes]
rs4362840	0.96[CEU][hapmap];0.90[CHB][hapmap];0.93[JPT][hapmap];1.00[AFR][1000 genomes];0.94[AMR][1000 genomes];0.93[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4975185	0.87[AFR][1000 genomes];0.95[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs6534687	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6534691	0.84[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs6821679	0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6840580	0.83[CEU][hapmap];0.82[CHB][hapmap];0.82[JPT][hapmap];0.87[AFR][1000 genomes];0.84[AMR][1000 genomes]
rs6849290	1.00[CEU][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs7441245	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]

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

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv869258	chr4:129191619-130138148	Weak transcription Enhancers Flanking Active TSS Strong transcription Active TSS ZNF genes & repeats Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	79 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:65 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:129425800-129445600	Weak transcription	Gastric	stomach
2	chr4:129431200-129440800	Weak transcription	Left Ventricle	heart
3	chr4:129433400-129443200	Weak transcription	Lung	lung
4	chr4:129437000-129443400	Enhancers	NHLF	lung
5	chr4:129437200-129441000	Enhancers	Fetal Lung	lung
6	chr4:129437400-129441400	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
7	chr4:129437400-129442200	Enhancers	Fetal Muscle Leg	muscle
8	chr4:129437600-129440200	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
9	chr4:129437600-129440200	Enhancers	Right Atrium	heart
10	chr4:129437600-129440800	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
11	chr4:129437600-129447400	Enhancers	HUVEC	blood vessel
12	chr4:129438200-129441200	Enhancers	Psoas Muscle	Psoas
13	chr4:129438200-129441200	Enhancers	Skeletal Muscle Male	skeletal muscle
14	chr4:129438200-129441400	Enhancers	NH-A	brain
15	chr4:129438400-129440200	Enhancers	HepG2	liver
16	chr4:129438400-129441200	Enhancers	Skeletal Muscle Female	skeletal muscle
17	chr4:129438600-129440200	Enhancers	HUES6 Cell Line	embryonic stem cell
18	chr4:129438800-129441000	Enhancers	Right Ventricle	heart
19	chr4:129439000-129440800	Enhancers	HSMM	muscle
20	chr4:129439000-129441200	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
21	chr4:129439200-129440600	Weak transcription	Fetal Muscle Trunk	muscle
22	chr4:129439200-129440800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
23	chr4:129439200-129441200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
24	chr4:129439200-129441200	Enhancers	HSMMtube	muscle
25	chr4:129439200-129443600	Weak transcription	Aorta	Aorta
26	chr4:129439200-129449400	Weak transcription	Stomach Smooth Muscle	stomach
27	chr4:129439200-129450000	Weak transcription	Rectal Smooth Muscle	rectum
28	chr4:129439400-129440200	Enhancers	Hela-S3	cervix
29	chr4:129439400-129440200	Flanking Active TSS	NHDF-Ad	bronchial
30	chr4:129439400-129440400	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
31	chr4:129439400-129441800	Weak transcription	HUES64 Cell Line	embryonic stem cell
32	chr4:129439400-129442000	Weak transcription	Fetal Heart	heart
33	chr4:129439400-129442200	Weak transcription	Stomach Mucosa	stomach
34	chr4:129439400-129442400	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
35	chr4:129439400-129442600	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
36	chr4:129439600-129440600	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
37	chr4:129439600-129440600	Weak transcription	Ovary	ovary
38	chr4:129439600-129441000	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
39	chr4:129439600-129441400	Enhancers	Muscle Satellite Cultured Cells	--
40	chr4:129439600-129441400	Enhancers	Osteobl	bone
41	chr4:129439600-129441800	Weak transcription	Placenta	Placenta
42	chr4:129439600-129442000	Weak transcription	Small Intestine	intestine
43	chr4:129439600-129442200	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
44	chr4:129439600-129442600	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
45	chr4:129439600-129443000	Weak transcription	iPS-15b Cell Line	embryonic stem cell
46	chr4:129439600-129443600	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
47	chr4:129439600-129444000	Enhancers	K562	blood
48	chr4:129439600-129445000	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
49	chr4:129439600-129445200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
50	chr4:129439600-129445400	Weak transcription	Placenta Amnion	Placenta Amnion

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