Variant report

Variant	rs3891262
Chromosome Location	chr12:121563481-121563482
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr12:121562465..121564050-chr12:121566966..121568974,2	MCF-7	breast:
2	chr12:121563121..121566575-chr12:121568260..121572155,4	K562	blood:
3	chr12:121561171..121566774-chr12:121646455..121649214,5	MCF-7	breast:

Variant related genes	Relation type
ENSG00000135124	Chromatin interaction
ENSG00000089041	Chromatin interaction

Extended variants
information (count: 47 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:34)

rs_ID	r²[population]
rs10849843	0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10849845	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10849846	0.83[AMR][1000 genomes];0.80[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10849848	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs10849849	1.00[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs10849850	0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs10849851	0.97[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs11065428	0.89[AFR][1000 genomes];0.87[AMR][1000 genomes];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11065433	0.93[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11065435	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11065436	0.80[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11065437	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11065440	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11065441	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11065443	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11065445	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11065453	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11065458	0.97[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs208292	0.93[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2393800	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs3861798	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3900976	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4077055	0.99[ASN][1000 genomes]
rs4559762	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.93[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs520396	0.81[AFR][1000 genomes]
rs58717055	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6489794	0.91[ASN][1000 genomes]
rs684201	0.94[AMR][1000 genomes];0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7298521	0.94[AFR][1000 genomes];0.87[AMR][1000 genomes];0.93[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7302184	0.94[AFR][1000 genomes];0.87[AMR][1000 genomes];0.93[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7310821	0.83[AMR][1000 genomes];0.80[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7313004	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7314706	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7954687	0.99[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:13 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv521928	chr12:121041728-121761800	Genic enhancers Flanking Active TSS Weak transcription Transcr. at gene 5' and 3' Enhancers Strong transcription ZNF genes & repeats Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	68 gene(s)	inside rSNPs	diseases
2	nsv899559	chr12:121324727-121592689	Active TSS Enhancers Weak transcription Flanking Bivalent TSS/Enh Flanking Active TSS Genic enhancers Bivalent/Poised TSS Strong transcription Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	31 gene(s)	inside rSNPs	diseases
3	nsv899562	chr12:121376416-121565870	Weak transcription Flanking Active TSS Active TSS Strong transcription Enhancers Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	24 gene(s)	inside rSNPs	diseases
4	esv2758318	chr12:121415845-121584813	Weak transcription Flanking Active TSS Strong transcription Enhancers Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	21 gene(s)	inside rSNPs	diseases
5	esv2759917	chr12:121415845-121584813	Enhancers Weak transcription ZNF genes & repeats Active TSS Flanking Active TSS Strong transcription Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	21 gene(s)	inside rSNPs	diseases
6	nsv832531	chr12:121440495-121604232	Flanking Active TSS Enhancers Active TSS Strong transcription Weak transcription Genic enhancers Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	15 gene(s)	inside rSNPs	diseases
7	nsv560454	chr12:121457073-121745742	Strong transcription Enhancers Active TSS Weak transcription Flanking Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	29 gene(s)	inside rSNPs	diseases
8	nsv430537	chr12:121487632-121579955	Enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Active TSS Flanking Active TSS Weak transcription Genic enhancers ZNF genes & repeats Bivalent Enhancer Strong transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
9	nsv1054878	chr12:121519880-121761800	Flanking Active TSS Genic enhancers Strong transcription Weak transcription Enhancers Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	26 gene(s)	inside rSNPs	diseases
10	nsv455729	chr12:121525591-121761800	Enhancers Strong transcription Genic enhancers Flanking Active TSS Weak transcription Active TSS ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	25 gene(s)	inside rSNPs	diseases
11	nsv560455	chr12:121525591-121761800	Weak transcription Strong transcription Enhancers Genic enhancers Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	25 gene(s)	inside rSNPs	diseases
12	nsv899563	chr12:121543011-121600529	Enhancers Weak transcription Flanking Active TSS Strong transcription Active TSS Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
13	nsv1050519	chr12:121552964-121756420	Enhancers Flanking Active TSS Weak transcription Active TSS Genic enhancers Strong transcription ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	22 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:42 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:121555400-121565800	Weak transcription	Gastric	stomach
2	chr12:121559000-121563600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
3	chr12:121559600-121564000	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
4	chr12:121561400-121565800	Enhancers	HepG2	liver
5	chr12:121561600-121566200	Weak transcription	Thymus	Thymus
6	chr12:121562200-121564000	Weak transcription	Liver	Liver
7	chr12:121562200-121566000	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
8	chr12:121562200-121566000	Weak transcription	K562	blood
9	chr12:121562200-121566600	Weak transcription	Breast Myoepithelial Primary Cells	Breast
10	chr12:121562400-121565800	Weak transcription	Fetal Thymus	thymus
11	chr12:121562400-121566800	Enhancers	Primary hematopoietic stem cells	blood
12	chr12:121562400-121570600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
13	chr12:121562600-121563600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
14	chr12:121562600-121565800	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
15	chr12:121562600-121565800	Weak transcription	Rectal Mucosa Donor 31	rectum
16	chr12:121562600-121566000	Weak transcription	Primary T helper naive cells from peripheral blood	blood
17	chr12:121562600-121566400	Weak transcription	Sigmoid Colon	Sigmoid Colon
18	chr12:121562600-121566600	Weak transcription	Primary T killer memory cells from peripheral blood	blood
19	chr12:121562600-121566600	Weak transcription	Skeletal Muscle Male	skeletal muscle
20	chr12:121562600-121566800	Weak transcription	A549	lung
21	chr12:121562800-121564000	Weak transcription	Primary hematopoietic stem cells short term culture	blood
22	chr12:121562800-121564000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
23	chr12:121562800-121565000	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
24	chr12:121562800-121565400	Weak transcription	Primary T helper cells fromperipheralblood	blood
25	chr12:121562800-121565600	Weak transcription	Primary T cells from cord blood	blood
26	chr12:121562800-121566000	Weak transcription	Primary T cells fromperipheralblood	blood
27	chr12:121562800-121566000	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
28	chr12:121562800-121566000	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
29	chr12:121562800-121566000	Weak transcription	Skeletal Muscle Female	skeletal muscle
30	chr12:121562800-121566000	Weak transcription	HUVEC	blood vessel
31	chr12:121562800-121566200	Weak transcription	Fetal Muscle Trunk	muscle
32	chr12:121562800-121566800	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
33	chr12:121562800-121566800	Weak transcription	Fetal Heart	heart
34	chr12:121562800-121569200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
35	chr12:121562800-121570400	Weak transcription	Ovary	ovary
36	chr12:121563000-121565000	Weak transcription	Stomach Mucosa	stomach
37	chr12:121563000-121566800	Weak transcription	NHEK	skin
38	chr12:121563000-121569400	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
39	chr12:121563200-121565800	Weak transcription	Primary T helper cells PMA-I stimulated	--
40	chr12:121563200-121565800	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
41	chr12:121563200-121565800	Weak transcription	Left Ventricle	heart
42	chr12:121563400-121565800	Weak transcription	Placenta	Placenta

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