Variant report

Variant	rs502643
Chromosome Location	chr3:121245041-121245042
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 109 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:101)

rs_ID	r²[population]
rs10451895	0.85[CHB][hapmap];1.00[JPT][hapmap];0.98[ASN][1000 genomes]
rs10934551	0.85[CHB][hapmap];1.00[JPT][hapmap];0.88[ASN][1000 genomes]
rs11705939	0.81[ASN][1000 genomes]
rs11706583	0.98[ASN][1000 genomes]
rs11709378	0.93[ASN][1000 genomes]
rs11709726	1.00[JPT][hapmap]
rs11711667	0.91[ASN][1000 genomes]
rs11713643	0.85[CHB][hapmap];1.00[JPT][hapmap];0.81[ASN][1000 genomes]
rs11714746	1.00[ASN][1000 genomes]
rs11714774	0.98[ASN][1000 genomes]
rs11718918	0.91[ASN][1000 genomes]
rs12488196	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs12496163	0.88[ASN][1000 genomes]
rs12632308	0.91[ASN][1000 genomes]
rs12634017	0.82[ASN][1000 genomes]
rs12635218	0.91[ASN][1000 genomes]
rs13059229	0.86[CHB][hapmap];1.00[JPT][hapmap];0.98[ASN][1000 genomes]
rs13065220	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs13077237	0.92[ASN][1000 genomes]
rs13077305	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs13080007	0.91[ASN][1000 genomes]
rs13082118	1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[ASN][1000 genomes]
rs13085365	0.98[ASN][1000 genomes]
rs13095550	0.88[ASN][1000 genomes]
rs13097659	0.86[CHB][hapmap];1.00[JPT][hapmap];0.91[ASN][1000 genomes]
rs13100579	1.00[ASN][1000 genomes]
rs1381057	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs1381058	1.00[JPT][hapmap];0.81[ASN][1000 genomes]
rs1381059	0.85[CHB][hapmap];1.00[JPT][hapmap];0.91[ASN][1000 genomes]
rs1877968	0.93[ASN][1000 genomes]
rs1877969	0.93[ASN][1000 genomes]
rs1987098	0.82[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs2030531	0.85[CHB][hapmap];1.00[JPT][hapmap]
rs2126139	0.83[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs2127024	0.81[EUR][1000 genomes]
rs2169301	0.98[ASN][1000 genomes]
rs2331962	0.98[ASN][1000 genomes]
rs28406368	0.91[ASN][1000 genomes]
rs3101345	0.89[CEU][hapmap]
rs3218649	0.86[CHB][hapmap];1.00[JPT][hapmap];0.91[ASN][1000 genomes]
rs3732406	1.00[JPT][hapmap];0.91[ASN][1000 genomes]
rs3772122	0.85[CHB][hapmap];1.00[JPT][hapmap];0.91[ASN][1000 genomes]
rs3772124	0.93[ASN][1000 genomes]
rs3806614	0.85[CHB][hapmap];1.00[JPT][hapmap];0.96[ASN][1000 genomes]
rs3843345	0.81[ASN][1000 genomes]
rs3845860	0.93[ASN][1000 genomes]
rs3845863	0.93[ASN][1000 genomes]
rs3911713	0.85[CHB][hapmap];1.00[JPT][hapmap];0.91[ASN][1000 genomes]
rs4107754	0.81[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs4346498	0.81[AMR][1000 genomes]
rs4525804	0.81[AMR][1000 genomes]
rs4555467	0.85[CHB][hapmap];1.00[JPT][hapmap];0.91[ASN][1000 genomes]
rs4676677	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs4676680	0.87[ASN][1000 genomes]
rs4676719	0.81[AMR][1000 genomes]
rs4676728	0.93[ASN][1000 genomes]
rs488636	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs500100	0.93[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs500103	0.81[AMR][1000 genomes];0.93[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs513380	0.81[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs524026	0.90[AFR][1000 genomes];0.94[AMR][1000 genomes];0.92[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs541818	0.82[AFR][1000 genomes];0.94[AMR][1000 genomes];0.91[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs575913	0.87[AFR][1000 genomes];0.97[AMR][1000 genomes];0.92[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs587553	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.93[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs61796946	0.87[ASN][1000 genomes]
rs6438630	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs6438633	0.86[CHB][hapmap];1.00[JPT][hapmap];0.81[ASN][1000 genomes]
rs66922316	0.93[ASN][1000 genomes]
rs6769377	0.85[CHB][hapmap];1.00[JPT][hapmap]
rs6778684	0.91[ASN][1000 genomes]
rs6782025	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[EUR][1000 genomes]
rs6782033	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[EUR][1000 genomes]
rs6784324	0.89[ASN][1000 genomes]
rs6787048	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[EUR][1000 genomes]
rs6793252	1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[ASN][1000 genomes]
rs6797376	0.85[CHB][hapmap];1.00[JPT][hapmap];0.81[ASN][1000 genomes]
rs6797682	0.95[ASN][1000 genomes]
rs6798699	1.00[JPT][hapmap]
rs6806191	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.86[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs693403	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs702019	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7609781	0.83[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs7612018	0.86[CHB][hapmap];1.00[JPT][hapmap];0.96[ASN][1000 genomes]
rs7613752	0.81[ASN][1000 genomes]
rs7615529	0.86[CHB][hapmap];1.00[JPT][hapmap];0.88[ASN][1000 genomes]
rs7617748	0.98[ASN][1000 genomes]
rs7621376	0.86[CHB][hapmap];1.00[JPT][hapmap]
rs7622867	0.86[CHB][hapmap];1.00[JPT][hapmap];0.98[ASN][1000 genomes]
rs7622881	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs7622897	0.91[ASN][1000 genomes]
rs7627978	0.81[AFR][1000 genomes];0.83[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs7628081	1.00[ASN][1000 genomes]
rs7632907	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[EUR][1000 genomes]
rs7633930	1.00[CHB][hapmap];0.88[JPT][hapmap];1.00[ASN][1000 genomes]
rs7634611	0.81[AFR][1000 genomes];0.83[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs7645027	0.86[CHB][hapmap];1.00[JPT][hapmap];0.81[ASN][1000 genomes]
rs7645050	0.98[ASN][1000 genomes]
rs7645849	0.81[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs7645869	0.81[ASN][1000 genomes]
rs7650658	0.82[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs9849118	0.81[AFR][1000 genomes];0.83[AMR][1000 genomes];0.82[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:8 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv998555	chr3:120700604-121348015	Weak transcription Strong transcription Enhancers Active TSS ZNF genes & repeats Flanking Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA	19 gene(s)	inside rSNPs	diseases
2	nsv591395	chr3:120970900-121501070	Flanking Active TSS Weak transcription Enhancers ZNF genes & repeats Strong transcription Transcr. at gene 5' and 3' Genic enhancers Active TSS Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	47 gene(s)	inside rSNPs	diseases
3	nsv591396	chr3:120970900-121557533	Strong transcription Active TSS Flanking Active TSS Enhancers Weak transcription Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	50 gene(s)	inside rSNPs	diseases
4	nsv591397	chr3:120977383-121505882	Strong transcription Weak transcription Enhancers Active TSS Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	47 gene(s)	inside rSNPs	diseases
5	nsv591400	chr3:121070299-121339354	Strong transcription Weak transcription Active TSS Genic enhancers Enhancers Flanking Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	diseases
6	nsv999335	chr3:121100283-121408766	Weak transcription Strong transcription Genic enhancers Flanking Active TSS Active TSS Enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	18 gene(s)	inside rSNPs	diseases
7	nsv877381	chr3:121192350-121343500	Strong transcription Enhancers Weak transcription Flanking Active TSS Active TSS ZNF genes & repeats 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	14 gene(s)	inside rSNPs	diseases
8	nsv1007522	chr3:121200563-121374051	Enhancers Weak transcription Strong transcription Active TSS Flanking Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	15 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:67 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:121151200-121263800	Weak transcription	Duodenum Mucosa	Duodenum
2	chr3:121178200-121263800	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
3	chr3:121186400-121255600	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
4	chr3:121200600-121264000	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
5	chr3:121201000-121250600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
6	chr3:121202400-121263200	Weak transcription	NHLF	lung
7	chr3:121202400-121263800	Weak transcription	HSMM	muscle
8	chr3:121209400-121263600	Weak transcription	NHDF-Ad	bronchial
9	chr3:121210000-121246400	Weak transcription	iPS-15b Cell Line	embryonic stem cell
10	chr3:121229000-121253200	Weak transcription	HepG2	liver
11	chr3:121229600-121263000	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
12	chr3:121230800-121260200	Strong transcription	Dnd41	blood
13	chr3:121232200-121263800	Weak transcription	Fetal Heart	heart
14	chr3:121233400-121263000	Strong transcription	Primary hematopoietic stem cells short term culture	blood
15	chr3:121233600-121245600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
16	chr3:121233800-121248800	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
17	chr3:121234000-121264000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
18	chr3:121234200-121263600	Weak transcription	Osteobl	bone
19	chr3:121234200-121264000	Weak transcription	Fetal Intestine Large	intestine
20	chr3:121234400-121263200	Strong transcription	HUES64 Cell Line	embryonic stem cell
21	chr3:121234600-121245800	Weak transcription	H9 Cell Line	embryonic stem cell
22	chr3:121234600-121263600	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
23	chr3:121235000-121263800	Weak transcription	Primary B cells from cord blood	blood
24	chr3:121235000-121264000	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
25	chr3:121235400-121263600	Weak transcription	Brain Germinal Matrix	brain
26	chr3:121235600-121262600	Strong transcription	HUES48 Cell Line	embryonic stem cell
27	chr3:121235600-121263600	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
28	chr3:121235600-121263600	Weak transcription	NH-A	brain
29	chr3:121235800-121263400	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
30	chr3:121236000-121262600	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
31	chr3:121236600-121263400	Weak transcription	Fetal Intestine Small	intestine
32	chr3:121236600-121264000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
33	chr3:121236600-121264200	Weak transcription	Sigmoid Colon	Sigmoid Colon
34	chr3:121237200-121247400	Strong transcription	GM12878-XiMat	blood
35	chr3:121237400-121264000	Weak transcription	Fetal Muscle Trunk	muscle
36	chr3:121237600-121263600	Weak transcription	Muscle Satellite Cultured Cells	--
37	chr3:121237600-121264000	Weak transcription	Fetal Lung	lung
38	chr3:121239200-121263200	Weak transcription	NHEK	skin
39	chr3:121239600-121249400	Weak transcription	Thymus	Thymus
40	chr3:121239600-121251600	Weak transcription	HUVEC	blood vessel
41	chr3:121239600-121264000	Weak transcription	Fetal Stomach	stomach
42	chr3:121241000-121245600	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
43	chr3:121241800-121263600	Weak transcription	Fetal Muscle Leg	muscle
44	chr3:121242000-121249000	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
45	chr3:121243000-121248800	Strong transcription	A549	lung
46	chr3:121243000-121259600	Strong transcription	Primary monocytes fromperipheralblood	blood
47	chr3:121243000-121262800	Strong transcription	iPS-18 Cell Line	embryonic stem cell
48	chr3:121243000-121263000	Strong transcription	HUES6 Cell Line	embryonic stem cell
49	chr3:121243200-121247000	Strong transcription	Monocytes-CD14+_RO01746	blood
50	chr3:121243400-121246800	Strong transcription	Primary hematopoietic stem cells	blood

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