Variant report

Variant	rs12089375
Chromosome Location	chr1:174939348-174939349
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr1:174937958..174940794-chr1:174967575..174969945,2	MCF-7	breast:
2	chr1:174937198..174939859-chr1:174967245..174970067,3	MCF-7	breast:
3	chr1:174932632..174935531-chr1:174937722..174939666,3	MCF-7	breast:
4	chr1:174938092..174940324-chr1:174940877..174942790,2	MCF-7	breast:
5	chr1:174939098..174941697-chr1:174958676..174960962,2	K562	blood:
6	chr1:174927580..174945830-chr1:174955726..174971213,32	K562	blood:

Variant related genes	Relation type
ENSG00000116161	Chromatin interaction
ENSG00000152061	Chromatin interaction
ENSG00000252552	Chromatin interaction

Extended variants
information (count: 26 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:25)

rs_ID	r²[population]
rs10489331	0.93[YRI][hapmap];0.90[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs10489334	1.00[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs10912852	1.00[EUR][1000 genomes]
rs10912862	1.00[EUR][1000 genomes]
rs10912866	1.00[EUR][1000 genomes]
rs10912869	1.00[EUR][1000 genomes]
rs11806870	0.84[AMR][1000 genomes]
rs12061403	1.00[EUR][1000 genomes]
rs12062145	0.89[YRI][hapmap];0.89[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs12072529	0.83[YRI][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs12075140	1.00[YRI][hapmap];0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs13376513	1.00[EUR][1000 genomes]
rs16847652	0.90[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs16847670	1.00[EUR][1000 genomes]
rs16847689	1.00[EUR][1000 genomes]
rs16847701	0.93[YRI][hapmap];0.93[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs1894679	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs4650677	1.00[EUR][1000 genomes]
rs57512007	1.00[EUR][1000 genomes]
rs58503437	1.00[EUR][1000 genomes]
rs60411387	0.93[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs6425311	1.00[EUR][1000 genomes]
rs6689751	0.93[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs74128526	1.00[EUR][1000 genomes]
rs74128530	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	esv2755184	chr1:174388343-174970343	Flanking Active TSS Weak transcription Enhancers Strong transcription Transcr. at gene 5' and 3' Genic enhancers Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	54 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:103 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:174910800-174957000	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
2	chr1:174924200-174967800	Weak transcription	Brain Germinal Matrix	brain
3	chr1:174924400-174958200	Weak transcription	Fetal Brain Male	brain
4	chr1:174925000-174940800	Weak transcription	Gastric	stomach
5	chr1:174932600-174941600	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
6	chr1:174933000-174953600	Weak transcription	Fetal Heart	heart
7	chr1:174934600-174943800	Weak transcription	Pancreas	Pancrea
8	chr1:174934800-174940400	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
9	chr1:174934800-174943800	Weak transcription	Aorta	Aorta
10	chr1:174935000-174942200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
11	chr1:174935000-174943800	Weak transcription	Lung	lung
12	chr1:174935000-174959000	Weak transcription	Skeletal Muscle Male	skeletal muscle
13	chr1:174935000-174964000	Strong transcription	HUES48 Cell Line	embryonic stem cell
14	chr1:174935000-174967000	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
15	chr1:174935200-174943400	Weak transcription	Brain Angular Gyrus	brain
16	chr1:174935200-174943400	Weak transcription	Rectal Smooth Muscle	rectum
17	chr1:174935200-174943800	Weak transcription	Fetal Muscle Leg	muscle
18	chr1:174935200-174959000	Weak transcription	Stomach Smooth Muscle	stomach
19	chr1:174935200-174959600	Weak transcription	Esophagus	oesophagus
20	chr1:174935400-174943600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
21	chr1:174935400-174958400	Weak transcription	Skeletal Muscle Female	skeletal muscle
22	chr1:174935600-174943800	Weak transcription	Brain Hippocampus Middle	brain
23	chr1:174935800-174959600	Weak transcription	Fetal Kidney	kidney
24	chr1:174936000-174940600	Weak transcription	Brain Inferior Temporal Lobe	brain
25	chr1:174936000-174943800	Weak transcription	Breast Myoepithelial Primary Cells	Breast
26	chr1:174936000-174944600	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
27	chr1:174936000-174945000	Weak transcription	NHEK	skin
28	chr1:174936000-174946200	Weak transcription	Brain Cingulate Gyrus	brain
29	chr1:174936000-174950600	Weak transcription	Fetal Brain Female	brain
30	chr1:174936000-174958600	Weak transcription	Brain Substantia Nigra	brain
31	chr1:174936400-174939600	Enhancers	HSMMtube	muscle
32	chr1:174936600-174943400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
33	chr1:174936600-174945400	Weak transcription	Fetal Lung	lung
34	chr1:174937000-174940800	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
35	chr1:174937000-174943800	Weak transcription	Ovary	ovary
36	chr1:174937000-174963600	Strong transcription	iPS-20b Cell Line	embryonic stem cell
37	chr1:174937200-174939400	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
38	chr1:174937200-174939600	Enhancers	HSMM	muscle
39	chr1:174937200-174940600	Weak transcription	Stomach Mucosa	stomach
40	chr1:174937200-174955000	Strong transcription	HUES64 Cell Line	embryonic stem cell
41	chr1:174937400-174939400	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
42	chr1:174937400-174944200	Weak transcription	Duodenum Smooth Muscle	Duodenum
43	chr1:174937400-174963600	Strong transcription	iPS-18 Cell Line	embryonic stem cell
44	chr1:174937600-174940600	Weak transcription	Pancreatic Islets	Pancreatic Islet
45	chr1:174937800-174939400	Enhancers	Fetal Thymus	thymus
46	chr1:174937800-174939800	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
47	chr1:174937800-174942200	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
48	chr1:174938000-174939600	Enhancers	Primary hematopoietic stem cells short term culture	blood
49	chr1:174938000-174939600	Genic enhancers	K562	blood
50	chr1:174938000-174940800	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived

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