Variant report

Variant	rs6852878
Chromosome Location	chr4:159043138-159043139
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr4:159040586..159043659-chr4:159090356..159092814,3	MCF-7	breast:
2	chr4:159014385..159016745-chr4:159041064..159043729,3	MCF-7	breast:
3	chr4:159041667..159043431-chr4:159082269..159084157,2	MCF-7	breast:
4	chr4:159041377..159043283-chr4:159093182..159095252,2	MCF-7	breast:
5	chr4:159042649..159044924-chr4:159061563..159064027,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000164125	Chromatin interaction
ENSG00000248429	Chromatin interaction

Extended variants
information (count: 27 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:23)

rs_ID	r²[population]
rs10008208	0.85[AMR][1000 genomes];0.84[ASN][1000 genomes]
rs10012339	0.87[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs10028490	0.95[AFR][1000 genomes];0.93[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs12645131	0.85[AMR][1000 genomes];0.84[ASN][1000 genomes]
rs12648410	0.83[AMR][1000 genomes]
rs14202	0.94[AFR][1000 genomes];0.93[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs1879659	0.87[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs2346321	0.82[AMR][1000 genomes]
rs2346781	0.85[AMR][1000 genomes];0.84[ASN][1000 genomes]
rs2346784	0.85[AMR][1000 genomes];0.84[ASN][1000 genomes]
rs2881373	0.83[AMR][1000 genomes]
rs4234917	0.87[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs4309890	0.87[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs4317248	0.87[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs4345228	0.87[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs4501266	0.87[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs4691455	0.83[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs4691461	0.85[AMR][1000 genomes];0.84[ASN][1000 genomes]
rs6536299	0.87[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs6820988	0.84[ASN][1000 genomes]
rs6830702	0.83[AMR][1000 genomes]
rs6833198	0.85[AMR][1000 genomes];0.84[ASN][1000 genomes]
rs8370	0.87[AMR][1000 genomes];0.90[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv993476	chr4:158550643-159202015	Weak transcription Enhancers Flanking Active TSS Active TSS Strong transcription ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	16 gene(s)	inside rSNPs	diseases
2	nsv1030124	chr4:158758675-159251140	Bivalent/Poised TSS Enhancers Active TSS Flanking Active TSS Weak transcription Genic enhancers ZNF genes & repeats Strong transcription Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	13 gene(s)	inside rSNPs	diseases
3	nsv1021067	chr4:158972282-159175475	Enhancers Flanking Active TSS Active TSS Strong transcription Weak transcription Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	10 gene(s)	inside rSNPs	diseases
4	nsv880293	chr4:159012365-159049020	Enhancers Weak transcription Flanking Active TSS Strong transcription Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Genic enhancers	Chromatin interactive region miRNA target site	2 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs6852878	TMEM144	cis	Esophagus Muscularis	GTEx

Chromatin state (count:46 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:159034200-159046200	Weak transcription	HUVEC	blood vessel
2	chr4:159041200-159043800	Enhancers	Primary monocytes fromperipheralblood	blood
3	chr4:159041200-159043800	Enhancers	Fetal Stomach	stomach
4	chr4:159041400-159044600	Enhancers	HSMM	muscle
5	chr4:159041600-159043800	Weak transcription	NHLF	lung
6	chr4:159041600-159044200	Enhancers	Fetal Lung	lung
7	chr4:159042000-159044400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
8	chr4:159042000-159046800	Weak transcription	Breast Myoepithelial Primary Cells	Breast
9	chr4:159042200-159048000	Weak transcription	Fetal Intestine Large	intestine
10	chr4:159042200-159051400	Weak transcription	Duodenum Smooth Muscle	Duodenum
11	chr4:159042400-159044000	Enhancers	Muscle Satellite Cultured Cells	--
12	chr4:159042400-159044200	Enhancers	Osteobl	bone
13	chr4:159042400-159044600	Enhancers	NHDF-Ad	bronchial
14	chr4:159042400-159050800	Weak transcription	Aorta	Aorta
15	chr4:159042600-159043800	Weak transcription	Fetal Kidney	kidney
16	chr4:159042600-159044400	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
17	chr4:159042600-159044600	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
18	chr4:159042600-159053400	Weak transcription	Right Atrium	heart
19	chr4:159042600-159053600	Weak transcription	Brain Anterior Caudate	brain
20	chr4:159042600-159060200	Weak transcription	Brain Substantia Nigra	brain
21	chr4:159042800-159043800	Weak transcription	Stomach Smooth Muscle	stomach
22	chr4:159042800-159043800	Enhancers	Monocytes-CD14+_RO01746	blood
23	chr4:159042800-159044000	Enhancers	NH-A	brain
24	chr4:159042800-159044400	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
25	chr4:159042800-159044600	Enhancers	Colon Smooth Muscle	Colon
26	chr4:159042800-159044600	Enhancers	HSMMtube	muscle
27	chr4:159042800-159046400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
28	chr4:159042800-159046400	Weak transcription	HUES48 Cell Line	embryonic stem cell
29	chr4:159042800-159046400	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
30	chr4:159042800-159047000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
31	chr4:159042800-159047200	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
32	chr4:159042800-159047200	Weak transcription	Adipose Nuclei	Adipose
33	chr4:159042800-159047400	Weak transcription	HMEC	breast
34	chr4:159042800-159048000	Weak transcription	HepG2	liver
35	chr4:159042800-159049000	Weak transcription	Ovary	ovary
36	chr4:159042800-159050000	Weak transcription	Brain Hippocampus Middle	brain
37	chr4:159042800-159053400	Weak transcription	Fetal Muscle Trunk	muscle
38	chr4:159042800-159053800	Weak transcription	Brain Inferior Temporal Lobe	brain
39	chr4:159042800-159054800	Weak transcription	Fetal Heart	heart
40	chr4:159042800-159083600	Weak transcription	Fetal Muscle Leg	muscle
41	chr4:159043000-159043200	Enhancers	Left Ventricle	heart
42	chr4:159043000-159043200	Weak transcription	Placenta Amnion	Placenta Amnion
43	chr4:159043000-159043400	Weak transcription	Rectal Smooth Muscle	rectum
44	chr4:159043000-159043600	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
45	chr4:159043000-159044000	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
46	chr4:159043000-159044800	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung

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