Variant report

Variant	rs6841016
Chromosome Location	chr4:57203152-57203153
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 43 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:37)

rs_ID	r²[population]
rs10031550	0.90[AMR][1000 genomes];0.91[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs13114104	0.81[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs13133016	0.84[EUR][1000 genomes]
rs13141793	0.81[EUR][1000 genomes]
rs13147824	0.86[EUR][1000 genomes]
rs1356788	0.82[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs1401912	0.81[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs1464286	0.81[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs1976815	0.81[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs1996650	0.81[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs2030365	0.87[EUR][1000 genomes]
rs2139512	0.86[EUR][1000 genomes]
rs28559894	0.81[EUR][1000 genomes]
rs2899063	0.85[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs3796542	0.81[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs3796547	0.81[EUR][1000 genomes]
rs3822003	0.80[EUR][1000 genomes]
rs4167	0.85[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs4865087	0.81[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs4865100	0.81[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs4865101	0.81[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs57503982	0.81[EUR][1000 genomes]
rs62310633	0.80[EUR][1000 genomes]
rs6554349	0.84[EUR][1000 genomes]
rs6554352	0.85[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs6554355	0.81[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs6554356	0.81[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs6812041	0.81[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs6826795	0.82[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs7657711	0.81[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs7661712	0.81[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs7683781	0.85[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs7692385	0.85[EUR][1000 genomes]
rs7693683	0.81[EUR][1000 genomes]
rs9683679	0.81[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs9684298	0.81[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs9997639	0.81[AMR][1000 genomes];0.86[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv999639	chr4:56942917-57401310	Weak transcription Flanking Active TSS Bivalent/Poised TSS Active TSS Strong transcription Enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	50 gene(s)	inside rSNPs	diseases
2	nsv1014045	chr4:56942917-57404511	Weak transcription Strong transcription Enhancers Active TSS ZNF genes & repeats Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	50 gene(s)	inside rSNPs	diseases
3	esv3415289	chr4:57063312-57236755	Strong transcription Enhancers Weak transcription Bivalent Enhancer ZNF genes & repeats Flanking Active TSS Genic enhancers Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	10 gene(s)	inside rSNPs	diseases
4	nsv829940	chr4:57072341-57262730	Weak transcription Strong transcription Enhancers ZNF genes & repeats Active TSS Genic enhancers Bivalent Enhancer Flanking Active TSS 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	33 gene(s)	inside rSNPs	diseases
5	nsv868815	chr4:57114268-58084688	Weak transcription Bivalent Enhancer Flanking Active TSS Active TSS Enhancers Strong transcription Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	88 gene(s)	inside rSNPs	diseases
6	nsv530121	chr4:57167367-57695576	Flanking Bivalent TSS/Enh Enhancers Flanking Active TSS Weak transcription Active TSS Genic enhancers Strong transcription Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	59 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs6841016	PPAT	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:63 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:57167600-57203400	Weak transcription	Duodenum Smooth Muscle	Duodenum
2	chr4:57167800-57218600	Weak transcription	Small Intestine	intestine
3	chr4:57172000-57204000	Weak transcription	Stomach Mucosa	stomach
4	chr4:57174400-57203800	Weak transcription	Fetal Kidney	kidney
5	chr4:57177600-57215400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
6	chr4:57178200-57211800	Weak transcription	Brain Hippocampus Middle	brain
7	chr4:57181400-57203800	Weak transcription	HSMMtube	muscle
8	chr4:57184600-57211200	Weak transcription	Brain Cingulate Gyrus	brain
9	chr4:57188400-57203600	Weak transcription	Fetal Lung	lung
10	chr4:57190400-57203200	Weak transcription	Fetal Muscle Trunk	muscle
11	chr4:57190400-57203600	Weak transcription	Brain Inferior Temporal Lobe	brain
12	chr4:57190400-57214400	Weak transcription	Brain Anterior Caudate	brain
13	chr4:57190600-57214600	Weak transcription	Brain Substantia Nigra	brain
14	chr4:57190600-57252400	Weak transcription	Colonic Mucosa	Colon
15	chr4:57190800-57203200	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
16	chr4:57190800-57203600	Weak transcription	Fetal Brain Male	brain
17	chr4:57190800-57203800	Weak transcription	Rectal Smooth Muscle	rectum
18	chr4:57191000-57204000	Weak transcription	Brain Angular Gyrus	brain
19	chr4:57193000-57204000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
20	chr4:57193600-57213000	Weak transcription	Left Ventricle	heart
21	chr4:57195000-57214400	Weak transcription	Placenta	Placenta
22	chr4:57195200-57238000	Weak transcription	HUVEC	blood vessel
23	chr4:57195400-57203200	Weak transcription	Rectal Mucosa Donor 29	rectum
24	chr4:57195800-57203200	Weak transcription	iPS-18 Cell Line	embryonic stem cell
25	chr4:57196000-57204600	Weak transcription	HSMM	muscle
26	chr4:57196000-57238200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
27	chr4:57197200-57203200	Weak transcription	Ovary	ovary
28	chr4:57197200-57203800	Weak transcription	Rectal Mucosa Donor 31	rectum
29	chr4:57198800-57214400	Weak transcription	Gastric	stomach
30	chr4:57201800-57203600	Weak transcription	Psoas Muscle	Psoas
31	chr4:57201800-57204000	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
32	chr4:57201800-57212000	Weak transcription	Adipose Nuclei	Adipose
33	chr4:57202000-57212000	Weak transcription	Stomach Smooth Muscle	stomach
34	chr4:57202200-57203600	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
35	chr4:57202400-57204600	Weak transcription	Skeletal Muscle Female	skeletal muscle
36	chr4:57202400-57204800	ZNF genes & repeats	Primary hematopoietic stem cells G-CSF-mobilized Male	--
37	chr4:57202600-57203200	ZNF genes & repeats	Fetal Stomach	stomach
38	chr4:57202600-57204200	ZNF genes & repeats	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
39	chr4:57202600-57204200	Strong transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
40	chr4:57202600-57204200	ZNF genes & repeats	Cortex derived primary cultured neurospheres	brain
41	chr4:57202600-57204200	ZNF genes & repeats	Fetal Intestine Small	intestine
42	chr4:57202600-57204800	ZNF genes & repeats	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
43	chr4:57202600-57204800	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
44	chr4:57202600-57205000	ZNF genes & repeats	H1 Cell Line	embryonic stem cell
45	chr4:57202600-57205000	ZNF genes & repeats	HUES6 Cell Line	embryonic stem cell
46	chr4:57202600-57205000	Strong transcription	Fetal Intestine Large	intestine
47	chr4:57202600-57221400	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
48	chr4:57202800-57203200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
49	chr4:57202800-57204800	Strong transcription	Duodenum Mucosa	Duodenum
50	chr4:57202800-57204800	Strong transcription	Fetal Brain Female	brain

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