Variant report

Variant	rs12128424
Chromosome Location	chr1:184393091-184393092
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr1:184387289..184390944-chr1:184391179..184396690,9	MCF-7	breast:
2	chr1:184354551..184358785-chr1:184391255..184395551,10	MCF-7	breast:
3	chr1:184373706..184377617-chr1:184391429..184395529,4	MCF-7	breast:
4	chr1:184384049..184385572-chr1:184391897..184393944,2	K562	blood:
5	chr1:184353547..184356536-chr1:184392448..184394003,2	MCF-7	breast:
6	chr1:184379414..184382005-chr1:184392541..184395797,4	MCF-7	breast:
7	chr1:184392135..184393855-chr1:184396238..184398930,2	K562	blood:

Variant related genes	Relation type
ENSG00000271387	Chromatin interaction
ENSG00000116667	Chromatin interaction
ENSG00000230470	Chromatin interaction

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

rSNPs within LD-proxies of this variant (count:29)

rs_ID	r²[population]
rs10911597	1.00[EUR][1000 genomes]
rs11799574	1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[TSI][hapmap];0.97[EUR][1000 genomes]
rs12123538	1.00[CEU][hapmap];0.81[EUR][1000 genomes]
rs12128343	1.00[CEU][hapmap];0.80[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs12129504	1.00[CEU][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];0.90[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs12130008	1.00[CEU][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];0.90[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs12131730	0.96[AFR][1000 genomes];0.90[AMR][1000 genomes]
rs12135850	0.97[EUR][1000 genomes]
rs12136470	1.00[CEU][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];0.90[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs12138263	0.80[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs12142338	0.87[AFR][1000 genomes];0.80[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs12142568	1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[TSI][hapmap];0.97[EUR][1000 genomes]
rs12142676	0.93[AFR][1000 genomes];0.90[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs12145326	1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[TSI][hapmap];0.97[EUR][1000 genomes]
rs13374592	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.97[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];0.90[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs16823133	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];0.90[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs17577247	1.00[CEU][hapmap]
rs2224029	0.97[EUR][1000 genomes]
rs41263668	0.82[EUR][1000 genomes]
rs56173711	0.96[AFR][1000 genomes];0.90[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs59688287	0.97[EUR][1000 genomes]
rs60650088	0.92[AFR][1000 genomes];0.90[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs73063509	0.97[EUR][1000 genomes]
rs74131663	0.96[AFR][1000 genomes];0.90[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs74131671	0.97[EUR][1000 genomes]
rs74131672	0.87[AFR][1000 genomes];0.80[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs74131673	1.00[EUR][1000 genomes]
rs7531736	0.85[GIH][hapmap]
rs9970469	1.00[CEU][hapmap]

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	nsv530079	chr1:183797938-184639971	Enhancers Weak transcription Strong transcription Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	21 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:62 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:184378000-184395600	Weak transcription	Brain Germinal Matrix	brain
2	chr1:184378200-184402400	Weak transcription	Fetal Lung	lung
3	chr1:184378400-184394200	Weak transcription	Fetal Intestine Small	intestine
4	chr1:184378400-184397400	Weak transcription	Ovary	ovary
5	chr1:184383600-184394200	Weak transcription	Spleen	Spleen
6	chr1:184383800-184412400	Weak transcription	Fetal Stomach	stomach
7	chr1:184386400-184393600	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
8	chr1:184386600-184393200	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
9	chr1:184386600-184393600	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
10	chr1:184387000-184397000	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
11	chr1:184387000-184400200	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
12	chr1:184387200-184397800	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
13	chr1:184387200-184403400	Weak transcription	Aorta	Aorta
14	chr1:184387600-184394400	Weak transcription	Lung	lung
15	chr1:184387600-184394600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
16	chr1:184388000-184400000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
17	chr1:184388400-184397400	Enhancers	Rectal Mucosa Donor 31	rectum
18	chr1:184389000-184395200	Weak transcription	Fetal Muscle Leg	muscle
19	chr1:184389200-184393800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
20	chr1:184389200-184394600	Weak transcription	Right Ventricle	heart
21	chr1:184389200-184395800	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
22	chr1:184389200-184399800	Weak transcription	A549	lung
23	chr1:184389400-184395400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
24	chr1:184389400-184397800	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
25	chr1:184389400-184399400	Weak transcription	NHLF	lung
26	chr1:184389600-184394600	Weak transcription	Colon Smooth Muscle	Colon
27	chr1:184389800-184393600	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
28	chr1:184390600-184393800	Weak transcription	Left Ventricle	heart
29	chr1:184390600-184401600	Weak transcription	Primary hematopoietic stem cells short term culture	blood
30	chr1:184390600-184422400	Weak transcription	Cortex derived primary cultured neurospheres	brain
31	chr1:184391200-184395600	Enhancers	Small Intestine	intestine
32	chr1:184391400-184393600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
33	chr1:184391400-184393600	Enhancers	NHEK	skin
34	chr1:184391400-184394000	Weak transcription	Colonic Mucosa	Colon
35	chr1:184391400-184395400	Weak transcription	H1 Cell Line	embryonic stem cell
36	chr1:184391400-184398000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
37	chr1:184391600-184393200	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
38	chr1:184391600-184394800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
39	chr1:184391800-184394800	Weak transcription	iPS-15b Cell Line	embryonic stem cell
40	chr1:184391800-184395000	Weak transcription	HUES48 Cell Line	embryonic stem cell
41	chr1:184391800-184395200	Weak transcription	iPS-18 Cell Line	embryonic stem cell
42	chr1:184391800-184395200	Weak transcription	iPS-20b Cell Line	embryonic stem cell
43	chr1:184391800-184395800	Enhancers	Duodenum Mucosa	Duodenum
44	chr1:184391800-184396200	Enhancers	Breast Myoepithelial Primary Cells	Breast
45	chr1:184392000-184393600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
46	chr1:184392000-184393800	Weak transcription	Skeletal Muscle Male	skeletal muscle
47	chr1:184392000-184393800	Weak transcription	Skeletal Muscle Female	skeletal muscle
48	chr1:184392000-184395200	Weak transcription	HUES64 Cell Line	embryonic stem cell
49	chr1:184392200-184395400	Weak transcription	H9 Cell Line	embryonic stem cell
50	chr1:184392200-184395600	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast

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