Variant report

Variant	rs33999879
Chromosome Location	chr3:160131347-160131348
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr3:160131304-160131529	Hela-S3	cervix:	n/a	n/a
2	CTCF	chr3:160131252-160131793	HCT-116	colon:	n/a	chr3:160131618-160131627 chr3:160131607-160131628 chr3:160131612-160131630
3	RAD21	chr3:160130856-160131996	SK-N-SH	brain:	n/a	chr3:160131610-160131629
4	POLR2A	chr3:160131335-160131840	K562	blood:	n/a	n/a
5	RAD21	chr3:160131313-160131762	MCF-7	breast:	n/a	chr3:160131610-160131629
6	CTCF	chr3:160131347-160131874	HCT-116	colon:	n/a	chr3:160131618-160131627 chr3:160131607-160131628 chr3:160131612-160131630
7	RAD21	chr3:160131334-160131811	HepG2	liver:	n/a	chr3:160131610-160131629
8	RAD21	chr3:160131337-160131860	HCT-116	colon:	n/a	chr3:160131610-160131629
9	ZNF384	chr3:160131233-160131760	K562	blood:	n/a	n/a
10	RAD21	chr3:160131344-160131828	A549	lung:	n/a	chr3:160131610-160131629
11	SMC3	chr3:160131232-160132292	SK-N-SH	brain:	n/a	chr3:160131614-160131628
12	FOS	chr3:160131335-160131761	MCF10A-Er-Src	breast:	n/a	n/a
13	POLR2A	chr3:160131323-160131766	GM12892	blood:	n/a	n/a
14	RAD21	chr3:160131326-160131821	A549	lung:	n/a	chr3:160131610-160131629
15	CTCF	chr3:160131340-160131999	SK-N-SH	brain:	n/a	chr3:160131618-160131627 chr3:160131607-160131628 chr3:160131612-160131630
16	RAD21	chr3:160131252-160131919	HCT-116	colon:	n/a	chr3:160131610-160131629
17	CTCF	chr3:160130978-160132596	A549	lung:	n/a	chr3:160131618-160131627 chr3:160131607-160131628 chr3:160131612-160131630
18	POLR2A	chr3:160127070-160138790	K562	blood:	n/a	n/a

Variant related genes	Relation type
SMC4	TF binding region

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

rSNPs within LD-proxies of this variant (count:100)

rs_ID	r²[population]
rs10513550	0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11920289	0.95[EUR][1000 genomes]
rs12233589	0.95[EUR][1000 genomes]
rs2275153	1.00[AFR][1000 genomes];0.85[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2305401	1.00[AMR][1000 genomes];0.91[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2305406	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3736627	1.00[AMR][1000 genomes];0.87[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs3773371	0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3806629	0.85[AMR][1000 genomes];0.84[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs41272959	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4532176	0.81[ASN][1000 genomes]
rs55815116	0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs56119270	0.95[EUR][1000 genomes]
rs56124988	0.91[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs56150006	0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs56343019	0.83[ASN][1000 genomes]
rs56396435	0.85[AMR][1000 genomes];0.82[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs56401539	0.95[EUR][1000 genomes]
rs57030267	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs57050097	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs57277659	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs57285344	1.00[AFR][1000 genomes];0.85[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs57328745	0.82[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs57555307	1.00[AMR][1000 genomes];0.94[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs58377812	0.86[AMR][1000 genomes]
rs58627305	0.95[EUR][1000 genomes]
rs58654032	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs58776572	0.95[EUR][1000 genomes]
rs58915028	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs59695030	1.00[AMR][1000 genomes];0.87[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs59799252	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs60066272	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];0.91[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs60153357	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs60222090	1.00[AFR][1000 genomes];0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs60517889	1.00[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs60607858	0.95[EUR][1000 genomes]
rs60640467	0.87[AFR][1000 genomes]
rs60914777	1.00[AFR][1000 genomes];0.85[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61066536	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62272169	0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62272171	0.84[AMR][1000 genomes]
rs62272176	1.00[AFR][1000 genomes];0.85[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62272179	0.85[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62272180	0.95[EUR][1000 genomes]
rs62272181	0.96[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs62272185	0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62272187	1.00[AFR][1000 genomes];0.85[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62272188	0.85[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62272190	1.00[AFR][1000 genomes];0.85[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62272191	1.00[AFR][1000 genomes];0.85[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62272193	1.00[AFR][1000 genomes];0.85[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62272196	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62272197	0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62272198	1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62272205	0.81[EUR][1000 genomes]
rs62272207	0.95[EUR][1000 genomes]
rs62272231	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62272236	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62272237	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62272243	0.84[AMR][1000 genomes]
rs62272245	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62272247	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62272249	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs62272251	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.91[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs62272253	0.84[AMR][1000 genomes]
rs62272254	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs62272255	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs62272256	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs62272257	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs62272258	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs62272259	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs62272780	0.91[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs62272781	1.00[AMR][1000 genomes];0.91[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs62272783	1.00[AMR][1000 genomes];0.91[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs62272785	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];0.91[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs62272787	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];0.91[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs62272788	1.00[AMR][1000 genomes];0.91[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs62272790	1.00[AMR][1000 genomes];0.87[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs62272793	1.00[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs62272799	1.00[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs62272804	0.83[ASN][1000 genomes]
rs62272805	0.83[ASN][1000 genomes]
rs62272806	0.85[AMR][1000 genomes];0.84[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs62272831	0.85[AMR][1000 genomes];0.80[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs62272833	0.85[AMR][1000 genomes];0.82[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs62272836	0.85[AMR][1000 genomes];0.82[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs62272838	0.82[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs66769612	0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs66850724	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs68069205	0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73154564	0.84[AMR][1000 genomes]
rs73154582	1.00[AFR][1000 genomes];0.92[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs73154583	1.00[AFR][1000 genomes];0.83[ASN][1000 genomes]
rs73154587	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73155914	1.00[AMR][1000 genomes];0.94[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs7614701	0.95[EUR][1000 genomes]
rs7618017	0.96[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7645798	0.94[EUR][1000 genomes]
rs7648832	1.00[AMR][1000 genomes];0.94[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs9637414	1.00[AFR][1000 genomes];0.85[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]

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	nsv532666	chr3:159777847-160703202	Enhancers Weak transcription ZNF genes & repeats Strong transcription Bivalent/Poised TSS Active TSS Transcr. at gene 5' and 3' Flanking Active TSS Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	271 gene(s)	inside rSNPs	diseases
2	nsv1000453	chr3:159853305-160366357	Active TSS Flanking Active TSS Enhancers Weak transcription Genic enhancers Strong transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	259 gene(s)	inside rSNPs	diseases
3	nsv536779	chr3:159853305-160366357	Strong transcription Enhancers Transcr. at gene 5' and 3' Weak transcription Flanking Bivalent TSS/Enh Active TSS ZNF genes & repeats Genic enhancers Flanking Active TSS Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	259 gene(s)	inside rSNPs	diseases
4	esv1800136	chr3:159950498-160278160	Enhancers Weak transcription Active TSS Strong transcription Genic enhancers Flanking Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	213 gene(s)	inside rSNPs	diseases
5	esv1801767	chr3:159950498-160279411	Strong transcription Active TSS Weak transcription Enhancers Flanking Active TSS Bivalent/Poised TSS Genic enhancers ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	213 gene(s)	inside rSNPs	diseases
6	esv1801474	chr3:160012843-160153305	Active TSS Weak transcription Strong transcription Enhancers Genic enhancers Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	206 gene(s)	inside rSNPs	diseases
7	nsv1008519	chr3:160038710-160292589	Flanking Active TSS Weak transcription Strong transcription ZNF genes & repeats Enhancers Active TSS Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	255 gene(s)	inside rSNPs	diseases
8	esv1795255	chr3:160089896-160153305	Weak transcription Enhancers Strong transcription Active TSS Flanking Active TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA	205 gene(s)	inside rSNPs	diseases
9	esv1801686	chr3:160089896-160248363	Strong transcription Weak transcription Flanking Active TSS Enhancers Genic enhancers Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	211 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:121 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:160119000-160144600	Weak transcription	Spleen	Spleen
2	chr3:160119000-160145200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
3	chr3:160119400-160137800	Weak transcription	Skeletal Muscle Male	skeletal muscle
4	chr3:160119400-160144400	Weak transcription	Pancreas	Pancrea
5	chr3:160119400-160144600	Weak transcription	Gastric	stomach
6	chr3:160119600-160133800	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
7	chr3:160119800-160132400	Weak transcription	Sigmoid Colon	Sigmoid Colon
8	chr3:160119800-160132400	Weak transcription	Skeletal Muscle Female	skeletal muscle
9	chr3:160119800-160142000	Weak transcription	Psoas Muscle	Psoas
10	chr3:160119800-160144400	Weak transcription	Esophagus	oesophagus
11	chr3:160119800-160144600	Weak transcription	Lung	lung
12	chr3:160119800-160144600	Weak transcription	Ovary	ovary
13	chr3:160119800-160144600	Weak transcription	Placenta Amnion	Placenta Amnion
14	chr3:160119800-160145200	Weak transcription	Brain Hippocampus Middle	brain
15	chr3:160119800-160146600	Weak transcription	HSMMtube	muscle
16	chr3:160119800-160151800	Weak transcription	Brain Substantia Nigra	brain
17	chr3:160120000-160132400	Weak transcription	Right Ventricle	heart
18	chr3:160120200-160132200	Weak transcription	Adipose Nuclei	Adipose
19	chr3:160120200-160152400	Weak transcription	Brain Inferior Temporal Lobe	brain
20	chr3:160120200-160164400	Weak transcription	Fetal Brain Male	brain
21	chr3:160120400-160134800	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
22	chr3:160120600-160132400	Weak transcription	Fetal Muscle Trunk	muscle
23	chr3:160120800-160133400	Weak transcription	Stomach Smooth Muscle	stomach
24	chr3:160121000-160131800	Weak transcription	iPS-15b Cell Line	embryonic stem cell
25	chr3:160121000-160132000	Weak transcription	Duodenum Mucosa	Duodenum
26	chr3:160121200-160132400	Weak transcription	Fetal Kidney	kidney
27	chr3:160121200-160144400	Weak transcription	Colonic Mucosa	Colon
28	chr3:160121200-160157200	Strong transcription	iPS-20b Cell Line	embryonic stem cell
29	chr3:160121200-160157400	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
30	chr3:160121200-160157800	Strong transcription	iPS-18 Cell Line	embryonic stem cell
31	chr3:160121800-160134000	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
32	chr3:160122000-160133200	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
33	chr3:160122000-160139800	Weak transcription	Primary T killer memory cells from peripheral blood	blood
34	chr3:160122000-160144800	Weak transcription	Primary T helper naive cells from peripheral blood	blood
35	chr3:160122000-160161000	Strong transcription	HUES6 Cell Line	embryonic stem cell
36	chr3:160122000-160164400	Strong transcription	HUES64 Cell Line	embryonic stem cell
37	chr3:160122000-160164600	Strong transcription	HUES48 Cell Line	embryonic stem cell
38	chr3:160122200-160132400	Weak transcription	Brain Germinal Matrix	brain
39	chr3:160122200-160157400	Strong transcription	Fetal Thymus	thymus
40	chr3:160122400-160132400	Strong transcription	Primary hematopoietic stem cells short term culture	blood
41	chr3:160122400-160134200	Weak transcription	Fetal Brain Female	brain
42	chr3:160122400-160135000	Weak transcription	Duodenum Smooth Muscle	Duodenum
43	chr3:160122600-160132400	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
44	chr3:160122600-160132400	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
45	chr3:160122600-160155000	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
46	chr3:160122600-160156600	Strong transcription	K562	blood
47	chr3:160122800-160154200	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
48	chr3:160123000-160132000	Weak transcription	Primary T helper cells fromperipheralblood	blood
49	chr3:160123000-160132200	Weak transcription	Primary T helper cells PMA-I stimulated	--
50	chr3:160123000-160153600	Weak transcription	Brain Anterior Caudate	brain

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