Variant report

Variant	rs59540486
Chromosome Location	chr4:129892006-129892007
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 57 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:33)

rs_ID	r²[population]
rs1030830	0.92[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs12500341	0.88[AMR][1000 genomes];0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12503465	0.90[AMR][1000 genomes];0.99[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs12504200	0.81[AFR][1000 genomes];0.84[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12512345	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs17416188	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17416706	0.89[AMR][1000 genomes];0.99[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1900397	0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2044523	0.90[AMR][1000 genomes];0.99[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs36195612	0.82[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs3980331	0.88[AMR][1000 genomes];0.98[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4975191	0.90[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4975293	0.87[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4975294	0.81[AFR][1000 genomes];0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs55925207	0.81[AMR][1000 genomes];0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6830023	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6845314	0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6847784	0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs72683669	0.80[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs72683673	0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs72683684	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs72683693	0.87[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs72685321	0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs72685324	0.81[AFR][1000 genomes];0.80[AMR][1000 genomes];0.93[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs72685328	0.81[AFR][1000 genomes];0.81[AMR][1000 genomes];0.93[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs72685351	0.90[ASN][1000 genomes]
rs72685352	0.81[AFR][1000 genomes];0.92[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs72685353	0.92[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs72685365	0.92[EUR][1000 genomes]
rs7675408	0.84[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs921375	0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs921376	0.85[AMR][1000 genomes];0.81[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs921377	0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:24 , 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	nsv517249	chr4:129738328-129927804	Genic enhancers Weak transcription Strong transcription Enhancers ZNF genes & repeats Active TSS Flanking Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region miRNA target site	4 gene(s)	inside rSNPs	diseases
3	nsv1026938	chr4:129770961-129936205	Weak transcription Strong transcription Enhancers Flanking Active TSS Genic enhancers ZNF genes & repeats 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
4	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
5	nsv870175	chr4:129771718-129937945	Genic enhancers Weak transcription Strong 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
6	nsv1026772	chr4:129773881-129936205	ZNF genes & repeats Flanking Active TSS Weak transcription Strong transcription Genic enhancers Enhancers 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
7	nsv461637	chr4:129774375-129924977	Weak transcription Strong transcription Enhancers Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Active TSS Active TSS	TF binding region CpG island Chromatin interactive region miRNA target site	4 gene(s)	inside rSNPs	diseases
8	nsv595397	chr4:129774375-129924977	Transcr. at gene 5' and 3' Weak transcription Genic enhancers Strong transcription Enhancers ZNF genes & repeats Flanking Active TSS Active TSS	TF binding region CpG island Chromatin interactive region miRNA target site	4 gene(s)	inside rSNPs	diseases
9	nsv461638	chr4:129774375-129927804	Weak transcription Strong transcription Genic enhancers Enhancers Flanking Active TSS Transcr. at gene 5' and 3' Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region miRNA target site	4 gene(s)	inside rSNPs	diseases
10	nsv595398	chr4:129774375-129927804	Weak transcription Strong transcription Genic enhancers Flanking Active TSS Enhancers ZNF genes & repeats 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
11	nsv1018994	chr4:129775612-129933968	Enhancers Strong transcription Weak transcription Genic 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
12	nsv1034996	chr4:129777825-129905255	Genic enhancers Strong transcription Weak transcription Flanking Active TSS Enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Active TSS	TF binding region CpG island Chromatin interactive region miRNA target site	4 gene(s)	inside rSNPs	diseases
13	nsv537249	chr4:129777825-129905255	Weak transcription Strong transcription Genic enhancers Enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Active TSS Active TSS	TF binding region CpG island Chromatin interactive region miRNA target site	4 gene(s)	inside rSNPs	diseases
14	nsv1022446	chr4:129778025-129905116	Enhancers Strong transcription Weak transcription Genic enhancers Flanking Active TSS ZNF genes & repeats 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
15	nsv537250	chr4:129778025-129905116	Strong transcription Weak transcription Enhancers Genic enhancers ZNF genes & repeats Flanking Active TSS Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region miRNA target site	4 gene(s)	inside rSNPs	diseases
16	nsv1030296	chr4:129778025-129920680	Weak transcription Genic enhancers Strong transcription Enhancers Transcr. at gene 5' and 3' Flanking Active TSS Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region miRNA target site	4 gene(s)	inside rSNPs	diseases
17	nsv537251	chr4:129778025-129920680	Genic enhancers Weak transcription ZNF genes & repeats Strong transcription Transcr. at gene 5' and 3' Enhancers Flanking Active TSS Active TSS	TF binding region CpG island Chromatin interactive region miRNA target site	4 gene(s)	inside rSNPs	diseases
18	esv2830419	chr4:129785483-129905256	Strong transcription Weak transcription Enhancers Genic enhancers ZNF genes & repeats Flanking Active TSS Active TSS	TF binding region CpG island Chromatin interactive region miRNA target site	3 gene(s)	inside rSNPs	diseases
19	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
20	nsv1026722	chr4:129801602-129929219	Weak transcription Enhancers Strong transcription ZNF genes & repeats Flanking Active TSS Active TSS Genic enhancers	TF binding region CpG island Chromatin interactive region	3 gene(s)	inside rSNPs	diseases
21	nsv537252	chr4:129801602-129929219	Weak transcription Enhancers ZNF genes & repeats Strong transcription Active TSS Genic enhancers Flanking Active TSS	TF binding region CpG island Chromatin interactive region	3 gene(s)	inside rSNPs	diseases
22	nsv595399	chr4:129835649-129924852	Enhancers Weak transcription ZNF genes & repeats Strong transcription Flanking Active TSS Active TSS Genic enhancers	TF binding region Chromatin interactive region	2 gene(s)	inside rSNPs	diseases
23	nsv1020327	chr4:129859624-129914665	Strong transcription Weak transcription Enhancers ZNF genes & repeats Flanking Active TSS Active TSS Genic enhancers	TF binding region Chromatin interactive region	2 gene(s)	inside rSNPs	diseases
24	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

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs59540486	SCLT1	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:73 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:129793800-129907200	Weak transcription	Sigmoid Colon	Sigmoid Colon
2	chr4:129834800-129907400	Weak transcription	Aorta	Aorta
3	chr4:129839800-129907800	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
4	chr4:129841000-129907400	Weak transcription	Rectal Mucosa Donor 31	rectum
5	chr4:129845400-129907400	Weak transcription	Brain Hippocampus Middle	brain
6	chr4:129845800-129907200	Weak transcription	Ovary	ovary
7	chr4:129847800-129895400	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
8	chr4:129855200-129907800	Weak transcription	K562	blood
9	chr4:129855400-129895200	Weak transcription	Fetal Kidney	kidney
10	chr4:129856400-129907200	Weak transcription	Rectal Mucosa Donor 29	rectum
11	chr4:129861000-129907200	Weak transcription	Thymus	Thymus
12	chr4:129862400-129924200	Weak transcription	Colonic Mucosa	Colon
13	chr4:129864000-129895400	Weak transcription	NHLF	lung
14	chr4:129864000-129918000	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
15	chr4:129864200-129895400	Weak transcription	Fetal Lung	lung
16	chr4:129864400-129901000	Weak transcription	A549	lung
17	chr4:129865600-129907200	Weak transcription	Pancreas	Pancrea
18	chr4:129866400-129907600	Weak transcription	Small Intestine	intestine
19	chr4:129866600-129916600	Weak transcription	Right Ventricle	heart
20	chr4:129866800-129916200	Weak transcription	Hela-S3	cervix
21	chr4:129867000-129907400	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
22	chr4:129868200-129935600	Weak transcription	HSMM	muscle
23	chr4:129868600-129895000	Weak transcription	Fetal Muscle Trunk	muscle
24	chr4:129868600-129907200	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
25	chr4:129868600-129907200	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
26	chr4:129868600-129907200	Weak transcription	Adipose Nuclei	Adipose
27	chr4:129868600-129907400	Weak transcription	Primary T cells fromperipheralblood	blood
28	chr4:129871600-129907600	Weak transcription	Liver	Liver
29	chr4:129873200-129900600	Weak transcription	NHDF-Ad	bronchial
30	chr4:129873800-129900600	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
31	chr4:129877400-129907200	Weak transcription	GM12878-XiMat	blood
32	chr4:129878400-129925600	Weak transcription	HSMMtube	muscle
33	chr4:129878600-129907400	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
34	chr4:129879400-129895400	Weak transcription	Fetal Intestine Small	intestine
35	chr4:129879800-129906600	Weak transcription	Primary B cells from peripheral blood	blood
36	chr4:129880000-129895200	Weak transcription	Fetal Intestine Large	intestine
37	chr4:129883200-129923400	Weak transcription	Primary T helper cells fromperipheralblood	blood
38	chr4:129883400-129893800	Weak transcription	Primary T helper naive cells from peripheral blood	blood
39	chr4:129883400-129894200	Strong transcription	Monocytes-CD14+_RO01746	blood
40	chr4:129883400-129907600	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
41	chr4:129883400-129912600	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
42	chr4:129883800-129895400	Weak transcription	Cortex derived primary cultured neurospheres	brain
43	chr4:129883800-129907600	Weak transcription	Primary T helper cells PMA-I stimulated	--
44	chr4:129884800-129909200	Weak transcription	Skeletal Muscle Male	skeletal muscle
45	chr4:129887000-129918800	Weak transcription	Psoas Muscle	Psoas
46	chr4:129887800-129918000	Weak transcription	Fetal Heart	heart
47	chr4:129888000-129894200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
48	chr4:129888600-129901000	Weak transcription	NHEK	skin
49	chr4:129888800-129895400	Weak transcription	Fetal Muscle Leg	muscle
50	chr4:129888800-129898200	Weak transcription	Primary T cells from cord blood	blood

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