Variant report

Variant	rs6446270
Chromosome Location	chr3:49445777-49445778
allele	A/C
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	SETDB1	chr3:49445703-49446390	U2OS	brain:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr3:49441705..49446563-chr3:49447849..49450189,5	MCF-7	breast:
2	chr3:49433997..49436498-chr3:49444708..49446631,2	K562	blood:
3	chr3:49441534..49443566-chr3:49445020..49447765,2	K562	blood:

Variant related genes	Relation type
TCTA	TF binding region
ENSG00000145022	Chromatin interaction
ENSG00000067560	Chromatin interaction

Extended variants
information (count: 78 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:77)

rs_ID	r²[population]
rs11130201	0.89[AFR][1000 genomes]
rs11717485	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs1522929	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs1568663	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs17080495	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs17080510	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs17080567	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs17080664	0.92[AFR][1000 genomes]
rs1996874	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2131107	0.89[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs2311794	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2311801	0.86[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs2329024	0.89[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs28615670	1.00[EUR][1000 genomes]
rs3870334	0.86[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs3870340	0.94[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs3912831	0.84[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs4241409	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs4452334	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs4527417	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs4855856	0.89[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs4855857	0.89[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs4855870	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs4855872	0.90[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs4855874	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs4855875	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs4855876	0.83[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs4855878	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs4855879	0.83[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs55677747	0.81[AFR][1000 genomes]
rs55808753	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs55990645	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs56101322	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs56760510	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs56897974	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs59579780	0.86[AFR][1000 genomes]
rs60011446	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs61749312	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs6446269	0.97[AFR][1000 genomes]
rs6446271	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs6446273	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs6446276	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs6446278	0.83[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs6446279	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs6446280	0.92[AFR][1000 genomes]
rs6446281	0.84[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs6446282	0.86[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs6446283	1.00[EUR][1000 genomes]
rs6766297	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs6787665	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs6793124	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs6797164	0.83[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs72936890	1.00[EUR][1000 genomes]
rs73830703	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73830704	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73830705	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73830706	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73831434	0.81[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs73831435	0.83[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs73831436	1.00[EUR][1000 genomes]
rs73831437	1.00[EUR][1000 genomes]
rs73831438	0.83[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs73831439	0.86[AFR][1000 genomes]
rs73831440	0.86[AFR][1000 genomes]
rs73831441	0.86[AFR][1000 genomes]
rs73831442	0.92[AFR][1000 genomes]
rs7646393	0.94[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs8179172	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs9311441	1.00[AFR][1000 genomes]
rs9811460	1.00[EUR][1000 genomes]
rs9814413	1.00[EUR][1000 genomes]
rs9830627	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs9837396	1.00[EUR][1000 genomes]
rs9849446	1.00[EUR][1000 genomes]
rs9861805	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs9869504	1.00[EUR][1000 genomes]
rs9875203	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]

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

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv237162	chr3:49444917-49446470	Enhancers Flanking Active TSS Weak transcription Genic enhancers Active TSS	TF binding region Chromatin interactive region	4 gene(s)	inside rSNPs	n/a

No data

Chromatin state (count:125 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:49399000-49448000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
2	chr3:49413200-49447400	Weak transcription	H9 Cell Line	embryonic stem cell
3	chr3:49427000-49448400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
4	chr3:49429000-49447200	Weak transcription	iPS-18 Cell Line	embryonic stem cell
5	chr3:49431200-49447200	Weak transcription	H1 Cell Line	embryonic stem cell
6	chr3:49433800-49447200	Weak transcription	Colonic Mucosa	Colon
7	chr3:49435400-49447000	Weak transcription	HSMMtube	muscle
8	chr3:49435400-49447800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
9	chr3:49435800-49446800	Weak transcription	Brain Angular Gyrus	brain
10	chr3:49438200-49446800	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
11	chr3:49439000-49447200	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
12	chr3:49439600-49447200	Weak transcription	HUES48 Cell Line	embryonic stem cell
13	chr3:49439800-49447000	Weak transcription	Brain Inferior Temporal Lobe	brain
14	chr3:49440200-49447000	Weak transcription	Fetal Lung	lung
15	chr3:49441400-49447000	Weak transcription	iPS-20b Cell Line	embryonic stem cell
16	chr3:49441400-49447000	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
17	chr3:49441400-49447200	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
18	chr3:49441600-49446000	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
19	chr3:49441600-49447000	Weak transcription	Fetal Brain Female	brain
20	chr3:49441600-49447200	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
21	chr3:49441600-49447600	Weak transcription	Placenta Amnion	Placenta Amnion
22	chr3:49441800-49447000	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
23	chr3:49441800-49447200	Weak transcription	Fetal Intestine Large	intestine
24	chr3:49442800-49446400	Enhancers	Skeletal Muscle Female	skeletal muscle
25	chr3:49442800-49447000	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
26	chr3:49442800-49447000	Enhancers	Primary T helper cells PMA-I stimulated	--
27	chr3:49442800-49447000	Enhancers	Fetal Muscle Leg	muscle
28	chr3:49442800-49447200	Enhancers	Primary T helper naive cells from peripheral blood	blood
29	chr3:49442800-49447200	Enhancers	Primary T helper cells fromperipheralblood	blood
30	chr3:49442800-49447400	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
31	chr3:49443000-49446200	Enhancers	Duodenum Mucosa	Duodenum
32	chr3:49443000-49446400	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
33	chr3:49443000-49447200	Enhancers	Primary T killer memory cells from peripheral blood	blood
34	chr3:49443000-49447200	Enhancers	Liver	Liver
35	chr3:49443200-49446000	Enhancers	Breast Myoepithelial Primary Cells	Breast
36	chr3:49443200-49446000	Enhancers	Stomach Mucosa	stomach
37	chr3:49443200-49446400	Enhancers	Primary T helper naive cells fromperipheralblood	blood
38	chr3:49443200-49446600	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
39	chr3:49443200-49447000	Enhancers	Primary T cells fromperipheralblood	blood
40	chr3:49443200-49447600	Enhancers	Primary T killer naive cells fromperipheralblood	blood
41	chr3:49443400-49446000	Enhancers	Skeletal Muscle Male	skeletal muscle
42	chr3:49443400-49446200	Enhancers	Duodenum Smooth Muscle	Duodenum
43	chr3:49443400-49446600	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
44	chr3:49443400-49447000	Weak transcription	Brain Germinal Matrix	brain
45	chr3:49443600-49446800	Weak transcription	Brain Anterior Caudate	brain
46	chr3:49443600-49447000	Enhancers	HepG2	liver
47	chr3:49443600-49447200	Enhancers	Primary T cells from cord blood	blood
48	chr3:49443600-49447200	Weak transcription	Brain Cingulate Gyrus	brain
49	chr3:49443600-49447200	Enhancers	Colon Smooth Muscle	Colon
50	chr3:49443800-49445800	Enhancers	Spleen	Spleen

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