Variant report

Variant	rs280601
Chromosome Location	chr4:129914268-129914269
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 61 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:42)

rs_ID	r²[population]
rs10028974	0.96[CEU][hapmap];0.95[CHB][hapmap];0.94[JPT][hapmap];0.98[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1030830	0.93[YRI][hapmap]
rs11098994	1.00[CEU][hapmap];1.00[CHB][hapmap];0.85[CHD][hapmap];0.89[GIH][hapmap];0.94[JPT][hapmap];0.83[LWK][hapmap];1.00[TSI][hapmap];0.84[AMR][1000 genomes];0.99[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs12504200	1.00[YRI][hapmap]
rs12512345	1.00[YRI][hapmap]
rs1376202	0.91[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.93[CHD][hapmap];0.92[GIH][hapmap];0.94[JPT][hapmap];0.97[LWK][hapmap];0.90[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap]
rs172168	1.00[ASW][hapmap];0.90[CHB][hapmap];0.95[CHD][hapmap];0.86[GIH][hapmap];0.89[JPT][hapmap];0.97[LWK][hapmap];0.87[MKK][hapmap];0.81[YRI][hapmap];0.89[AFR][1000 genomes];0.91[ASN][1000 genomes]
rs17416188	1.00[YRI][hapmap]
rs17416706	0.81[YRI][hapmap]
rs1756011	1.00[CEU][hapmap];0.90[CHB][hapmap];0.83[JPT][hapmap];0.93[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs1757926	0.93[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs1757929	0.93[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs1757937	0.95[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs1757938	1.00[ASW][hapmap];1.00[CEU][hapmap];0.81[CHB][hapmap];0.90[CHD][hapmap];0.97[GIH][hapmap];0.89[JPT][hapmap];0.80[LWK][hapmap];0.90[MKK][hapmap];0.98[TSI][hapmap];0.81[YRI][hapmap];0.81[AFR][1000 genomes];0.86[AMR][1000 genomes];0.95[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1757942	0.84[AFR][1000 genomes];0.83[AMR][1000 genomes];0.95[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs1838911	0.95[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs1877836	0.81[YRI][hapmap]
rs189236	1.00[CEU][hapmap];0.85[CHB][hapmap];0.83[JPT][hapmap];0.90[EUR][1000 genomes]
rs1900397	1.00[YRI][hapmap]
rs2044523	0.81[YRI][hapmap]
rs2118045	0.95[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2592948	1.00[ASW][hapmap];1.00[CEU][hapmap];0.90[CHB][hapmap];0.93[CHD][hapmap];0.97[GIH][hapmap];0.89[JPT][hapmap];0.80[LWK][hapmap];0.91[MKK][hapmap];0.97[TSI][hapmap];0.81[YRI][hapmap];0.81[AFR][1000 genomes];0.83[AMR][1000 genomes];0.95[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2597837	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];1.00[GIH][hapmap];0.94[JPT][hapmap];0.97[LWK][hapmap];0.97[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2655311	1.00[CEU][hapmap];0.93[CHB][hapmap];0.88[JPT][hapmap];0.84[YRI][hapmap];0.81[AFR][1000 genomes];0.87[AMR][1000 genomes];0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2777822	0.92[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2777823	0.81[AFR][1000 genomes];0.83[AMR][1000 genomes];0.92[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs280594	1.00[CEU][hapmap];0.90[CHB][hapmap];0.89[JPT][hapmap];0.82[AMR][1000 genomes];0.96[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs280596	0.89[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs280597	0.82[AMR][1000 genomes];0.97[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs3099902	1.00[CEU][hapmap];0.90[CHB][hapmap];0.89[JPT][hapmap];0.81[YRI][hapmap];0.81[AFR][1000 genomes];0.87[AMR][1000 genomes];0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs3099903	1.00[CEU][hapmap];0.90[CHB][hapmap];0.83[JPT][hapmap];0.94[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs3113487	1.00[CEU][hapmap];0.90[CHB][hapmap];0.90[CHD][hapmap];0.97[GIH][hapmap];0.89[JPT][hapmap];0.98[TSI][hapmap];0.86[AMR][1000 genomes];0.98[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs3113488	0.88[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs337276	0.84[CEU][hapmap]
rs337279	0.90[EUR][1000 genomes]
rs4975294	1.00[YRI][hapmap]
rs55865936	0.86[AMR][1000 genomes];0.84[ASN][1000 genomes]
rs62316971	0.80[AFR][1000 genomes];0.87[AMR][1000 genomes];0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs62316978	0.95[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs6847784	0.81[YRI][hapmap]
rs7654405	0.81[AFR][1000 genomes];0.87[AMR][1000 genomes];0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs796886	0.84[AFR][1000 genomes];0.83[AMR][1000 genomes];0.95[EUR][1000 genomes];0.91[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:19 , 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	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
19	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:2)

SNP	Gene	Cis/trans	Tissue	Source
rs280601	C4orf33	cis	Artery Tibial	GTEx
rs280601	C4orf33	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:78 , 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	chr4:129866600-129916600	Weak transcription	Right Ventricle	heart
4	chr4:129866800-129916200	Weak transcription	Hela-S3	cervix
5	chr4:129868200-129935600	Weak transcription	HSMM	muscle
6	chr4:129878400-129925600	Weak transcription	HSMMtube	muscle
7	chr4:129883200-129923400	Weak transcription	Primary T helper cells fromperipheralblood	blood
8	chr4:129887000-129918800	Weak transcription	Psoas Muscle	Psoas
9	chr4:129887800-129918000	Weak transcription	Fetal Heart	heart
10	chr4:129895600-129916800	Weak transcription	Rectal Smooth Muscle	rectum
11	chr4:129901200-129918000	Weak transcription	HUVEC	blood vessel
12	chr4:129901800-129918600	Weak transcription	NHDF-Ad	bronchial
13	chr4:129901800-129920600	Weak transcription	Muscle Satellite Cultured Cells	--
14	chr4:129901800-129921200	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
15	chr4:129902400-129922400	Weak transcription	NH-A	brain
16	chr4:129903200-129920600	Strong transcription	Monocytes-CD14+_RO01746	blood
17	chr4:129905000-129917800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
18	chr4:129906200-129935800	Weak transcription	Stomach Smooth Muscle	stomach
19	chr4:129906400-129917400	Weak transcription	Stomach Mucosa	stomach
20	chr4:129907600-129920600	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
21	chr4:129908200-129916600	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
22	chr4:129908200-129916600	Weak transcription	Fetal Intestine Small	intestine
23	chr4:129908200-129916800	Weak transcription	Aorta	Aorta
24	chr4:129908200-129916800	Weak transcription	Esophagus	oesophagus
25	chr4:129908200-129916800	Weak transcription	Fetal Stomach	stomach
26	chr4:129908200-129916800	Weak transcription	Lung	lung
27	chr4:129908200-129916800	Weak transcription	Rectal Mucosa Donor 29	rectum
28	chr4:129908200-129917000	Weak transcription	Ovary	ovary
29	chr4:129908200-129917200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
30	chr4:129908200-129918000	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
31	chr4:129908200-129918800	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
32	chr4:129908200-129919400	Weak transcription	NHEK	skin
33	chr4:129908200-129921200	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
34	chr4:129908200-129921600	Weak transcription	Duodenum Smooth Muscle	Duodenum
35	chr4:129908200-129921800	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
36	chr4:129908200-129927000	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
37	chr4:129908400-129915600	Weak transcription	Small Intestine	intestine
38	chr4:129908400-129916200	Weak transcription	Fetal Thymus	thymus
39	chr4:129908400-129916600	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
40	chr4:129908400-129916600	Weak transcription	Liver	Liver
41	chr4:129908400-129916800	Weak transcription	Gastric	stomach
42	chr4:129908400-129916800	Weak transcription	Pancreas	Pancrea
43	chr4:129908400-129916800	Weak transcription	Thymus	Thymus
44	chr4:129908400-129918800	Weak transcription	Spleen	Spleen
45	chr4:129908400-129919000	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
46	chr4:129908400-129919000	Weak transcription	Sigmoid Colon	Sigmoid Colon
47	chr4:129908400-129921400	Weak transcription	K562	blood
48	chr4:129908400-129921800	Weak transcription	Brain Hippocampus Middle	brain
49	chr4:129908400-129922000	Weak transcription	Primary T helper cells PMA-I stimulated	--
50	chr4:129908400-129922400	Weak transcription	Fetal Muscle Leg	muscle

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