Variant report

Variant	rs12079458
Chromosome Location	chr1:180613034-180613035
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr1:180600492..180602685-chr1:180608487..180613245,4	MCF-7	breast:
2	chr1:180611817..180614490-chr1:180617185..180619103,2	K562	blood:
3	chr1:180612995..180614895-chr1:180645911..180648715,2	K562	blood:

Variant related genes	Relation type
ENSG00000143324	Chromatin interaction

Extended variants
information (count: 15 )
Associated
traits (count: 0)

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

rs_ID	r²[population]
rs10914059	1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs10914060	1.00[YRI][hapmap];0.83[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs10914092	1.00[YRI][hapmap]
rs12060280	1.00[YRI][hapmap]
rs12064567	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs12072401	0.83[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs12073365	1.00[AMR][1000 genomes]
rs12076333	1.00[YRI][hapmap]
rs12084365	1.00[YRI][hapmap];0.90[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs12085100	1.00[YRI][hapmap]
rs12093933	1.00[YRI][hapmap]
rs7521560	1.00[AMR][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	nsv1003359	chr1:180300936-180727561	Enhancers Strong transcription Active TSS Weak transcription Flanking Active TSS ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA	48 gene(s)	inside rSNPs	diseases
2	nsv949311	chr1:180438895-180692815	ZNF genes & repeats Enhancers Flanking Active TSS Active TSS Weak transcription Strong transcription Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	46 gene(s)	inside rSNPs	diseases
3	nsv872578	chr1:180510771-180842344	Enhancers Weak transcription Active TSS Strong transcription Flanking Active TSS Bivalent/Poised TSS ZNF genes & repeats Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:66 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:180602000-180615800	Weak transcription	Lung	lung
2	chr1:180602000-180618800	Weak transcription	Pancreas	Pancrea
3	chr1:180602000-180645200	Weak transcription	Gastric	stomach
4	chr1:180603000-180614800	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
5	chr1:180603200-180614400	Weak transcription	Primary B cells from cord blood	blood
6	chr1:180603200-180615200	Weak transcription	HSMM	muscle
7	chr1:180603200-180615800	Weak transcription	HUES6 Cell Line	embryonic stem cell
8	chr1:180603200-180616400	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
9	chr1:180603200-180622400	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
10	chr1:180603400-180614800	Weak transcription	Sigmoid Colon	Sigmoid Colon
11	chr1:180603400-180615400	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
12	chr1:180603400-180615600	Weak transcription	HUVEC	blood vessel
13	chr1:180603400-180617000	Weak transcription	Monocytes-CD14+_RO01746	blood
14	chr1:180603400-180619400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
15	chr1:180603600-180626400	Weak transcription	Fetal Lung	lung
16	chr1:180603800-180613400	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
17	chr1:180603800-180614600	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
18	chr1:180604000-180613200	Weak transcription	Brain Germinal Matrix	brain
19	chr1:180604000-180623200	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
20	chr1:180604800-180617000	Weak transcription	Dnd41	blood
21	chr1:180605600-180625800	Weak transcription	Primary T killer memory cells from peripheral blood	blood
22	chr1:180605800-180613200	Weak transcription	Fetal Brain Female	brain
23	chr1:180605800-180615000	Weak transcription	HUES64 Cell Line	embryonic stem cell
24	chr1:180605800-180622000	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
25	chr1:180605800-180625000	Weak transcription	Primary T helper cells fromperipheralblood	blood
26	chr1:180606000-180614000	Weak transcription	Left Ventricle	heart
27	chr1:180606000-180618200	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
28	chr1:180608200-180617000	Weak transcription	Fetal Intestine Large	intestine
29	chr1:180608600-180615600	Enhancers	Fetal Heart	heart
30	chr1:180609800-180614800	Weak transcription	Small Intestine	intestine
31	chr1:180609800-180625800	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
32	chr1:180610000-180615400	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
33	chr1:180610200-180617000	Weak transcription	Primary B cells from peripheral blood	blood
34	chr1:180610600-180614800	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
35	chr1:180611200-180615400	Genic enhancers	K562	blood
36	chr1:180611600-180615200	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
37	chr1:180612000-180613200	Enhancers	Cortex derived primary cultured neurospheres	brain
38	chr1:180612200-180613400	Enhancers	Skeletal Muscle Male	skeletal muscle
39	chr1:180612400-180613200	Enhancers	A549	lung
40	chr1:180612400-180613400	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
41	chr1:180612400-180613400	Enhancers	Brain Substantia Nigra	brain
42	chr1:180612400-180613400	Enhancers	Colon Smooth Muscle	Colon
43	chr1:180612400-180613400	Enhancers	Duodenum Smooth Muscle	Duodenum
44	chr1:180612400-180615200	Enhancers	Breast Myoepithelial Primary Cells	Breast
45	chr1:180612600-180613200	Enhancers	Muscle Satellite Cultured Cells	--
46	chr1:180612600-180613200	Enhancers	Brain Inferior Temporal Lobe	brain
47	chr1:180612600-180613400	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
48	chr1:180612600-180613400	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
49	chr1:180612600-180613400	Enhancers	Adipose Nuclei	Adipose
50	chr1:180612600-180613400	Enhancers	Brain Hippocampus Middle	brain

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