Variant report

Variant	rs12271959
Chromosome Location	chr11:63650925-63650926
allele	A/G
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	MXI1	chr11:63650020-63651062	SK-N-SH	brain:	n/a	chr11:63650510-63650525

No.	Distal block	Cell Line	Cell type
1	chr11:63644143..63645756-chr11:63650897..63653554,2	MCF-7	breast:
2	chr11:63639014..63641483-chr11:63650269..63652057,2	MCF-7	breast:
3	chr11:63535711..63538179-chr11:63649382..63651942,2	K562	blood:

Variant related genes	Relation type
RNU6-1306P	TF binding region
ENSG00000255651	Chromatin interaction

Extended variants
information (count: 46 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:40)

rs_ID	r²[population]
rs10897460	0.82[ASW][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.88[MKK][hapmap];1.00[TSI][hapmap];0.82[AFR][1000 genomes];0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11231632	1.00[EUR][1000 genomes]
rs11231634	0.80[AFR][1000 genomes];0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11822339	1.00[JPT][hapmap]
rs12099085	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[TSI][hapmap];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12277386	1.00[EUR][1000 genomes]
rs12277838	1.00[EUR][1000 genomes]
rs12288290	1.00[EUR][1000 genomes]
rs12291042	1.00[EUR][1000 genomes]
rs12295918	1.00[EUR][1000 genomes]
rs13377315	1.00[EUR][1000 genomes]
rs1392118	0.91[ASN][1000 genomes]
rs17403349	1.00[TSI][hapmap]
rs2133548	1.00[JPT][hapmap]
rs320110	0.82[ASW][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.88[MKK][hapmap];1.00[TSI][hapmap];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs320115	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];1.00[TSI][hapmap];1.00[ASN][1000 genomes]
rs57219930	0.81[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs57864399	1.00[EUR][1000 genomes]
rs58678024	0.82[AFR][1000 genomes];0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs59423787	1.00[EUR][1000 genomes]
rs59642000	1.00[EUR][1000 genomes]
rs60107756	1.00[EUR][1000 genomes]
rs60791209	0.91[ASN][1000 genomes]
rs61141225	0.91[ASN][1000 genomes]
rs61475860	1.00[EUR][1000 genomes]
rs684865	1.00[TSI][hapmap]
rs7110433	1.00[EUR][1000 genomes]
rs7123788	1.00[TSI][hapmap]
rs7127354	1.00[GIH][hapmap];1.00[JPT][hapmap]
rs7130187	1.00[GIH][hapmap];1.00[JPT][hapmap]
rs73494120	1.00[ASN][1000 genomes]
rs7929867	1.00[EUR][1000 genomes]
rs7933899	1.00[TSI][hapmap];1.00[EUR][1000 genomes]
rs7948681	1.00[TSI][hapmap];1.00[EUR][1000 genomes]
rs7952003	1.00[TSI][hapmap];1.00[EUR][1000 genomes]
rs9630214	1.00[EUR][1000 genomes]
rs9630215	1.00[EUR][1000 genomes]
rs9804541	1.00[TSI][hapmap]
rs9888136	1.00[EUR][1000 genomes]
rs9888177	1.00[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1051171	chr11:62987064-63835715	Genic enhancers Enhancers Weak transcription Flanking Active TSS Active TSS Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	100 gene(s)	inside rSNPs	diseases
2	nsv468589	chr11:63515752-63713239	Weak transcription Strong transcription Transcr. at gene 5' and 3' Genic enhancers Active TSS Enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	39 gene(s)	inside rSNPs	diseases
3	nsv555180	chr11:63515752-63713239	Weak transcription Strong transcription Flanking Active TSS Enhancers Genic enhancers Bivalent Enhancer Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	39 gene(s)	inside rSNPs	diseases
4	esv1839119	chr11:63615554-63680052	Enhancers Flanking Active TSS Weak transcription Genic enhancers Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats Active TSS	TF binding region CpG island Chromatin interactive region miRNA target site	8 gene(s)	inside rSNPs	diseases
5	nsv468590	chr11:63639881-63783352	Flanking Active TSS Bivalent Enhancer Active TSS Strong transcription Weak transcription Genic enhancers Flanking Bivalent TSS/Enh Enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	41 gene(s)	inside rSNPs	diseases
6	nsv555181	chr11:63639881-63783352	Weak transcription Enhancers Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Strong transcription Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	41 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:118 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:63637800-63653200	Enhancers	Primary T helper cells PMA-I stimulated	--
2	chr11:63641000-63654800	Weak transcription	HepG2	liver
3	chr11:63642200-63654800	Weak transcription	Fetal Lung	lung
4	chr11:63642400-63654400	Weak transcription	Colon Smooth Muscle	Colon
5	chr11:63642400-63655000	Weak transcription	Placenta Amnion	Placenta Amnion
6	chr11:63643600-63655800	Weak transcription	Aorta	Aorta
7	chr11:63643800-63652400	Enhancers	Cortex derived primary cultured neurospheres	brain
8	chr11:63644600-63655200	Enhancers	Primary T helper cells fromperipheralblood	blood
9	chr11:63645000-63652400	Enhancers	Primary T killer naive cells fromperipheralblood	blood
10	chr11:63645800-63654600	Weak transcription	Skeletal Muscle Male	skeletal muscle
11	chr11:63646400-63652200	Enhancers	Primary T killer memory cells from peripheral blood	blood
12	chr11:63646600-63652000	Enhancers	Primary T helper naive cells from peripheral blood	blood
13	chr11:63646600-63652600	Enhancers	Fetal Thymus	thymus
14	chr11:63646800-63651000	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
15	chr11:63646800-63652200	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
16	chr11:63646800-63652200	Enhancers	Brain Inferior Temporal Lobe	brain
17	chr11:63647000-63651000	Enhancers	iPS-18 Cell Line	embryonic stem cell
18	chr11:63647000-63651400	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
19	chr11:63647000-63651800	Enhancers	Thymus	Thymus
20	chr11:63647000-63652000	Enhancers	Primary T cells fromperipheralblood	blood
21	chr11:63647400-63652000	Enhancers	Primary hematopoietic stem cells	blood
22	chr11:63647600-63651200	Strong transcription	Fetal Intestine Small	intestine
23	chr11:63647600-63651600	Enhancers	Primary T cells effector/memory enriched fromperipheralblood	blood
24	chr11:63647600-63654200	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
25	chr11:63647600-63654400	Weak transcription	Liver	Liver
26	chr11:63648000-63654200	Weak transcription	A549	lung
27	chr11:63648000-63654400	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
28	chr11:63648200-63652000	Enhancers	Primary T helper naive cells fromperipheralblood	blood
29	chr11:63648200-63653800	Weak transcription	K562	blood
30	chr11:63648200-63654400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
31	chr11:63648200-63654600	Weak transcription	HMEC	breast
32	chr11:63648200-63654800	Weak transcription	NHEK	skin
33	chr11:63648400-63651000	Weak transcription	Skeletal Muscle Female	skeletal muscle
34	chr11:63648400-63651400	Weak transcription	Colonic Mucosa	Colon
35	chr11:63648400-63651600	Weak transcription	Sigmoid Colon	Sigmoid Colon
36	chr11:63648400-63651800	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
37	chr11:63648400-63652400	Enhancers	Brain Anterior Caudate	brain
38	chr11:63648400-63654400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
39	chr11:63648400-63654400	Weak transcription	Muscle Satellite Cultured Cells	--
40	chr11:63648400-63654400	Weak transcription	Small Intestine	intestine
41	chr11:63648400-63654600	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
42	chr11:63648400-63654600	Weak transcription	Osteobl	bone
43	chr11:63648400-63654800	Weak transcription	HSMM	muscle
44	chr11:63648400-63655000	Weak transcription	Hela-S3	cervix
45	chr11:63648400-63655000	Weak transcription	NH-A	brain
46	chr11:63648400-63655200	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
47	chr11:63648600-63655000	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
48	chr11:63648800-63651600	Enhancers	Primary monocytes fromperipheralblood	blood
49	chr11:63648800-63651800	Enhancers	Breast Myoepithelial Primary Cells	Breast
50	chr11:63649000-63651400	Weak transcription	Rectal Mucosa Donor 29	rectum

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