Variant report

Variant	rs3980331
Chromosome Location	chr4:129943636-129943637
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 46 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:41)

rs_ID	r²[population]
rs1030830	0.82[AMR][1000 genomes];0.93[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs12500341	0.93[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12503465	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12504200	0.90[AFR][1000 genomes];0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12512345	0.88[AMR][1000 genomes];0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs17416188	0.88[AMR][1000 genomes];0.98[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs17416706	1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1757938	0.81[AFR][1000 genomes]
rs1757942	0.81[AFR][1000 genomes]
rs1900397	0.87[AFR][1000 genomes];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2044523	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2592948	0.81[AFR][1000 genomes]
rs2655311	0.81[AFR][1000 genomes]
rs2777823	0.81[AFR][1000 genomes]
rs3099902	0.81[AFR][1000 genomes]
rs36195612	0.91[AFR][1000 genomes];0.82[AMR][1000 genomes];0.84[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs4975191	0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4975293	0.84[AFR][1000 genomes];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4975294	0.90[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs55925207	0.85[AFR][1000 genomes];0.88[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs59540486	0.88[AMR][1000 genomes];0.98[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6830023	0.81[AFR][1000 genomes];0.88[AMR][1000 genomes];0.98[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6845314	1.00[AFR][1000 genomes];0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6847784	1.00[AFR][1000 genomes];0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs72683669	0.96[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs72683673	0.81[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs72683684	0.81[AFR][1000 genomes];0.88[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs72683693	0.84[AFR][1000 genomes];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs72685321	1.00[AFR][1000 genomes];0.89[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs72685324	0.90[AFR][1000 genomes];0.87[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs72685328	0.90[AFR][1000 genomes];0.88[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs72685351	0.95[ASN][1000 genomes]
rs72685352	0.90[AFR][1000 genomes];0.84[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs72685353	0.97[AFR][1000 genomes];0.86[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs72685365	0.88[AFR][1000 genomes];0.80[AMR][1000 genomes];0.94[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs7654405	0.81[AFR][1000 genomes]
rs7675408	0.81[AFR][1000 genomes];0.89[AMR][1000 genomes];0.98[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs796886	0.81[AFR][1000 genomes]
rs921375	0.84[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs921376	0.95[ASN][1000 genomes]
rs921377	0.84[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 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
2	nsv1030513	chr4:129770961-129965026	Strong transcription Genic enhancers Weak transcription Enhancers ZNF genes & repeats Flanking Active TSS Transcr. at gene 5' and 3' Active TSS	TF binding region CpG island Chromatin interactive region miRNA target site	4 gene(s)	inside rSNPs	diseases
3	nsv534538	chr4:129799138-130431688	Enhancers Weak transcription Strong transcription Active TSS ZNF genes & repeats Flanking Active TSS Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases
4	nsv522694	chr4:129862073-129994690	Weak transcription Strong transcription ZNF genes & repeats Genic enhancers Enhancers Active TSS Flanking Active TSS	TF binding region Chromatin interactive region	2 gene(s)	inside rSNPs	diseases
5	nsv879931	chr4:129939775-130178102	Weak transcription Strong transcription ZNF genes & repeats Enhancers Flanking Active TSS Active TSS Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs3980331	SCLT1	Cis_1M	lymphoblastoid	RTeQTL

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:129932000-129944000	Weak transcription	Muscle Satellite Cultured Cells	--
2	chr4:129932200-129947000	Weak transcription	Rectal Smooth Muscle	rectum
3	chr4:129934200-129944200	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
4	chr4:129934600-129944200	Weak transcription	Primary T cells fromperipheralblood	blood
5	chr4:129934600-129944200	Weak transcription	Pancreatic Islets	Pancreatic Islet
6	chr4:129935800-129943800	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
7	chr4:129935800-129944400	Weak transcription	Skeletal Muscle Male	skeletal muscle
8	chr4:129936800-129943800	Weak transcription	Stomach Smooth Muscle	stomach
9	chr4:129936800-129944000	Weak transcription	NHLF	lung
10	chr4:129937200-129964000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
11	chr4:129937800-129943800	Weak transcription	Adipose Nuclei	Adipose
12	chr4:129937800-129947000	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
13	chr4:129941200-129943800	Weak transcription	Small Intestine	intestine
14	chr4:129941200-129945600	ZNF genes & repeats	Primary hematopoietic stem cells G-CSF-mobilized Male	--
15	chr4:129941200-129945800	Weak transcription	Colon Smooth Muscle	Colon
16	chr4:129941400-129944400	ZNF genes & repeats	Primary hematopoietic stem cells	blood
17	chr4:129941400-129945000	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
18	chr4:129942000-129944200	ZNF genes & repeats	Breast Myoepithelial Primary Cells	Breast
19	chr4:129942000-129944600	ZNF genes & repeats	Fetal Muscle Leg	muscle
20	chr4:129942200-129944000	ZNF genes & repeats	Foreskin Keratinocyte Primary Cells skin03	Skin
21	chr4:129942200-129944600	ZNF genes & repeats	Dnd41	blood
22	chr4:129942200-129944800	ZNF genes & repeats	Primary hematopoietic stem cells G-CSF-mobilized Female	--
23	chr4:129942200-129945200	ZNF genes & repeats	Monocytes-CD14+_RO01746	blood
24	chr4:129942400-129944400	ZNF genes & repeats	Primary neutrophils fromperipheralblood	blood
25	chr4:129942400-129944800	ZNF genes & repeats	Primary hematopoietic stem cells short term culture	blood
26	chr4:129942400-129944800	ZNF genes & repeats	Liver	Liver
27	chr4:129942600-129944600	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
28	chr4:129942800-129944800	Weak transcription	Gastric	stomach
29	chr4:129942800-129952200	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
30	chr4:129943000-129943800	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
31	chr4:129943000-129944200	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
32	chr4:129943000-129944600	Weak transcription	Ovary	ovary
33	chr4:129943200-129943800	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
34	chr4:129943200-129943800	Strong transcription	Fetal Lung	lung
35	chr4:129943200-129944000	Weak transcription	Right Ventricle	heart
36	chr4:129943200-129944200	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
37	chr4:129943200-129944400	Weak transcription	Primary monocytes fromperipheralblood	blood
38	chr4:129943200-129944400	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
39	chr4:129943200-129944400	Weak transcription	Left Ventricle	heart
40	chr4:129943200-129944800	Weak transcription	Pancreas	Pancrea
41	chr4:129943200-129954600	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
42	chr4:129943200-129960200	Weak transcription	Primary B cells from cord blood	blood
43	chr4:129943400-129944200	Weak transcription	Primary T helper cells fromperipheralblood	blood
44	chr4:129943400-129944600	ZNF genes & repeats	Duodenum Mucosa	Duodenum
45	chr4:129943400-129944600	ZNF genes & repeats	Rectal Mucosa Donor 31	rectum
46	chr4:129943600-129944400	ZNF genes & repeats	Primary T cells from cord blood	blood
47	chr4:129943600-129944400	ZNF genes & repeats	Fetal Adrenal Gland	Adrenal Gland
48	chr4:129943600-129944800	ZNF genes & repeats	HUES64 Cell Line	embryonic stem cell
49	chr4:129943600-129944800	ZNF genes & repeats	Duodenum Smooth Muscle	Duodenum
50	chr4:129943600-129945000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin

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