Variant report

Variant	rs6857561
Chromosome Location	chr4:57193303-57193304
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 62 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:56)

rs_ID	r²[population]
rs1042040	0.92[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs1124570	0.90[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs11538098	0.91[EUR][1000 genomes]
rs11722404	0.97[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs11723379	0.84[EUR][1000 genomes]
rs11728068	0.88[EUR][1000 genomes]
rs11732985	0.92[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs11734595	0.97[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs11935357	0.89[EUR][1000 genomes]
rs11937997	0.98[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs11943048	0.92[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs11946745	0.91[EUR][1000 genomes]
rs13109030	0.96[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs13114481	0.91[EUR][1000 genomes]
rs13122196	0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs13122422	0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs13122832	0.96[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs13123542	0.83[ASN][1000 genomes]
rs13124065	0.92[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs13129188	0.97[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs13131846	0.85[AFR][1000 genomes];0.84[AMR][1000 genomes];0.96[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs13132553	0.87[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13135151	0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs13140746	0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs13146014	0.88[EUR][1000 genomes]
rs13148435	0.92[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs13148656	0.98[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs13150967	0.97[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs1401908	0.82[EUR][1000 genomes]
rs1401911	0.92[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2030363	0.82[EUR][1000 genomes]
rs3796544	0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6554346	0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6554350	0.96[AFR][1000 genomes];0.81[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6554353	0.98[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs6554354	0.98[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs6811153	0.88[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6811616	0.88[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6811652	0.82[EUR][1000 genomes]
rs6812222	0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6815480	0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6818283	0.88[EUR][1000 genomes]
rs6818340	0.88[EUR][1000 genomes]
rs6820922	0.88[EUR][1000 genomes]
rs6823339	0.86[EUR][1000 genomes]
rs6854326	0.91[EUR][1000 genomes]
rs7437329	0.82[EUR][1000 genomes]
rs7654543	0.89[EUR][1000 genomes]
rs7656361	0.87[AFR][1000 genomes];0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7673373	0.92[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs7682041	0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7682608	0.85[AMR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7695701	1.00[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7699157	0.98[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs956275	0.92[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs9995463	0.89[AMR][1000 genomes];0.98[EUR][1000 genomes];0.89[ASN][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:4)

SNP	Gene	Cis/trans	Tissue	Source
rs6857561	AASDH	cis	multi-tissue	Pritchard
rs6857561	AASDH	Cis_1M	lymphoblastoid	RTeQTL
rs6857561	PPAT	Cis_1M	lymphoblastoid	RTeQTL
rs6857561	AASDH	cis	Skin Sun Exposed Lower leg	GTEx

Chromatin state (count:56 , 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	chr4:57173200-57202800	Weak transcription	H9 Cell Line	embryonic stem cell
5	chr4:57174400-57195000	Strong transcription	Fetal Intestine Small	intestine
6	chr4:57174400-57203800	Weak transcription	Fetal Kidney	kidney
7	chr4:57174600-57197200	Strong transcription	Duodenum Mucosa	Duodenum
8	chr4:57177600-57215400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
9	chr4:57178200-57211800	Weak transcription	Brain Hippocampus Middle	brain
10	chr4:57180800-57197200	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
11	chr4:57181200-57196400	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
12	chr4:57181400-57203800	Weak transcription	HSMMtube	muscle
13	chr4:57181800-57196200	Strong transcription	Fetal Intestine Large	intestine
14	chr4:57182800-57196800	Weak transcription	Ovary	ovary
15	chr4:57183000-57193800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
16	chr4:57183200-57194400	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
17	chr4:57184600-57211200	Weak transcription	Brain Cingulate Gyrus	brain
18	chr4:57187200-57202600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
19	chr4:57188400-57203600	Weak transcription	Fetal Lung	lung
20	chr4:57188600-57197800	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
21	chr4:57189000-57195800	Strong transcription	Brain Germinal Matrix	brain
22	chr4:57189400-57195800	Strong transcription	Primary hematopoietic stem cells short term culture	blood
23	chr4:57189600-57194000	Weak transcription	Placenta	Placenta
24	chr4:57190400-57203000	Weak transcription	Primary hematopoietic stem cells	blood
25	chr4:57190400-57203200	Weak transcription	Fetal Muscle Trunk	muscle
26	chr4:57190400-57203600	Weak transcription	Brain Inferior Temporal Lobe	brain
27	chr4:57190400-57214400	Weak transcription	Brain Anterior Caudate	brain
28	chr4:57190600-57193800	Weak transcription	HUES64 Cell Line	embryonic stem cell
29	chr4:57190600-57194200	Weak transcription	Rectal Mucosa Donor 29	rectum
30	chr4:57190600-57214600	Weak transcription	Brain Substantia Nigra	brain
31	chr4:57190600-57252400	Weak transcription	Colonic Mucosa	Colon
32	chr4:57190800-57194400	Weak transcription	Sigmoid Colon	Sigmoid Colon
33	chr4:57190800-57194600	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
34	chr4:57190800-57196400	Weak transcription	Fetal Muscle Leg	muscle
35	chr4:57190800-57197000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
36	chr4:57190800-57202600	Weak transcription	H1 Cell Line	embryonic stem cell
37	chr4:57190800-57202600	Weak transcription	HUES6 Cell Line	embryonic stem cell
38	chr4:57190800-57203200	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
39	chr4:57190800-57203600	Weak transcription	Fetal Brain Male	brain
40	chr4:57190800-57203800	Weak transcription	Rectal Smooth Muscle	rectum
41	chr4:57191000-57193800	Weak transcription	HUES48 Cell Line	embryonic stem cell
42	chr4:57191000-57194000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
43	chr4:57191000-57204000	Weak transcription	Brain Angular Gyrus	brain
44	chr4:57191200-57193600	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
45	chr4:57191200-57194200	Weak transcription	iPS-20b Cell Line	embryonic stem cell
46	chr4:57191800-57193800	Weak transcription	Fetal Stomach	stomach
47	chr4:57192000-57194200	Weak transcription	iPS-18 Cell Line	embryonic stem cell
48	chr4:57192200-57195400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
49	chr4:57192600-57197200	Strong transcription	Rectal Mucosa Donor 31	rectum
50	chr4:57192800-57193600	Weak transcription	Cortex derived primary cultured neurospheres	brain

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