Variant report

Variant	rs11169158
Chromosome Location	chr12:50192968-50192969
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:5)
CpG islands
(count:0)
Chromatin interactive
region (count:6)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:5 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	CTCF	chr12:50192832-50192990	K562	blood:	n/a	n/a
2	CTCF	chr12:50192840-50192990	WERI-Rb-1	eye:	n/a	n/a
3	CTCF	chr12:50192803-50193012	H1-hESC	embryonic stem cell:	n/a	n/a
4	RAD21	chr12:50192692-50193080	H1-hESC	embryonic stem cell:	n/a	chr12:50192924-50192938
5	ZBTB7A	chr12:50192835-50193004	K562	blood:	n/a	n/a

No data

(count:6 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr12:50191000..50193803-chr12:50196375..50198903,2	MCF-7	breast:
2	chr12:50190700..50193578-chr12:50220244..50222518,3	MCF-7	breast:
3	chr12:50192057..50194728-chr12:50200116..50202021,2	MCF-7	breast:
4	chr12:50191850..50193529-chr12:50199593..50201536,2	K562	blood:
5	chr12:50192465..50194419-chr13:20355646..20358127,2	MCF-7	breast:
6	chr12:50191925..50194204-chr12:50203904..50205859,2	K562	blood:

No data

Variant related genes	Relation type
NCKAP5L	TF binding region
ENSG00000258057	Chromatin interaction
ENSG00000121390	Chromatin interaction
ENSG00000167566	Chromatin interaction

Extended variants
information (count: 14 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:12)

rs_ID	r²[population]
rs11169159	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12305896	0.97[ASN][1000 genomes]
rs12313989	0.87[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs12316892	0.87[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs2603113	0.97[ASN][1000 genomes]
rs2720288	0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2720289	0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs3741556	0.87[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs67453698	0.82[ASN][1000 genomes]
rs72644870	0.87[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs72644871	0.92[ASN][1000 genomes]
rs897055	0.87[AMR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1045327	chr12:49975040-50551375	Strong transcription Weak transcription Enhancers Genic enhancers Flanking Active TSS Active TSS Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	170 gene(s)	inside rSNPs	diseases
2	nsv541490	chr12:49975040-50551375	Weak transcription Transcr. at gene 5' and 3' Enhancers Genic enhancers Active TSS Strong transcription Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	170 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	chr12:50174400-50209600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
2	chr12:50177800-50203400	Weak transcription	Fetal Kidney	kidney
3	chr12:50178400-50194000	Weak transcription	NH-A	brain
4	chr12:50178400-50195000	Weak transcription	Rectal Smooth Muscle	rectum
5	chr12:50179200-50213600	Weak transcription	Hela-S3	cervix
6	chr12:50179600-50195200	Weak transcription	Fetal Brain Male	brain
7	chr12:50183200-50197600	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
8	chr12:50183200-50200600	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
9	chr12:50183200-50201400	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
10	chr12:50183200-50203400	Strong transcription	Primary hematopoietic stem cells short term culture	blood
11	chr12:50183400-50193200	Strong transcription	Skeletal Muscle Female	skeletal muscle
12	chr12:50183400-50193400	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
13	chr12:50183400-50193400	Strong transcription	Adipose Nuclei	Adipose
14	chr12:50183400-50197600	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
15	chr12:50183400-50200000	Strong transcription	Brain Hippocampus Middle	brain
16	chr12:50183400-50200000	Strong transcription	Brain Inferior Temporal Lobe	brain
17	chr12:50183400-50200200	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
18	chr12:50183400-50200200	Strong transcription	Stomach Smooth Muscle	stomach
19	chr12:50183400-50200600	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
20	chr12:50183400-50200600	Strong transcription	Fetal Brain Female	brain
21	chr12:50183400-50202200	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
22	chr12:50183400-50202200	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
23	chr12:50183400-50202600	Strong transcription	NHLF	lung
24	chr12:50183800-50199800	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
25	chr12:50184400-50193000	Strong transcription	Brain Cingulate Gyrus	brain
26	chr12:50184400-50200000	Strong transcription	Lung	lung
27	chr12:50184400-50200000	Strong transcription	Spleen	Spleen
28	chr12:50184400-50200200	Strong transcription	Brain Germinal Matrix	brain
29	chr12:50184400-50203200	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
30	chr12:50184600-50193400	Strong transcription	Skeletal Muscle Male	skeletal muscle
31	chr12:50184600-50194000	Strong transcription	Right Ventricle	heart
32	chr12:50184600-50199800	Strong transcription	Brain Anterior Caudate	brain
33	chr12:50184800-50194200	Strong transcription	Fetal Intestine Small	intestine
34	chr12:50184800-50199800	Strong transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
35	chr12:50185000-50202400	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
36	chr12:50185200-50196400	Weak transcription	Primary hematopoietic stem cells	blood
37	chr12:50185200-50200000	Strong transcription	Gastric	stomach
38	chr12:50185200-50200200	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
39	chr12:50185200-50200200	Strong transcription	Fetal Thymus	thymus
40	chr12:50185200-50200400	Strong transcription	Cortex derived primary cultured neurospheres	brain
41	chr12:50185400-50194000	Weak transcription	Psoas Muscle	Psoas
42	chr12:50185600-50201200	Strong transcription	Fetal Stomach	stomach
43	chr12:50185800-50199800	Strong transcription	Placenta	Placenta
44	chr12:50185800-50200400	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
45	chr12:50186000-50195000	Strong transcription	Foreskin Fibroblast Primary Cells skin01	Skin
46	chr12:50186200-50200400	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
47	chr12:50187000-50199800	Strong transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
48	chr12:50187200-50203000	Strong transcription	Primary T cells from cord blood	blood
49	chr12:50187200-50214800	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
50	chr12:50188000-50193000	Strong transcription	Fetal Intestine Large	intestine

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