Variant report

Variant	rs4466058
Chromosome Location	chr4:129923879-129923880
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 95 )
Associated
traits (count: 8 )

rSNPs within LD-proxies of this variant (count:79)

rs_ID	r²[population]
rs10002332	1.00[CEU][hapmap];0.84[CHB][hapmap];0.90[JPT][hapmap];0.88[AMR][1000 genomes];0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs10032000	0.93[CEU][hapmap];0.85[JPT][hapmap]
rs1030831	1.00[CEU][hapmap];1.00[CHB][hapmap];0.92[JPT][hapmap];0.95[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs1037147	0.95[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs12171333	1.00[CEU][hapmap];1.00[CHB][hapmap];0.92[JPT][hapmap];0.87[AMR][1000 genomes];0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs13109003	0.92[AFR][1000 genomes];0.86[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs13130762	0.95[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs1374491	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[AFR][1000 genomes];0.86[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1596963	0.86[AMR][1000 genomes];0.81[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs1668289	0.93[CEU][hapmap];0.85[JPT][hapmap]
rs1699379	0.92[AFR][1000 genomes];0.84[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1699380	0.93[CEU][hapmap];0.94[EUR][1000 genomes]
rs1699384	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[AFR][1000 genomes];0.83[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1699385	0.91[AFR][1000 genomes];0.84[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1699387	0.93[CEU][hapmap];0.88[CHB][hapmap];0.94[EUR][1000 genomes]
rs1699388	1.00[CEU][hapmap];0.89[CHB][hapmap];1.00[JPT][hapmap];0.92[AFR][1000 genomes];0.84[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1699389	0.92[AFR][1000 genomes];0.84[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1699391	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[AFR][1000 genomes];0.84[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1699393	1.00[CEU][hapmap];1.00[CHB][hapmap];0.93[JPT][hapmap];0.81[AFR][1000 genomes];0.83[AMR][1000 genomes];0.96[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1699394	0.80[AMR][1000 genomes];0.93[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs17014265	0.89[CHB][hapmap]
rs1709419	0.92[EUR][1000 genomes]
rs1756012	1.00[CEU][hapmap];1.00[CHB][hapmap];0.93[JPT][hapmap];0.82[AMR][1000 genomes];0.95[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1757924	0.95[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs1757925	1.00[CEU][hapmap];1.00[CHB][hapmap];0.92[JPT][hapmap];0.95[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs1757927	0.95[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs1757928	0.93[CEU][hapmap];1.00[CHB][hapmap];0.92[JPT][hapmap];0.95[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs1757930	0.80[AMR][1000 genomes];0.95[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs1757935	1.00[CEU][hapmap];1.00[CHB][hapmap];0.93[JPT][hapmap];0.95[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs1854773	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[AFR][1000 genomes];0.84[AMR][1000 genomes];0.92[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1854774	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs189235	0.94[EUR][1000 genomes]
rs2034498	0.81[AFR][1000 genomes];0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2083634	1.00[CEU][hapmap]
rs2162126	0.85[JPT][hapmap]
rs2198042	1.00[CEU][hapmap];1.00[CHB][hapmap];0.91[JPT][hapmap];0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2217023	0.80[JPT][hapmap]
rs2597836	0.96[AMR][1000 genomes];0.93[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2655310	1.00[CEU][hapmap];1.00[CHB][hapmap];0.85[JPT][hapmap];0.95[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs280603	1.00[CEU][hapmap];0.88[CHB][hapmap];0.91[JPT][hapmap];1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs280604	1.00[CEU][hapmap];0.94[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs3099899	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]
rs3105369	0.95[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs3113407	0.93[CEU][hapmap];0.82[JPT][hapmap]
rs3113489	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]
rs318502	0.86[JPT][hapmap]
rs318503	0.91[JPT][hapmap]
rs318536	0.93[CEU][hapmap];0.85[JPT][hapmap]
rs318543	0.93[CEU][hapmap];0.85[JPT][hapmap]
rs318552	0.93[CEU][hapmap];0.85[JPT][hapmap]
rs337263	0.93[CEU][hapmap];0.91[EUR][1000 genomes]
rs337270	0.91[EUR][1000 genomes]
rs337275	0.92[EUR][1000 genomes]
rs337277	0.93[CEU][hapmap];0.88[CHB][hapmap];0.94[EUR][1000 genomes]
rs337278	0.95[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs35006492	0.87[AMR][1000 genomes];0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs389376	0.93[CEU][hapmap];0.94[EUR][1000 genomes]
rs390260	0.93[CEU][hapmap];0.94[EUR][1000 genomes]
rs391396	0.92[EUR][1000 genomes]
rs395864	0.94[CEU][hapmap];0.89[CHB][hapmap];0.92[EUR][1000 genomes]
rs426521	0.93[CEU][hapmap];0.94[EUR][1000 genomes]
rs4394010	0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs445294	0.94[EUR][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];1.00[JPT][hapmap];0.94[AFR][1000 genomes];0.84[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4975194	0.94[AFR][1000 genomes];0.84[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4975274	0.85[JPT][hapmap]
rs517659	0.92[EUR][1000 genomes]
rs57501568	0.86[AMR][1000 genomes];0.99[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs576492	0.91[EUR][1000 genomes]
rs58689608	0.92[AFR][1000 genomes];0.84[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6534707	0.87[AFR][1000 genomes];0.84[AMR][1000 genomes];0.91[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs66921209	0.88[AMR][1000 genomes];0.96[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs6812361	0.82[AMR][1000 genomes]
rs7655841	1.00[CEU][hapmap];1.00[CHB][hapmap];0.85[JPT][hapmap];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs7687562	0.85[JPT][hapmap]

Variant overlapped rSNPs/rCNVs (count:16 , 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	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
13	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
14	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
15	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
16	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
rs4466058	C4orf33	cis	Artery Tibial	GTEx
rs4466058	C4orf33	Cis_1M	lymphoblastoid	RTeQTL
rs4466058	LOC132321	cis	normal skin	skin_eQTL
rs4466058	C4orf33	cis	Lymphoblastoid	GTEx
rs4466058	SCLT1	Cis_1M	lymphoblastoid	RTeQTL
rs4466058	C4orf33	cis	Whole Blood	GTEx
rs4466058	C4orf33	cis	multi-tissue	Pritchard
rs4466058	PHF17	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:22 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:129862400-129924200	Weak transcription	Colonic Mucosa	Colon
2	chr4:129868200-129935600	Weak transcription	HSMM	muscle
3	chr4:129878400-129925600	Weak transcription	HSMMtube	muscle
4	chr4:129906200-129935800	Weak transcription	Stomach Smooth Muscle	stomach
5	chr4:129908200-129927000	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
6	chr4:129911400-129936800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
7	chr4:129917200-129926000	Weak transcription	Ovary	ovary
8	chr4:129917400-129924200	Weak transcription	Rectal Smooth Muscle	rectum
9	chr4:129917400-129927200	Weak transcription	Primary B cells from cord blood	blood
10	chr4:129917400-129935800	Weak transcription	Pancreas	Pancrea
11	chr4:129917400-129936000	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
12	chr4:129917400-129936200	Weak transcription	Left Ventricle	heart
13	chr4:129917400-129942400	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
14	chr4:129917600-129924000	Weak transcription	Dnd41	blood
15	chr4:129917600-129926800	Weak transcription	Primary hematopoietic stem cells	blood
16	chr4:129920200-129926000	Weak transcription	Breast Myoepithelial Primary Cells	Breast
17	chr4:129920400-129925000	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
18	chr4:129920600-129924400	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
19	chr4:129920600-129926800	Weak transcription	NHDF-Ad	bronchial
20	chr4:129920600-129927600	Weak transcription	Monocytes-CD14+_RO01746	blood
21	chr4:129920600-129936000	Weak transcription	Fetal Thymus	thymus
22	chr4:129920800-129927000	Weak transcription	Primary neutrophils fromperipheralblood	blood

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links