Variant report

Variant	rs4676677
Chromosome Location	chr3:121160369-121160370
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr3:121152541..121155166-chr3:121158856..121160501,2	K562	blood:

Extended variants
information (count: 98 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:88)

rs_ID	r²[population]
rs10451895	1.00[ASW][hapmap];0.85[CHB][hapmap];0.94[CHD][hapmap];1.00[JPT][hapmap];0.95[LWK][hapmap];0.90[MEX][hapmap];0.98[MKK][hapmap];1.00[YRI][hapmap]
rs10934551	0.85[CHB][hapmap];0.94[CHD][hapmap];1.00[JPT][hapmap];0.90[MEX][hapmap]
rs11705939	0.86[AFR][1000 genomes]
rs11707252	0.84[ASN][1000 genomes]
rs11708438	0.85[ASN][1000 genomes]
rs11709726	1.00[JPT][hapmap]
rs11713643	0.82[CHB][hapmap];1.00[JPT][hapmap]
rs11714746	0.85[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs11714774	0.82[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs11715085	0.86[AFR][1000 genomes];0.87[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs12233510	0.85[ASN][1000 genomes]
rs12488196	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.81[AFR][1000 genomes];0.85[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs12634017	0.85[AFR][1000 genomes];0.91[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs13059229	0.85[CHB][hapmap];1.00[JPT][hapmap]
rs13065220	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.95[LWK][hapmap];0.95[MEX][hapmap];0.98[MKK][hapmap];0.97[TSI][hapmap];1.00[YRI][hapmap]
rs13076688	0.85[ASN][1000 genomes]
rs13077305	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.95[LWK][hapmap];0.95[MEX][hapmap];0.98[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.81[AFR][1000 genomes];0.85[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs13080007	0.84[AFR][1000 genomes]
rs13081748	0.85[ASN][1000 genomes]
rs13082118	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.81[EUR][1000 genomes]
rs13086811	0.85[ASN][1000 genomes]
rs13095550	0.83[AMR][1000 genomes]
rs13095841	0.85[ASN][1000 genomes]
rs13097659	0.85[CHB][hapmap];1.00[JPT][hapmap]
rs13100579	0.83[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs1381057	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];0.87[ASN][1000 genomes]
rs1381058	0.94[CHD][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap]
rs1381059	0.85[CHB][hapmap];0.94[CHD][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap]
rs1986730	0.85[ASN][1000 genomes]
rs1987097	0.85[ASN][1000 genomes]
rs1987098	0.87[ASN][1000 genomes]
rs2030531	0.85[CHB][hapmap];0.94[CHD][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];0.85[ASN][1000 genomes]
rs2126139	0.87[ASN][1000 genomes]
rs2126140	0.85[ASN][1000 genomes]
rs2127024	0.87[ASN][1000 genomes]
rs2169300	0.85[ASN][1000 genomes]
rs2331921	0.82[ASN][1000 genomes]
rs3218649	0.85[CHB][hapmap];1.00[JPT][hapmap]
rs3732406	1.00[ASW][hapmap];0.94[CHD][hapmap];1.00[JPT][hapmap];0.93[LWK][hapmap];0.81[MEX][hapmap];0.98[MKK][hapmap];0.96[YRI][hapmap]
rs3772122	0.85[CHB][hapmap];0.94[CHD][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap]
rs3772124	0.82[AFR][1000 genomes];0.88[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs3806614	0.85[CHB][hapmap];0.94[CHD][hapmap];1.00[JPT][hapmap];0.90[MEX][hapmap]
rs3845860	0.84[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs3911713	0.85[CHB][hapmap];0.88[CHD][hapmap];1.00[JPT][hapmap];0.90[MEX][hapmap]
rs4107754	0.84[ASN][1000 genomes]
rs4346498	0.84[ASN][1000 genomes]
rs4555467	0.85[CHB][hapmap];0.94[CHD][hapmap];1.00[JPT][hapmap];0.90[MEX][hapmap]
rs502643	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs587553	1.00[CHB][hapmap];1.00[CHD][hapmap];0.90[GIH][hapmap];1.00[JPT][hapmap]
rs61796944	0.85[ASN][1000 genomes]
rs6438625	0.85[ASN][1000 genomes]
rs6438626	0.89[ASN][1000 genomes]
rs6438630	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.92[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs6438633	0.85[CHB][hapmap];1.00[JPT][hapmap]
rs66922316	0.81[AFR][1000 genomes];0.85[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs6765310	0.85[ASN][1000 genomes]
rs6769377	0.85[CHB][hapmap];0.94[CHD][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];0.85[ASN][1000 genomes]
rs6782025	1.00[CHB][hapmap];1.00[CHD][hapmap];0.90[GIH][hapmap];1.00[JPT][hapmap];0.87[ASN][1000 genomes]
rs6782033	1.00[CHB][hapmap];1.00[CHD][hapmap];0.90[GIH][hapmap];1.00[JPT][hapmap];0.87[ASN][1000 genomes]
rs6784324	0.85[AFR][1000 genomes];0.89[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs6787048	1.00[CHB][hapmap];1.00[CHD][hapmap];0.90[GIH][hapmap];1.00[JPT][hapmap];0.87[ASN][1000 genomes]
rs6793029	0.84[ASN][1000 genomes]
rs6793252	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.95[LWK][hapmap];0.95[MEX][hapmap];0.98[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.81[AFR][1000 genomes];0.85[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs6796068	0.85[ASN][1000 genomes]
rs6797376	0.85[CHB][hapmap];0.94[CHD][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap]
rs6797682	0.81[EUR][1000 genomes]
rs6798699	0.87[CHD][hapmap];1.00[JPT][hapmap];0.86[MEX][hapmap];0.82[ASN][1000 genomes]
rs6806191	1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[ASN][1000 genomes]
rs693403	1.00[CHB][hapmap];1.00[CHD][hapmap];0.90[GIH][hapmap];1.00[JPT][hapmap]
rs702019	1.00[CHB][hapmap];1.00[CHD][hapmap];0.90[GIH][hapmap];1.00[JPT][hapmap]
rs7609781	0.87[ASN][1000 genomes]
rs7612018	0.85[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap]
rs7615529	0.85[CHB][hapmap];1.00[JPT][hapmap]
rs7618570	0.85[ASN][1000 genomes]
rs7621376	0.85[CHB][hapmap];1.00[JPT][hapmap];0.85[ASN][1000 genomes]
rs7622867	0.85[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap]
rs7622881	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.81[AFR][1000 genomes];0.85[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs7627978	0.87[ASN][1000 genomes]
rs7628081	0.81[AFR][1000 genomes];0.83[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs7632907	1.00[CHB][hapmap];1.00[CHD][hapmap];0.90[GIH][hapmap];1.00[JPT][hapmap];0.87[ASN][1000 genomes]
rs7633930	1.00[CHB][hapmap];0.88[JPT][hapmap];0.95[YRI][hapmap];0.83[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs7634611	0.87[ASN][1000 genomes]
rs7645027	0.85[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.86[AFR][1000 genomes]
rs7645544	0.84[ASN][1000 genomes]
rs7645849	0.87[ASN][1000 genomes]
rs7650439	0.87[ASN][1000 genomes]
rs7650658	0.87[ASN][1000 genomes]
rs9849118	0.87[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:10 , 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	nsv521397	chr3:120970900-121192350	Weak transcription Strong transcription Active TSS Enhancers ZNF genes & repeats Flanking Active TSS Genic enhancers Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
3	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
4	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
5	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
6	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
7	nsv591399	chr3:121046468-121160369	Enhancers Active TSS Weak transcription Strong transcription Flanking Active TSS ZNF genes & repeats Genic enhancers Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
8	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
9	nsv591401	chr3:121094592-121160369	Strong transcription Flanking Active TSS Weak transcription Enhancers Active TSS Genic enhancers ZNF genes & repeats	Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
10	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

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs4676677	CHST13	cis	parietal	SCAN

Chromatin state (count:54 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:121139200-121186000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
2	chr3:121140600-121170800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
3	chr3:121141200-121186000	Weak transcription	NHEK	skin
4	chr3:121142200-121161600	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
5	chr3:121145400-121160600	Strong transcription	HUES48 Cell Line	embryonic stem cell
6	chr3:121145800-121161200	Strong transcription	iPS-20b Cell Line	embryonic stem cell
7	chr3:121146000-121177400	Weak transcription	Fetal Muscle Leg	muscle
8	chr3:121146000-121185800	Weak transcription	Fetal Stomach	stomach
9	chr3:121146200-121185600	Weak transcription	Fetal Muscle Trunk	muscle
10	chr3:121146400-121185800	Weak transcription	Fetal Intestine Large	intestine
11	chr3:121148000-121170800	Weak transcription	iPS-15b Cell Line	embryonic stem cell
12	chr3:121148400-121199600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
13	chr3:121149400-121181000	Weak transcription	HMEC	breast
14	chr3:121149400-121196600	Weak transcription	NH-A	brain
15	chr3:121149400-121199600	Weak transcription	Fetal Lung	lung
16	chr3:121149800-121177400	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
17	chr3:121149800-121177400	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
18	chr3:121150000-121166200	Weak transcription	Cortex derived primary cultured neurospheres	brain
19	chr3:121151200-121185800	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
20	chr3:121151200-121193400	Weak transcription	HSMM	muscle
21	chr3:121151200-121263800	Weak transcription	Duodenum Mucosa	Duodenum
22	chr3:121151400-121185600	Weak transcription	HUVEC	blood vessel
23	chr3:121151600-121166600	Weak transcription	Primary B cells from cord blood	blood
24	chr3:121151800-121162000	Weak transcription	NHLF	lung
25	chr3:121151800-121166400	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
26	chr3:121151800-121171000	Weak transcription	HepG2	liver
27	chr3:121151800-121177600	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
28	chr3:121152600-121177400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
29	chr3:121153200-121167400	Weak transcription	A549	lung
30	chr3:121153200-121170400	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
31	chr3:121153200-121177600	Weak transcription	K562	blood
32	chr3:121153800-121160800	Strong transcription	Dnd41	blood
33	chr3:121153800-121177400	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
34	chr3:121154800-121160400	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
35	chr3:121155200-121168000	Weak transcription	Hela-S3	cervix
36	chr3:121155400-121168200	Weak transcription	Fetal Thymus	thymus
37	chr3:121155600-121162400	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
38	chr3:121155600-121177400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
39	chr3:121155800-121163800	Weak transcription	Primary hematopoietic stem cells	blood
40	chr3:121155800-121170400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
41	chr3:121155800-121177600	Weak transcription	Thymus	Thymus
42	chr3:121156200-121160600	Strong transcription	GM12878-XiMat	blood
43	chr3:121157400-121170400	Weak transcription	H1 Cell Line	embryonic stem cell
44	chr3:121157800-121167600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
45	chr3:121158200-121168000	Weak transcription	Primary neutrophils fromperipheralblood	blood
46	chr3:121158400-121160400	Strong transcription	iPS-18 Cell Line	embryonic stem cell
47	chr3:121159600-121165400	Weak transcription	Primary hematopoietic stem cells short term culture	blood
48	chr3:121159600-121165800	Weak transcription	HUES6 Cell Line	embryonic stem cell
49	chr3:121159600-121177400	Weak transcription	H9 Cell Line	embryonic stem cell
50	chr3:121160000-121164400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--

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