Variant report

Variant	rs12059402
Chromosome Location	chr1:185017172-185017173
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr1:185016945..185018901-chr1:185045228..185047270,2	MCF-7	breast:
2	chr1:185016452..185019529-chr1:185020434..185022223,3	MCF-7	breast:
3	chr1:185010844..185012522-chr1:185016130..185018992,2	MCF-7	breast:
4	chr1:185014501..185017888-chr1:185123055..185126846,5	MCF-7	breast:
5	chr1:185012738..185017820-chr1:185123187..185127311,9	K562	blood:
6	chr1:185016719..185019700-chr1:185022718..185024922,3	MCF-7	breast:
7	chr1:185016066..185017861-chr1:185027232..185029137,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000121486	Chromatin interaction
ENSG00000116668	Chromatin interaction

Extended variants
information (count: 13 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:9)

rs_ID	r²[population]
rs10911672	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs12062374	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs12076847	1.00[AMR][1000 genomes]
rs12090423	1.00[AMR][1000 genomes]
rs12093884	1.00[AMR][1000 genomes]
rs55855715	1.00[AMR][1000 genomes]
rs74134431	1.00[AMR][1000 genomes]
rs74134432	1.00[AMR][1000 genomes]
rs74134441	1.00[AMR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1001323	chr1:184525419-185315876	Weak transcription Active TSS Enhancers Strong transcription ZNF genes & repeats Flanking Active TSS Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	69 gene(s)	inside rSNPs	diseases
2	nsv535222	chr1:184525419-185315876	Weak transcription Enhancers Strong transcription Genic enhancers Bivalent Enhancer Active TSS Flanking Active TSS Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	69 gene(s)	inside rSNPs	diseases
3	nsv525731	chr1:184812165-185038104	Weak transcription Enhancers Strong transcription Flanking Active TSS Active TSS Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases
4	nsv947340	chr1:185012848-185017415	Bivalent/Poised TSS Active TSS Weak transcription Enhancers Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	8 gene(s)	inside rSNPs	n/a

No data

Chromatin state (count:115 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:185014200-185017200	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
2	chr1:185015000-185017200	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
3	chr1:185015600-185017200	Weak transcription	Lung	lung
4	chr1:185015600-185017400	Flanking Active TSS	Dnd41	blood
5	chr1:185015600-185018800	Weak transcription	Sigmoid Colon	Sigmoid Colon
6	chr1:185015600-185034200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
7	chr1:185015600-185037000	Weak transcription	Spleen	Spleen
8	chr1:185015600-185037600	Weak transcription	Pancreas	Pancrea
9	chr1:185015800-185017400	Enhancers	Stomach Mucosa	stomach
10	chr1:185015800-185018800	Weak transcription	Left Ventricle	heart
11	chr1:185015800-185023400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
12	chr1:185015800-185037600	Weak transcription	Aorta	Aorta
13	chr1:185015800-185043400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
14	chr1:185016000-185017200	Flanking Active TSS	iPS-18 Cell Line	embryonic stem cell
15	chr1:185016000-185017200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
16	chr1:185016000-185017200	Enhancers	Colon Smooth Muscle	Colon
17	chr1:185016000-185017200	Enhancers	Placenta Amnion	Placenta Amnion
18	chr1:185016000-185017400	Flanking Active TSS	HUES64 Cell Line	embryonic stem cell
19	chr1:185016000-185017400	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
20	chr1:185016000-185017400	Enhancers	Primary T killer naive cells fromperipheralblood	blood
21	chr1:185016000-185017400	Enhancers	Brain Inferior Temporal Lobe	brain
22	chr1:185016000-185017400	Enhancers	Rectal Mucosa Donor 31	rectum
23	chr1:185016000-185017400	Enhancers	Skeletal Muscle Female	skeletal muscle
24	chr1:185016000-185017600	Enhancers	Fetal Intestine Small	intestine
25	chr1:185016000-185025600	Weak transcription	Ovary	ovary
26	chr1:185016000-185026600	Weak transcription	Psoas Muscle	Psoas
27	chr1:185016000-185026600	Weak transcription	Right Atrium	heart
28	chr1:185016000-185034400	Weak transcription	Fetal Muscle Trunk	muscle
29	chr1:185016200-185017200	Enhancers	Brain Germinal Matrix	brain
30	chr1:185016200-185017400	Flanking Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
31	chr1:185016200-185017400	Flanking Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
32	chr1:185016200-185017400	Enhancers	Breast Myoepithelial Primary Cells	Breast
33	chr1:185016200-185017400	Enhancers	Primary monocytes fromperipheralblood	blood
34	chr1:185016200-185017400	Enhancers	Primary T helper cells fromperipheralblood	blood
35	chr1:185016200-185017400	Enhancers	Brain Dorsolateral Prefrontal Cortex	brain
36	chr1:185016200-185017600	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
37	chr1:185016200-185017600	Flanking Active TSS	H9 Derived Neuron Cultured Cells	ES cell derived
38	chr1:185016200-185017600	Enhancers	Fetal Heart	heart
39	chr1:185016200-185017600	Enhancers	Fetal Lung	lung
40	chr1:185016200-185017600	Enhancers	Fetal Stomach	stomach
41	chr1:185016200-185018000	Enhancers	Primary T helper naive cells fromperipheralblood	blood
42	chr1:185016200-185018000	Enhancers	Primary T regulatory cells fromperipheralblood	blood
43	chr1:185016200-185018000	Enhancers	Fetal Adrenal Gland	Adrenal Gland
44	chr1:185016200-185018400	Enhancers	Fetal Brain Male	brain
45	chr1:185016200-185023600	Weak transcription	Primary T cells fromperipheralblood	blood
46	chr1:185016400-185017200	Enhancers	HUVEC	blood vessel
47	chr1:185016400-185017400	Enhancers	H9 Cell Line	embryonic stem cell
48	chr1:185016400-185017400	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
49	chr1:185016400-185017400	Enhancers	Duodenum Smooth Muscle	Duodenum
50	chr1:185016400-185017400	Enhancers	Fetal Intestine Large	intestine

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