Variant report

Variant	rs3099899
Chromosome Location	chr4:129917368-129917369
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 107 )
Associated
traits (count: 8 )

rSNPs within LD-proxies of this variant (count:89)

rs_ID	r²[population]
rs10002332	1.00[CEU][hapmap];0.84[CHB][hapmap];1.00[JPT][hapmap];0.88[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs10032000	0.92[CEU][hapmap];0.93[JPT][hapmap]
rs1030831	1.00[CEU][hapmap];1.00[CHB][hapmap];0.85[JPT][hapmap];0.95[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs1037147	0.95[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs12171333	1.00[CEU][hapmap];0.89[CHB][hapmap];1.00[JPT][hapmap];0.87[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs13109003	0.91[AFR][1000 genomes];0.86[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs13130762	0.95[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs13143771	0.86[JPT][hapmap]
rs1374491	1.00[CEU][hapmap];1.00[CHB][hapmap];0.93[JPT][hapmap];0.97[YRI][hapmap];0.90[AFR][1000 genomes];0.86[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1596963	0.86[AMR][1000 genomes];0.81[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1648062	0.81[JPT][hapmap]
rs1668289	0.93[CEU][hapmap];0.93[JPT][hapmap]
rs1699379	0.94[AFR][1000 genomes];0.84[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1699380	0.92[CEU][hapmap];0.94[EUR][1000 genomes]
rs1699384	1.00[CEU][hapmap];1.00[CHB][hapmap];0.93[JPT][hapmap];0.80[AFR][1000 genomes];0.83[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1699385	0.93[AFR][1000 genomes];0.84[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1699387	0.92[CEU][hapmap];0.88[CHB][hapmap];0.94[EUR][1000 genomes]
rs1699388	1.00[CEU][hapmap];0.89[CHB][hapmap];0.93[JPT][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];0.84[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1699389	0.94[AFR][1000 genomes];0.84[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1699391	1.00[CEU][hapmap];1.00[CHB][hapmap];0.93[JPT][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];0.84[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1699393	1.00[CEU][hapmap];1.00[CHB][hapmap];0.86[JPT][hapmap];0.87[YRI][hapmap];0.83[AMR][1000 genomes];0.96[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs1699394	0.80[AMR][1000 genomes];0.93[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs17014265	0.89[CHB][hapmap]
rs1709419	0.92[EUR][1000 genomes]
rs1709422	0.84[YRI][hapmap]
rs1756012	1.00[CEU][hapmap];1.00[CHB][hapmap];0.86[JPT][hapmap];0.80[YRI][hapmap];0.82[AMR][1000 genomes];0.95[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs1757924	0.95[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs1757925	1.00[CEU][hapmap];1.00[CHB][hapmap];0.85[JPT][hapmap];0.95[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs1757927	0.95[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs1757928	0.92[CEU][hapmap];1.00[CHB][hapmap];0.84[JPT][hapmap];0.95[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs1757930	0.81[AFR][1000 genomes];0.80[AMR][1000 genomes];0.95[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs1757935	1.00[CEU][hapmap];1.00[CHB][hapmap];0.86[JPT][hapmap];0.95[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs1757936	0.85[YRI][hapmap]
rs1854773	1.00[CEU][hapmap];1.00[CHB][hapmap];0.84[JPT][hapmap];1.00[YRI][hapmap];0.90[AFR][1000 genomes];0.84[AMR][1000 genomes];0.92[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1854774	1.00[CEU][hapmap];1.00[CHB][hapmap];0.93[JPT][hapmap];0.87[YRI][hapmap];0.81[EUR][1000 genomes]
rs189235	0.94[EUR][1000 genomes]
rs2034498	0.83[AFR][1000 genomes];0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2083634	1.00[CEU][hapmap]
rs2162126	0.93[JPT][hapmap]
rs2198042	1.00[CEU][hapmap];0.89[CHB][hapmap];1.00[JPT][hapmap];0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2217023	0.87[JPT][hapmap]
rs2597836	0.96[AMR][1000 genomes];0.93[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2655310	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs280594	0.81[YRI][hapmap]
rs280603	1.00[CEU][hapmap];0.92[JPT][hapmap];0.98[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs280604	1.00[CEU][hapmap];0.96[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs3105369	0.95[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs3113407	0.93[CEU][hapmap];0.91[JPT][hapmap]
rs3113489	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]
rs3113490	0.80[YRI][hapmap]
rs318502	0.93[JPT][hapmap]
rs318503	0.84[JPT][hapmap]
rs318536	0.92[CEU][hapmap];0.93[JPT][hapmap]
rs318543	0.92[CEU][hapmap];0.93[JPT][hapmap]
rs318552	0.93[CEU][hapmap];0.93[JPT][hapmap]
rs318556	0.81[JPT][hapmap]
rs337263	0.92[CEU][hapmap];0.89[YRI][hapmap];0.91[EUR][1000 genomes]
rs337270	0.91[EUR][1000 genomes]
rs337275	0.92[EUR][1000 genomes]
rs337277	0.92[CEU][hapmap];0.88[CHB][hapmap];0.94[EUR][1000 genomes]
rs337278	0.95[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs35006492	0.87[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs389376	0.92[CEU][hapmap];0.89[YRI][hapmap];0.94[EUR][1000 genomes]
rs390260	0.92[CEU][hapmap];0.94[EUR][1000 genomes]
rs391396	0.92[EUR][1000 genomes]
rs395864	0.93[CEU][hapmap];0.89[CHB][hapmap];0.90[YRI][hapmap];0.92[EUR][1000 genomes]
rs426521	0.92[CEU][hapmap];0.94[EUR][1000 genomes]
rs4394010	0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs445294	0.94[EUR][1000 genomes]
rs4466058	1.00[CEU][hapmap];1.00[CHB][hapmap];0.93[JPT][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs474667	0.91[EUR][1000 genomes]
rs474794	0.92[EUR][1000 genomes]
rs487233	0.94[EUR][1000 genomes]
rs487501	0.94[EUR][1000 genomes]
rs4975193	1.00[CEU][hapmap];1.00[CHB][hapmap];0.92[JPT][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];0.84[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4975194	0.96[AFR][1000 genomes];0.84[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4975269	0.81[JPT][hapmap]
rs4975274	0.93[JPT][hapmap]
rs517659	0.92[EUR][1000 genomes]
rs57501568	0.86[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs576492	0.91[EUR][1000 genomes]
rs58689608	0.94[AFR][1000 genomes];0.84[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6534707	0.86[AFR][1000 genomes];0.84[AMR][1000 genomes];0.91[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs66921209	0.88[AMR][1000 genomes];0.96[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs6812361	0.82[AMR][1000 genomes]
rs6857659	0.81[JPT][hapmap]
rs7655841	1.00[CEU][hapmap];0.88[CHB][hapmap];0.93[JPT][hapmap];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7671508	0.85[YRI][hapmap]
rs7687562	0.92[JPT][hapmap]

Variant overlapped rSNPs/rCNVs (count:18 , 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	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
13	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
14	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
15	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
16	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
17	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
18	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:8)

SNP	Gene	Cis/trans	Tissue	Source
rs3099899	C4orf33	cis	Lymphoblastoid	GTEx
rs3099899	C4orf33	cis	Whole Blood	GTEx
rs3099899	C4orf33	Cis_1M	lymphoblastoid	RTeQTL
rs3099899	LOC132321	cis	normal skin	skin_eQTL
rs3099899	SCLT1	Cis_1M	lymphoblastoid	RTeQTL
rs3099899	C4orf33	cis	Artery Tibial	GTEx
rs3099899	C4orf33	cis	multi-tissue	Pritchard
rs3099899	PHF17	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:76 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:129862400-129924200	Weak transcription	Colonic Mucosa	Colon
2	chr4:129864000-129918000	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
3	chr4:129868200-129935600	Weak transcription	HSMM	muscle
4	chr4:129878400-129925600	Weak transcription	HSMMtube	muscle
5	chr4:129883200-129923400	Weak transcription	Primary T helper cells fromperipheralblood	blood
6	chr4:129887000-129918800	Weak transcription	Psoas Muscle	Psoas
7	chr4:129887800-129918000	Weak transcription	Fetal Heart	heart
8	chr4:129901200-129918000	Weak transcription	HUVEC	blood vessel
9	chr4:129901800-129918600	Weak transcription	NHDF-Ad	bronchial
10	chr4:129901800-129920600	Weak transcription	Muscle Satellite Cultured Cells	--
11	chr4:129901800-129921200	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
12	chr4:129902400-129922400	Weak transcription	NH-A	brain
13	chr4:129903200-129920600	Strong transcription	Monocytes-CD14+_RO01746	blood
14	chr4:129905000-129917800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
15	chr4:129906200-129935800	Weak transcription	Stomach Smooth Muscle	stomach
16	chr4:129906400-129917400	Weak transcription	Stomach Mucosa	stomach
17	chr4:129907600-129920600	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
18	chr4:129908200-129918000	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
19	chr4:129908200-129918800	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
20	chr4:129908200-129919400	Weak transcription	NHEK	skin
21	chr4:129908200-129921200	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
22	chr4:129908200-129921600	Weak transcription	Duodenum Smooth Muscle	Duodenum
23	chr4:129908200-129921800	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
24	chr4:129908200-129927000	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
25	chr4:129908400-129918800	Weak transcription	Spleen	Spleen
26	chr4:129908400-129919000	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
27	chr4:129908400-129919000	Weak transcription	Sigmoid Colon	Sigmoid Colon
28	chr4:129908400-129921400	Weak transcription	K562	blood
29	chr4:129908400-129921800	Weak transcription	Brain Hippocampus Middle	brain
30	chr4:129908400-129922000	Weak transcription	Primary T helper cells PMA-I stimulated	--
31	chr4:129908400-129922400	Weak transcription	Fetal Muscle Leg	muscle
32	chr4:129908600-129917600	Weak transcription	Primary B cells from peripheral blood	blood
33	chr4:129908600-129917600	Weak transcription	A549	lung
34	chr4:129909000-129920200	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
35	chr4:129909000-129923600	Weak transcription	Adipose Nuclei	Adipose
36	chr4:129910000-129918600	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
37	chr4:129910200-129918800	Weak transcription	Fetal Intestine Large	intestine
38	chr4:129910200-129919800	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
39	chr4:129910400-129918800	Weak transcription	GM12878-XiMat	blood
40	chr4:129911400-129936800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
41	chr4:129912000-129923600	Weak transcription	Fetal Lung	lung
42	chr4:129913000-129918000	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
43	chr4:129913600-129921000	Strong transcription	Primary monocytes fromperipheralblood	blood
44	chr4:129914400-129921000	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
45	chr4:129915400-129917600	Strong transcription	Primary hematopoietic stem cells	blood
46	chr4:129916200-129917600	Strong transcription	Fetal Thymus	thymus
47	chr4:129916400-129917400	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
48	chr4:129916600-129917400	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
49	chr4:129916600-129917400	Strong transcription	Primary neutrophils fromperipheralblood	blood
50	chr4:129916600-129917400	Strong transcription	Primary B cells from cord blood	blood

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