Variant report

Variant	rs3099903
Chromosome Location	chr4:129962072-129962073
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 39 )
Associated
traits (count: 5 )

rSNPs within LD-proxies of this variant (count:34)

rs_ID	r²[population]
rs10028974	0.96[CEU][hapmap];0.85[CHB][hapmap];0.88[JPT][hapmap];0.92[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs11098994	1.00[CEU][hapmap];0.90[CHB][hapmap];0.88[JPT][hapmap];0.84[AMR][1000 genomes];0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1376202	1.00[CEU][hapmap];0.90[CHB][hapmap];0.88[JPT][hapmap]
rs172168	1.00[CHB][hapmap];0.94[JPT][hapmap];0.93[ASN][1000 genomes]
rs1756011	1.00[CEU][hapmap];1.00[CHB][hapmap];0.89[JPT][hapmap];0.98[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs1757926	0.98[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs1757929	0.98[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs1757936	0.81[YRI][hapmap]
rs1757937	0.87[AFR][1000 genomes];0.90[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1757938	1.00[CEU][hapmap];0.90[CHB][hapmap];0.94[JPT][hapmap];0.85[AMR][1000 genomes];0.99[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1757942	0.82[AMR][1000 genomes];0.99[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1838911	0.87[AFR][1000 genomes];0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs189236	1.00[CEU][hapmap];0.95[CHB][hapmap];0.89[JPT][hapmap];0.95[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs2118045	0.88[AFR][1000 genomes];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2592948	1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];0.82[AMR][1000 genomes];0.99[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2597837	1.00[CEU][hapmap];0.90[CHB][hapmap];0.88[JPT][hapmap];0.94[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2655311	1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];0.86[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2777822	0.85[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2777823	0.82[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs280594	1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];0.80[YRI][hapmap];0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs280596	0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs280597	0.98[AFR][1000 genomes];0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs280601	1.00[CEU][hapmap];0.90[CHB][hapmap];0.83[JPT][hapmap];0.94[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs3099902	1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];0.86[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs3113487	1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];0.88[YRI][hapmap];0.89[AFR][1000 genomes];0.89[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs3113488	0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs337276	0.84[CEU][hapmap];0.89[CHB][hapmap];0.82[JPT][hapmap]
rs337279	0.95[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs55865936	0.85[ASN][1000 genomes]
rs62316971	0.86[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs62316978	0.87[AFR][1000 genomes];0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7654405	0.86[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7671508	0.81[YRI][hapmap]
rs796886	0.82[AMR][1000 genomes];0.99[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:5)

SNP	Gene	Cis/trans	Tissue	Source
rs3099903	SCLT1	cis	brain	BrainEAC
rs3099903	C4orf33	Cis_1M	lymphoblastoid	RTeQTL
rs3099903	LOC132321	cis	normal skin	skin_eQTL
rs3099903	C4orf33	cis	Artery Tibial	GTEx
rs3099903	SCLT1	cis	temporal cortex	BrainEAC

Chromatin state (count:46 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:129937200-129964000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
2	chr4:129944600-129962800	Weak transcription	Primary T cells fromperipheralblood	blood
3	chr4:129944800-129965400	Weak transcription	Ovary	ovary
4	chr4:129945600-129981800	Weak transcription	Thymus	Thymus
5	chr4:129951200-129962400	Weak transcription	Primary T helper cells fromperipheralblood	blood
6	chr4:129951200-129967200	Weak transcription	Rectal Mucosa Donor 31	rectum
7	chr4:129951400-129976200	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
8	chr4:129953400-129962600	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
9	chr4:129953600-129965600	Weak transcription	Primary hematopoietic stem cells short term culture	blood
10	chr4:129953600-129965600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
11	chr4:129954800-129964400	Strong transcription	Monocytes-CD14+_RO01746	blood
12	chr4:129955000-129965200	Weak transcription	K562	blood
13	chr4:129956000-129962600	Weak transcription	HMEC	breast
14	chr4:129956400-129962200	Weak transcription	Fetal Lung	lung
15	chr4:129956600-129962400	Weak transcription	Left Ventricle	heart
16	chr4:129956800-129962600	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
17	chr4:129956800-129962600	Weak transcription	Primary B cells from peripheral blood	blood
18	chr4:129957000-129963800	Weak transcription	Lung	lung
19	chr4:129957000-129965400	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
20	chr4:129957400-129964400	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
21	chr4:129957400-129964800	Weak transcription	Fetal Stomach	stomach
22	chr4:129958400-129964800	Weak transcription	Breast Myoepithelial Primary Cells	Breast
23	chr4:129958600-129963000	Weak transcription	Psoas Muscle	Psoas
24	chr4:129958800-129965400	Weak transcription	Adipose Nuclei	Adipose
25	chr4:129958800-129965400	Weak transcription	Liver	Liver
26	chr4:129958800-129966400	Weak transcription	Fetal Thymus	thymus
27	chr4:129959800-129965600	Weak transcription	Fetal Intestine Small	intestine
28	chr4:129959800-129966000	Weak transcription	Duodenum Smooth Muscle	Duodenum
29	chr4:129960000-129962200	Weak transcription	Primary T helper cells PMA-I stimulated	--
30	chr4:129960000-129962400	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
31	chr4:129960000-129962400	Weak transcription	Small Intestine	intestine
32	chr4:129960000-129964800	Weak transcription	Gastric	stomach
33	chr4:129960400-129963400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
34	chr4:129961000-129962800	Weak transcription	Duodenum Mucosa	Duodenum
35	chr4:129961200-129962200	Weak transcription	HUES48 Cell Line	embryonic stem cell
36	chr4:129961200-129965400	Weak transcription	Primary hematopoietic stem cells	blood
37	chr4:129961400-129963000	Weak transcription	Dnd41	blood
38	chr4:129961400-129963200	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
39	chr4:129961400-129963600	Weak transcription	GM12878-XiMat	blood
40	chr4:129961400-129965400	Weak transcription	Primary B cells from cord blood	blood
41	chr4:129961400-129965600	Weak transcription	Primary neutrophils fromperipheralblood	blood
42	chr4:129961400-129967800	Weak transcription	HSMM	muscle
43	chr4:129961600-129963200	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
44	chr4:129961600-129965200	Weak transcription	Primary monocytes fromperipheralblood	blood
45	chr4:129961600-129965200	Weak transcription	Primary T cells from cord blood	blood
46	chr4:129961600-129965400	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin

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