Variant report

Variant	rs17123778
Chromosome Location	chr12:49948841-49948842
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr12:49947021..49949486-chr12:49957820..49961447,4	K562	blood:
2	chr12:49740169..49741813-chr12:49946127..49949102,2	MCF-7	breast:
3	chr12:49751555..49753857-chr12:49947807..49949474,2	MCF-7	breast:
4	chr12:49936941..49938508-chr12:49948825..49950668,2	MCF-7	breast:
5	chr12:49759558..49762549-chr12:49947414..49949768,3	MCF-7	breast:
6	chr12:49932766..49934381-chr12:49946781..49949043,2	MCF-7	breast:
7	chr12:49946254..49948915-chr12:49954730..49957396,3	K562	blood:

Variant related genes	Relation type
ENSG00000187778	Chromatin interaction
ENSG00000123352	Chromatin interaction
ENSG00000178401	Chromatin interaction
ENSG00000135519	Chromatin interaction

Extended variants
information (count: 30 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:27)

rs_ID	r²[population]
rs11609068	0.86[YRI][hapmap]
rs12300376	1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs12300919	1.00[EUR][1000 genomes]
rs12300962	1.00[EUR][1000 genomes]
rs12306951	0.83[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs12316175	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs1317263	0.92[YRI][hapmap];1.00[EUR][1000 genomes]
rs17119738	0.85[YRI][hapmap];1.00[EUR][1000 genomes]
rs17123724	1.00[YRI][hapmap];1.00[EUR][1000 genomes]
rs17123729	1.00[EUR][1000 genomes]
rs17123787	1.00[YRI][hapmap];1.00[EUR][1000 genomes]
rs17123827	1.00[YRI][hapmap]
rs57625108	1.00[EUR][1000 genomes]
rs58039341	1.00[EUR][1000 genomes]
rs61438877	1.00[EUR][1000 genomes]
rs73305101	1.00[EUR][1000 genomes]
rs73306844	1.00[EUR][1000 genomes]
rs73306846	1.00[EUR][1000 genomes]
rs73306864	1.00[EUR][1000 genomes]
rs73306865	1.00[EUR][1000 genomes]
rs73306875	1.00[EUR][1000 genomes]
rs73306891	1.00[EUR][1000 genomes]
rs73309004	1.00[EUR][1000 genomes]
rs73309010	1.00[EUR][1000 genomes]
rs73309013	1.00[EUR][1000 genomes]
rs73309017	1.00[EUR][1000 genomes]
rs73309026	1.00[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv832406	chr12:49860693-50062136	Weak transcription Flanking Bivalent TSS/Enh Strong transcription Enhancers Genic enhancers Flanking Active TSS Active TSS Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	39 gene(s)	inside rSNPs	diseases
2	nsv482795	chr12:49897633-50068686	Flanking Active TSS Weak transcription Active TSS Enhancers Transcr. at gene 5' and 3' Strong transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Genic enhancers Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	39 gene(s)	inside rSNPs	diseases
3	nsv899071	chr12:49927148-49955935	Flanking Bivalent TSS/Enh ZNF genes & repeats Strong transcription Bivalent Enhancer Enhancers Active TSS Weak transcription Bivalent/Poised TSS Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:116 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:49943000-49950400	Weak transcription	GM12878-XiMat	blood
2	chr12:49943200-49951000	Weak transcription	Aorta	Aorta
3	chr12:49943200-49959600	Weak transcription	Right Atrium	heart
4	chr12:49943400-49949400	Weak transcription	Gastric	stomach
5	chr12:49943400-49949400	Weak transcription	Spleen	Spleen
6	chr12:49943400-49950000	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
7	chr12:49943400-49950200	Weak transcription	Primary B cells from cord blood	blood
8	chr12:49943400-49952600	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
9	chr12:49943600-49949800	Weak transcription	H9 Cell Line	embryonic stem cell
10	chr12:49943600-49949800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
11	chr12:49943600-49949800	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
12	chr12:49943600-49949800	Weak transcription	Fetal Lung	lung
13	chr12:49943600-49950000	Weak transcription	Cortex derived primary cultured neurospheres	brain
14	chr12:49943600-49950000	Weak transcription	Ovary	ovary
15	chr12:49943600-49950200	Weak transcription	Primary B cells from peripheral blood	blood
16	chr12:49943600-49950200	Weak transcription	Colon Smooth Muscle	Colon
17	chr12:49943600-49950400	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
18	chr12:49944200-49952200	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
19	chr12:49944800-49949800	Weak transcription	Duodenum Mucosa	Duodenum
20	chr12:49944800-49952400	Weak transcription	Fetal Kidney	kidney
21	chr12:49945000-49949400	Weak transcription	Thymus	Thymus
22	chr12:49945000-49952400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
23	chr12:49945200-49949800	Weak transcription	Sigmoid Colon	Sigmoid Colon
24	chr12:49945600-49950200	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
25	chr12:49946000-49960200	Weak transcription	Fetal Brain Male	brain
26	chr12:49946200-49949400	Weak transcription	Brain Germinal Matrix	brain
27	chr12:49946200-49949600	Weak transcription	Fetal Intestine Large	intestine
28	chr12:49946200-49949800	Weak transcription	Adipose Nuclei	Adipose
29	chr12:49946200-49949800	Weak transcription	Esophagus	oesophagus
30	chr12:49946200-49949800	Weak transcription	Lung	lung
31	chr12:49946200-49949800	Weak transcription	Stomach Smooth Muscle	stomach
32	chr12:49946200-49952200	Weak transcription	HSMMtube	muscle
33	chr12:49946200-49952400	Weak transcription	HMEC	breast
34	chr12:49946200-49955600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
35	chr12:49946400-49949400	Weak transcription	Brain Anterior Caudate	brain
36	chr12:49946400-49949600	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
37	chr12:49946400-49949600	Weak transcription	Brain Hippocampus Middle	brain
38	chr12:49946400-49949600	Weak transcription	Fetal Thymus	thymus
39	chr12:49946400-49949800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
40	chr12:49946400-49949800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
41	chr12:49946400-49949800	Weak transcription	Brain Inferior Temporal Lobe	brain
42	chr12:49946400-49949800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
43	chr12:49946400-49950000	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
44	chr12:49946400-49950000	Weak transcription	Brain Substantia Nigra	brain
45	chr12:49946400-49950000	Weak transcription	Psoas Muscle	Psoas
46	chr12:49946600-49949600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
47	chr12:49946600-49949600	Weak transcription	Brain Cingulate Gyrus	brain
48	chr12:49946600-49949600	Weak transcription	Fetal Muscle Leg	muscle
49	chr12:49946600-49949800	Weak transcription	Primary hematopoietic stem cells short term culture	blood
50	chr12:49946600-49949800	Weak transcription	Brain Angular Gyrus	brain

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