Variant report

Variant	rs3113489
Chromosome Location	chr4:129961179-129961180
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 88 )
Associated
traits (count: 14 )

rSNPs within LD-proxies of this variant (count:83)

rs_ID	r²[population]
rs10002332	0.93[CEU][hapmap];0.90[JPT][hapmap];0.90[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs10032000	0.87[CEU][hapmap];0.86[JPT][hapmap]
rs1030831	0.93[CEU][hapmap];0.88[CHB][hapmap];0.82[CHD][hapmap];0.92[JPT][hapmap];1.00[TSI][hapmap];0.85[AMR][1000 genomes];0.94[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs1037147	0.85[AMR][1000 genomes];0.94[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs11934740	0.81[TSI][hapmap]
rs12171333	0.93[CEU][hapmap];0.92[JPT][hapmap];0.90[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs13109003	0.86[AFR][1000 genomes];0.99[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs13130762	0.87[AMR][1000 genomes];0.94[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs1374491	0.93[CEU][hapmap];0.88[CHB][hapmap];1.00[JPT][hapmap];0.82[YRI][hapmap];0.85[AFR][1000 genomes];0.99[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1596963	0.84[ASN][1000 genomes]
rs1668289	0.87[CEU][hapmap];0.85[JPT][hapmap]
rs1699379	0.83[AFR][1000 genomes];0.97[AMR][1000 genomes];0.93[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1699380	0.87[CEU][hapmap];0.97[TSI][hapmap];0.88[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs1699384	0.93[CEU][hapmap];0.88[CHB][hapmap];1.00[JPT][hapmap];0.96[AFR][1000 genomes];0.99[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1699385	0.83[AFR][1000 genomes];0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1699387	0.87[CEU][hapmap];0.81[LWK][hapmap];0.97[TSI][hapmap];0.86[YRI][hapmap];0.85[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs1699388	0.93[CEU][hapmap];1.00[JPT][hapmap];0.86[YRI][hapmap];0.83[AFR][1000 genomes];0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1699389	0.83[AFR][1000 genomes];0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1699391	0.93[CEU][hapmap];0.88[CHB][hapmap];1.00[JPT][hapmap];0.86[YRI][hapmap];0.83[AFR][1000 genomes];0.97[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1699393	0.93[CEU][hapmap];0.88[CHB][hapmap];0.92[JPT][hapmap];1.00[YRI][hapmap];0.90[AFR][1000 genomes];0.98[AMR][1000 genomes];0.95[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs1699394	0.96[AMR][1000 genomes];0.92[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs1709419	0.86[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs1709422	0.85[YRI][hapmap]
rs17185550	0.82[YRI][hapmap]
rs1756012	0.93[CEU][hapmap];0.88[CHB][hapmap];0.92[JPT][hapmap];0.86[YRI][hapmap];0.82[AFR][1000 genomes];0.97[AMR][1000 genomes];0.94[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs1757924	0.84[AMR][1000 genomes];0.94[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs1757925	0.93[CEU][hapmap];0.88[CHB][hapmap];0.81[CHD][hapmap];0.92[JPT][hapmap];1.00[TSI][hapmap];0.85[AMR][1000 genomes];0.94[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs1757927	0.85[AMR][1000 genomes];0.94[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs1757928	0.87[CEU][hapmap];0.88[CHB][hapmap];0.92[JPT][hapmap];0.82[LWK][hapmap];0.81[MEX][hapmap];1.00[TSI][hapmap];0.85[AMR][1000 genomes];0.94[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs1757930	0.87[AFR][1000 genomes];0.96[AMR][1000 genomes];0.94[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs1757935	0.93[CEU][hapmap];0.88[CHB][hapmap];0.92[JPT][hapmap];0.85[AMR][1000 genomes];0.94[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs1757936	0.82[CHD][hapmap];0.81[MEX][hapmap];0.81[TSI][hapmap];0.85[AMR][1000 genomes]
rs1854773	0.93[CEU][hapmap];0.88[CHB][hapmap];0.91[JPT][hapmap];0.85[YRI][hapmap];0.85[AFR][1000 genomes];0.97[AMR][1000 genomes];0.91[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1854774	0.93[CEU][hapmap];0.88[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.89[AFR][1000 genomes];0.84[AMR][1000 genomes]
rs189235	0.85[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs2034498	0.80[AFR][1000 genomes];0.88[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2083634	0.93[CEU][hapmap]
rs2162126	0.86[JPT][hapmap]
rs2198042	0.93[CEU][hapmap];0.91[JPT][hapmap];0.92[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2597836	0.80[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs2655310	0.93[CEU][hapmap];0.88[CHB][hapmap];0.82[CHD][hapmap];0.85[JPT][hapmap];0.81[MEX][hapmap];0.91[MKK][hapmap];1.00[TSI][hapmap];0.86[AMR][1000 genomes];0.94[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs280603	0.93[CEU][hapmap];0.83[JPT][hapmap];0.83[AFR][1000 genomes];0.83[AMR][1000 genomes];0.92[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs280604	0.93[CEU][hapmap];0.83[AMR][1000 genomes];0.91[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs3099899	0.92[CEU][hapmap];0.88[CHB][hapmap];0.92[JPT][hapmap];0.86[YRI][hapmap];0.83[AFR][1000 genomes];0.84[AMR][1000 genomes];0.92[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs3105369	0.84[AMR][1000 genomes];0.94[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs3113407	0.86[CEU][hapmap];0.81[JPT][hapmap]
rs3113490	0.85[AMR][1000 genomes]
rs318502	0.86[JPT][hapmap]
rs318503	0.83[JPT][hapmap]
rs318536	0.87[CEU][hapmap];0.86[JPT][hapmap]
rs318543	0.87[CEU][hapmap];0.86[JPT][hapmap]
rs318552	0.87[CEU][hapmap];0.85[JPT][hapmap]
rs337263	0.87[CEU][hapmap];0.82[CHD][hapmap];0.89[LWK][hapmap];1.00[MEX][hapmap];0.93[MKK][hapmap];0.97[TSI][hapmap];0.96[YRI][hapmap];0.91[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs337270	0.81[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs337275	0.94[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs337277	0.87[CEU][hapmap];0.83[LWK][hapmap];0.97[TSI][hapmap];0.86[YRI][hapmap];0.85[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs337278	0.84[AMR][1000 genomes];0.94[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs35006492	0.90[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs389376	0.87[CEU][hapmap];0.82[CHD][hapmap];0.89[LWK][hapmap];1.00[MEX][hapmap];0.94[MKK][hapmap];0.97[TSI][hapmap];0.96[YRI][hapmap];0.81[AFR][1000 genomes];0.94[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs390260	0.87[CEU][hapmap];0.97[TSI][hapmap];0.85[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs391396	0.94[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs395864	0.87[CEU][hapmap];0.96[YRI][hapmap];0.94[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs426521	0.87[CEU][hapmap];0.97[TSI][hapmap];0.85[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs4394010	0.90[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs445294	0.86[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs4466058	0.93[CEU][hapmap];0.88[CHB][hapmap];1.00[JPT][hapmap];0.83[AFR][1000 genomes];0.84[AMR][1000 genomes];0.92[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs474667	0.86[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs474794	0.86[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs487233	0.81[AFR][1000 genomes];0.94[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs487501	0.81[AFR][1000 genomes];0.94[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs4975193	0.93[CEU][hapmap];0.88[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.89[LWK][hapmap];1.00[MEX][hapmap];0.91[MKK][hapmap];1.00[TSI][hapmap];0.86[YRI][hapmap];0.85[AFR][1000 genomes];0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4975194	0.85[AFR][1000 genomes];0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4975274	0.86[JPT][hapmap]
rs517659	0.94[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs57501568	0.91[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs576492	0.84[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs58689608	0.83[AFR][1000 genomes];0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6534707	0.82[AFR][1000 genomes];0.97[AMR][1000 genomes];0.90[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs66921209	0.89[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs6824219	0.80[TSI][hapmap]
rs7655841	0.93[CEU][hapmap];0.89[CHD][hapmap];1.00[GIH][hapmap];0.86[JPT][hapmap];0.93[MEX][hapmap];0.87[MKK][hapmap];1.00[TSI][hapmap];0.92[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs7671508	0.82[CHD][hapmap];0.81[MEX][hapmap];0.81[TSI][hapmap];0.85[AMR][1000 genomes]
rs789982	0.82[CHD][hapmap];0.81[MEX][hapmap];0.81[TSI][hapmap];0.85[AMR][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:14)

SNP	Gene	Cis/trans	Tissue	Source
rs3113489	SCLT1	Cis_1M	lymphoblastoid	RTeQTL
rs3113489	C4orf33	cis	Adipose Subcutaneous	GTEx
rs3113489	C4orf33	cis	Artery Tibial	GTEx
rs3113489	ZNF226	trans	cerebellum	SCAN
rs3113489	C4orf33	cis	Whole Blood	GTEx
rs3113489	LOC132321	cis	normal skin	skin_eQTL
rs3113489	C4orf33	cis	Lymphoblastoid	GTEx
rs3113489	SCLT1	cis	cerebellum	SCAN
rs3113489	C4orf33	cis	cerebellum	SCAN
rs3113489	C4orf33	Cis_1M	lymphoblastoid	RTeQTL
rs3113489	C4orf33	cis	parietal	SCAN
rs3113489	C4orf33	cis	multi-tissue	Pritchard
rs3113489	C4orf33	cis	lymphoblastoid	seeQTL
rs3113489	PHF17	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:49 , 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	chr4:129958000-129961200	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
23	chr4:129958400-129961600	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
24	chr4:129958400-129964800	Weak transcription	Breast Myoepithelial Primary Cells	Breast
25	chr4:129958600-129961600	Strong transcription	Primary monocytes fromperipheralblood	blood
26	chr4:129958600-129961600	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
27	chr4:129958600-129963000	Weak transcription	Psoas Muscle	Psoas
28	chr4:129958800-129961400	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
29	chr4:129958800-129965400	Weak transcription	Adipose Nuclei	Adipose
30	chr4:129958800-129965400	Weak transcription	Liver	Liver
31	chr4:129958800-129966400	Weak transcription	Fetal Thymus	thymus
32	chr4:129959400-129961800	Weak transcription	Fetal Muscle Leg	muscle
33	chr4:129959600-129961400	Strong transcription	Primary neutrophils fromperipheralblood	blood
34	chr4:129959800-129965600	Weak transcription	Fetal Intestine Small	intestine
35	chr4:129959800-129966000	Weak transcription	Duodenum Smooth Muscle	Duodenum
36	chr4:129960000-129961400	Strong transcription	Dnd41	blood
37	chr4:129960000-129962200	Weak transcription	Primary T helper cells PMA-I stimulated	--
38	chr4:129960000-129962400	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
39	chr4:129960000-129962400	Weak transcription	Small Intestine	intestine
40	chr4:129960000-129964800	Weak transcription	Gastric	stomach
41	chr4:129960200-129961400	Strong transcription	Primary B cells from cord blood	blood
42	chr4:129960400-129963400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
43	chr4:129960800-129961200	Strong transcription	Primary hematopoietic stem cells	blood
44	chr4:129960800-129961400	Strong transcription	HSMM	muscle
45	chr4:129961000-129961200	Enhancers	HUES48 Cell Line	embryonic stem cell
46	chr4:129961000-129961200	Enhancers	iPS DF 6.9 Cell Line	embryonic stem cell
47	chr4:129961000-129961400	ZNF genes & repeats	GM12878-XiMat	blood
48	chr4:129961000-129961600	Strong transcription	Primary T cells from cord blood	blood
49	chr4:129961000-129962800	Weak transcription	Duodenum Mucosa	Duodenum

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