Variant report

Variant	rs6771917
Chromosome Location	chr3:48108442-48108443
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 35 )
Associated
traits (count: 12 )

rSNPs within LD-proxies of this variant (count:24)

rs_ID	r²[population]
rs11130154	0.83[AFR][1000 genomes]
rs11130155	0.81[ASN][1000 genomes]
rs11710866	0.81[ASN][1000 genomes]
rs11720151	0.81[ASN][1000 genomes]
rs12486714	0.84[AFR][1000 genomes];0.81[ASN][1000 genomes]
rs12493348	0.84[AFR][1000 genomes];0.81[ASN][1000 genomes]
rs13075457	0.83[AFR][1000 genomes]
rs13080997	0.82[AFR][1000 genomes]
rs13085054	0.81[AFR][1000 genomes]
rs2121754	0.81[AFR][1000 genomes]
rs2361683	0.83[AFR][1000 genomes]
rs2361684	0.84[AFR][1000 genomes]
rs34597784	0.82[AFR][1000 genomes]
rs35689209	0.85[AFR][1000 genomes];0.90[ASN][1000 genomes]
rs4293721	0.81[AFR][1000 genomes]
rs4858880	0.80[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs4858881	0.92[AFR][1000 genomes];0.83[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs5012971	0.86[AFR][1000 genomes]
rs56067795	0.83[AFR][1000 genomes]
rs6791834	0.97[AFR][1000 genomes];0.83[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs6803741	0.84[ASN][1000 genomes]
rs7427648	0.86[AFR][1000 genomes]
rs7620736	0.95[AFR][1000 genomes];0.83[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs7627645	0.87[AFR][1000 genomes];0.81[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:11 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv529989	chr3:47909480-48301481	Genic enhancers Strong transcription Flanking Active TSS Weak transcription Enhancers Active TSS ZNF genes & repeats 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 miRNA target site	42 gene(s)	inside rSNPs	diseases
2	nsv1001056	chr3:47912342-48223849	Genic enhancers Strong transcription Enhancers Weak transcription Active TSS Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	21 gene(s)	inside rSNPs	diseases
3	esv1835684	chr3:47912703-48123540	Weak transcription Enhancers Strong transcription Genic enhancers Flanking Active TSS Active TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	7 gene(s)	inside rSNPs	diseases
4	esv1827272	chr3:47912703-48260968	Weak transcription Genic enhancers Strong transcription Enhancers Flanking Active TSS Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	39 gene(s)	inside rSNPs	diseases
5	nsv1009243	chr3:47935331-48340448	Enhancers Flanking Active TSS Weak transcription Strong transcription Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	45 gene(s)	inside rSNPs	diseases
6	nsv536562	chr3:47935331-48340448	Enhancers Active TSS Weak transcription Strong transcription Flanking Active TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	45 gene(s)	inside rSNPs	diseases
7	nsv1012828	chr3:47996472-48192862	Strong transcription Weak transcription Enhancers Active TSS Genic enhancers Flanking Active TSS ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	17 gene(s)	inside rSNPs	diseases
8	nsv1002067	chr3:47996472-48326518	Enhancers Weak transcription Genic enhancers ZNF genes & repeats Flanking Active TSS Strong transcription Active TSS 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 miRNA target site	43 gene(s)	inside rSNPs	diseases
9	nsv876760	chr3:48019258-48197614	Enhancers Genic enhancers Flanking Active TSS Active TSS Weak transcription ZNF genes & repeats Strong transcription Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	diseases
10	nsv834681	chr3:48032000-48181775	Enhancers Weak transcription Strong transcription Genic enhancers Flanking Active TSS Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases
11	nsv1004557	chr3:48056534-48256694	Weak transcription ZNF genes & repeats Enhancers Strong transcription Active TSS Flanking Active TSS Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	34 gene(s)	inside rSNPs	diseases

mRNA abundance (count:12)

SNP	Gene	Cis/trans	Tissue	Source
rs6771917	MRPS18AP1	cis	Nerve Tibial	GTEx
rs6771917	MAP4	Cis_1M	lymphoblastoid	RTeQTL
rs6771917	MRPS18AP1	cis	Muscle Skeletal	GTEx
rs6771917	MRPS18AP1	cis	Thyroid	GTEx
rs6771917	MRPS18AP1	cis	Esophagus Muscularis	GTEx
rs6771917	MRPS18AP1	cis	Artery Tibial	GTEx
rs6771917	CDC25A	cis	Muscle Skeletal	GTEx
rs6771917	CDC25A	cis	Thyroid	GTEx
rs6771917	ZNF589	cis	Adipose Subcutaneous	GTEx
rs6771917	ZNF589	cis	Nerve Tibial	GTEx
rs6771917	MRPS18AP1	cis	lung	GTEx
rs6771917	NME6	cis	Esophagus Muscularis	GTEx

Chromatin state (count:99 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:48051200-48128000	Weak transcription	Primary B cells from cord blood	blood
2	chr3:48059600-48128800	Weak transcription	Primary T cells from cord blood	blood
3	chr3:48064400-48128800	Weak transcription	Esophagus	oesophagus
4	chr3:48081400-48110600	Weak transcription	Duodenum Mucosa	Duodenum
5	chr3:48081400-48128400	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
6	chr3:48081800-48128400	Weak transcription	Primary hematopoietic stem cells	blood
7	chr3:48082200-48115000	Weak transcription	Primary B cells from peripheral blood	blood
8	chr3:48084000-48111800	Weak transcription	Cortex derived primary cultured neurospheres	brain
9	chr3:48089400-48128400	Weak transcription	Thymus	Thymus
10	chr3:48089400-48128600	Weak transcription	H9 Cell Line	embryonic stem cell
11	chr3:48089600-48128400	Weak transcription	Rectal Mucosa Donor 29	rectum
12	chr3:48089800-48128200	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
13	chr3:48089800-48128800	Weak transcription	Primary neutrophils fromperipheralblood	blood
14	chr3:48091000-48110200	Weak transcription	HepG2	liver
15	chr3:48091200-48110000	Weak transcription	Rectal Mucosa Donor 31	rectum
16	chr3:48091200-48110600	Weak transcription	Liver	Liver
17	chr3:48091200-48110800	Weak transcription	Sigmoid Colon	Sigmoid Colon
18	chr3:48091400-48111400	Weak transcription	Fetal Muscle Trunk	muscle
19	chr3:48091400-48112400	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
20	chr3:48092400-48111000	Weak transcription	Fetal Stomach	stomach
21	chr3:48092600-48110800	Weak transcription	Fetal Lung	lung
22	chr3:48093800-48128400	Weak transcription	Spleen	Spleen
23	chr3:48095000-48128400	Weak transcription	Primary T helper naive cells from peripheral blood	blood
24	chr3:48095200-48110200	Weak transcription	Hela-S3	cervix
25	chr3:48096600-48110800	Weak transcription	Fetal Muscle Leg	muscle
26	chr3:48096600-48126000	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
27	chr3:48100400-48110200	Weak transcription	Duodenum Smooth Muscle	Duodenum
28	chr3:48100800-48110200	Weak transcription	Breast Myoepithelial Primary Cells	Breast
29	chr3:48100800-48110800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
30	chr3:48100800-48110800	Weak transcription	Ovary	ovary
31	chr3:48100800-48112800	Weak transcription	Stomach Smooth Muscle	stomach
32	chr3:48100800-48113200	Weak transcription	Adipose Nuclei	Adipose
33	chr3:48100800-48123200	Weak transcription	GM12878-XiMat	blood
34	chr3:48100800-48128400	Weak transcription	Brain Substantia Nigra	brain
35	chr3:48100800-48128600	Weak transcription	Primary monocytes fromperipheralblood	blood
36	chr3:48100800-48128800	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
37	chr3:48101000-48111800	Weak transcription	Primary T cells fromperipheralblood	blood
38	chr3:48101000-48116400	Weak transcription	Primary T helper cells PMA-I stimulated	--
39	chr3:48101600-48113600	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
40	chr3:48101600-48128200	Weak transcription	Primary T helper cells fromperipheralblood	blood
41	chr3:48103000-48110200	Weak transcription	Fetal Intestine Small	intestine
42	chr3:48103600-48112200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
43	chr3:48103600-48112200	Weak transcription	Fetal Thymus	thymus
44	chr3:48103600-48128200	Weak transcription	Primary hematopoietic stem cells short term culture	blood
45	chr3:48104600-48108600	Enhancers	Psoas Muscle	Psoas
46	chr3:48104600-48110400	Weak transcription	Stomach Mucosa	stomach
47	chr3:48104800-48110600	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
48	chr3:48105000-48128200	Weak transcription	HUES48 Cell Line	embryonic stem cell
49	chr3:48105200-48110400	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
50	chr3:48105200-48125600	Weak transcription	Dnd41	blood

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