Variant report

Variant	rs693403
Chromosome Location	chr3:121227392-121227393
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 115 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:106)

rs_ID	r²[population]
rs10451895	0.85[CHB][hapmap];0.94[CHD][hapmap];1.00[JPT][hapmap];0.91[ASN][1000 genomes]
rs10934551	0.85[CHB][hapmap];0.94[CHD][hapmap];1.00[JPT][hapmap];0.95[ASN][1000 genomes]
rs11705939	0.88[ASN][1000 genomes]
rs11706583	0.91[ASN][1000 genomes]
rs11709378	0.86[ASN][1000 genomes]
rs11709726	1.00[JPT][hapmap]
rs11711667	0.98[ASN][1000 genomes]
rs11713643	0.82[CHB][hapmap];1.00[JPT][hapmap];0.88[ASN][1000 genomes]
rs11714746	0.93[ASN][1000 genomes]
rs11714774	0.91[ASN][1000 genomes]
rs11718918	0.98[ASN][1000 genomes]
rs12488196	1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[ASN][1000 genomes]
rs12496163	0.95[ASN][1000 genomes]
rs12632308	0.98[ASN][1000 genomes]
rs12634017	0.89[ASN][1000 genomes]
rs12635218	0.98[ASN][1000 genomes]
rs13059229	0.85[CHB][hapmap];1.00[JPT][hapmap];0.91[ASN][1000 genomes]
rs13065220	1.00[CHB][hapmap];1.00[CHD][hapmap];0.90[GIH][hapmap];1.00[JPT][hapmap]
rs13077237	0.85[ASN][1000 genomes]
rs13077305	1.00[CHB][hapmap];1.00[CHD][hapmap];0.90[GIH][hapmap];1.00[JPT][hapmap];0.93[ASN][1000 genomes]
rs13080007	0.98[ASN][1000 genomes]
rs13082118	1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[ASN][1000 genomes]
rs13085365	0.91[ASN][1000 genomes]
rs13095550	0.82[ASN][1000 genomes]
rs13097659	0.85[CHB][hapmap];1.00[JPT][hapmap];0.98[ASN][1000 genomes]
rs13100579	0.93[ASN][1000 genomes]
rs1381057	1.00[CHB][hapmap];1.00[CHD][hapmap];0.90[GIH][hapmap];1.00[JPT][hapmap]
rs1381058	0.94[CHD][hapmap];1.00[JPT][hapmap];0.88[ASN][1000 genomes]
rs1381059	0.85[CHB][hapmap];0.94[CHD][hapmap];1.00[JPT][hapmap];0.98[ASN][1000 genomes]
rs1877968	0.86[ASN][1000 genomes]
rs1877969	0.86[ASN][1000 genomes]
rs1987098	0.82[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs2030531	0.85[CHB][hapmap];0.94[CHD][hapmap];1.00[JPT][hapmap]
rs2126139	0.81[AFR][1000 genomes];0.83[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs2127024	0.83[EUR][1000 genomes]
rs2169301	0.91[ASN][1000 genomes]
rs2331962	0.91[ASN][1000 genomes]
rs28406368	0.98[ASN][1000 genomes]
rs3101345	0.88[CEU][hapmap]
rs3218649	0.85[CHB][hapmap];1.00[JPT][hapmap];0.98[ASN][1000 genomes]
rs35362700	0.83[ASN][1000 genomes]
rs3732405	0.81[ASN][1000 genomes]
rs3732406	0.94[CHD][hapmap];1.00[JPT][hapmap];0.98[ASN][1000 genomes]
rs3772122	0.85[CHB][hapmap];0.94[CHD][hapmap];1.00[JPT][hapmap];0.98[ASN][1000 genomes]
rs3772124	1.00[ASN][1000 genomes]
rs3806614	0.85[CHB][hapmap];0.94[CHD][hapmap];1.00[JPT][hapmap];0.89[ASN][1000 genomes]
rs3843345	0.88[ASN][1000 genomes]
rs3845860	1.00[ASN][1000 genomes]
rs3845863	0.86[ASN][1000 genomes]
rs3911713	0.85[CHB][hapmap];0.88[CHD][hapmap];1.00[JPT][hapmap];0.98[ASN][1000 genomes]
rs4107754	0.81[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs4346498	0.81[AMR][1000 genomes]
rs4525804	0.81[AMR][1000 genomes]
rs4555467	0.85[CHB][hapmap];0.94[CHD][hapmap];1.00[JPT][hapmap];0.98[ASN][1000 genomes]
rs4676677	1.00[CHB][hapmap];1.00[CHD][hapmap];0.90[GIH][hapmap];1.00[JPT][hapmap]
rs4676680	0.80[ASN][1000 genomes]
rs4676719	0.81[AMR][1000 genomes]
rs4676722	0.86[ASN][1000 genomes]
rs4676728	0.86[ASN][1000 genomes]
rs488636	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs500100	0.91[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs500103	0.81[AMR][1000 genomes];0.91[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs502643	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]
rs513380	0.81[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs524026	0.93[AFR][1000 genomes];0.94[AMR][1000 genomes];0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs541818	0.84[AFR][1000 genomes];0.94[AMR][1000 genomes];0.93[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs575913	0.94[AFR][1000 genomes];0.97[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs587553	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.93[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs61796946	0.95[ASN][1000 genomes]
rs6438630	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs6438633	0.85[CHB][hapmap];1.00[JPT][hapmap];0.88[ASN][1000 genomes]
rs66922316	1.00[ASN][1000 genomes]
rs6769377	0.85[CHB][hapmap];0.94[CHD][hapmap];1.00[JPT][hapmap]
rs6778684	0.98[ASN][1000 genomes]
rs6782025	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.97[TSI][hapmap];0.82[EUR][1000 genomes]
rs6782033	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.96[TSI][hapmap];0.82[EUR][1000 genomes]
rs6784324	0.96[ASN][1000 genomes]
rs6787048	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.97[TSI][hapmap];0.83[EUR][1000 genomes]
rs6793252	1.00[CHB][hapmap];1.00[CHD][hapmap];0.90[GIH][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs6797376	0.85[CHB][hapmap];0.94[CHD][hapmap];1.00[JPT][hapmap];0.88[ASN][1000 genomes]
rs6797682	0.88[ASN][1000 genomes]
rs6798699	0.86[CHD][hapmap];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]
rs702019	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7609781	0.83[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs7612018	0.85[CHB][hapmap];1.00[JPT][hapmap];0.89[ASN][1000 genomes]
rs7613752	0.88[ASN][1000 genomes]
rs7614639	0.83[ASN][1000 genomes]
rs7615529	0.85[CHB][hapmap];1.00[JPT][hapmap];0.95[ASN][1000 genomes]
rs7617748	0.91[ASN][1000 genomes]
rs7621376	0.85[CHB][hapmap];1.00[JPT][hapmap]
rs7622867	0.85[CHB][hapmap];1.00[JPT][hapmap];0.91[ASN][1000 genomes]
rs7622881	1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[ASN][1000 genomes]
rs7622897	0.98[ASN][1000 genomes]
rs7627978	0.84[AFR][1000 genomes];0.83[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs7628081	0.93[ASN][1000 genomes]
rs7632907	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.97[TSI][hapmap];0.83[EUR][1000 genomes]
rs7633930	1.00[CHB][hapmap];0.88[JPT][hapmap];0.93[ASN][1000 genomes]
rs7634611	0.84[AFR][1000 genomes];0.83[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs7645027	0.85[CHB][hapmap];1.00[JPT][hapmap];0.88[ASN][1000 genomes]
rs7645050	0.91[ASN][1000 genomes]
rs7645849	0.81[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs7645869	0.88[ASN][1000 genomes]
rs7650658	0.82[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs9849118	0.84[AFR][1000 genomes];0.83[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs9863608	0.83[TSI][hapmap]

Variant overlapped rSNPs/rCNVs (count:9 , 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	nsv829702	chr3:121045793-121227975	Weak transcription Strong transcription Flanking Active TSS Enhancers Active TSS ZNF genes & repeats Genic enhancers Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
6	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
7	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
8	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
9	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

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs693403	CHST13	cis	parietal	SCAN

Chromatin state (count:63 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:121151200-121263800	Weak transcription	Duodenum Mucosa	Duodenum
2	chr3:121177200-121237000	Weak transcription	Rectal Mucosa Donor 29	rectum
3	chr3:121178200-121263800	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
4	chr3:121183800-121234400	Weak transcription	Primary B cells from cord blood	blood
5	chr3:121186400-121255600	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
6	chr3:121192200-121233600	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
7	chr3:121193200-121237000	Weak transcription	Fetal Muscle Trunk	muscle
8	chr3:121195600-121233800	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
9	chr3:121197200-121233400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
10	chr3:121200600-121264000	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
11	chr3:121201000-121250600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
12	chr3:121202400-121263200	Weak transcription	NHLF	lung
13	chr3:121202400-121263800	Weak transcription	HSMM	muscle
14	chr3:121202600-121233400	Weak transcription	NHEK	skin
15	chr3:121202800-121236600	Weak transcription	Muscle Satellite Cultured Cells	--
16	chr3:121207200-121233400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
17	chr3:121208600-121233400	Weak transcription	Cortex derived primary cultured neurospheres	brain
18	chr3:121209400-121263600	Weak transcription	NHDF-Ad	bronchial
19	chr3:121209600-121227800	Weak transcription	HMEC	breast
20	chr3:121209800-121228800	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
21	chr3:121209800-121233400	Weak transcription	Thymus	Thymus
22	chr3:121210000-121246400	Weak transcription	iPS-15b Cell Line	embryonic stem cell
23	chr3:121210200-121241400	Weak transcription	Fetal Muscle Leg	muscle
24	chr3:121213200-121228200	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
25	chr3:121214000-121230400	Weak transcription	Fetal Stomach	stomach
26	chr3:121217800-121228200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
27	chr3:121220400-121228400	Weak transcription	Fetal Kidney	kidney
28	chr3:121220800-121230800	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
29	chr3:121221000-121229200	Strong transcription	Dnd41	blood
30	chr3:121221000-121232200	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
31	chr3:121221200-121229200	Strong transcription	HUES48 Cell Line	embryonic stem cell
32	chr3:121221400-121233400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
33	chr3:121221600-121229200	Strong transcription	iPS-20b Cell Line	embryonic stem cell
34	chr3:121221800-121229200	Strong transcription	iPS-18 Cell Line	embryonic stem cell
35	chr3:121222200-121232200	Strong transcription	Primary hematopoietic stem cells short term culture	blood
36	chr3:121222400-121231400	Weak transcription	Hela-S3	cervix
37	chr3:121222600-121228000	Weak transcription	HUVEC	blood vessel
38	chr3:121223400-121231400	Strong transcription	GM12878-XiMat	blood
39	chr3:121223800-121231600	Strong transcription	Primary monocytes fromperipheralblood	blood
40	chr3:121224400-121228400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
41	chr3:121224600-121234000	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
42	chr3:121225200-121229200	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
43	chr3:121225200-121229200	Strong transcription	Monocytes-CD14+_RO01746	blood
44	chr3:121225200-121234800	Weak transcription	Brain Germinal Matrix	brain
45	chr3:121225400-121227800	Strong transcription	A549	lung
46	chr3:121225400-121229200	Strong transcription	Primary neutrophils fromperipheralblood	blood
47	chr3:121225400-121231400	Strong transcription	HUES64 Cell Line	embryonic stem cell
48	chr3:121225600-121236400	Weak transcription	Fetal Lung	lung
49	chr3:121225800-121236200	Weak transcription	K562	blood
50	chr3:121226200-121227400	Strong transcription	Primary hematopoietic stem cells	blood

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