Variant report

Variant	rs2430610
Chromosome Location	chr12:12245254-12245255
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr12:12242492..12245826-chr12:12250715..12252862,3	MCF-7	breast:
2	chr12:12243605..12245833-chr12:12417112..12419056,2	MCF-7	breast:

Extended variants
information (count: 28 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:26)

rs_ID	r²[population]
rs1612841	0.95[CEU][hapmap];0.90[JPT][hapmap];0.83[AMR][1000 genomes];0.89[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs1628766	1.00[CEU][hapmap];0.85[CHB][hapmap];0.90[JPT][hapmap];0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs1630467	1.00[CEU][hapmap];0.85[CHB][hapmap];0.90[JPT][hapmap];0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs1641727	0.95[CEU][hapmap];0.82[CHB][hapmap];0.95[JPT][hapmap];0.81[AMR][1000 genomes];0.88[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs1641728	1.00[CEU][hapmap];1.00[CHB][hapmap];0.90[JPT][hapmap];0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs1641729	1.00[CEU][hapmap];0.90[CHB][hapmap];0.90[JPT][hapmap];0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs1797646	1.00[CEU][hapmap];0.86[CHB][hapmap];0.90[JPT][hapmap];0.89[AMR][1000 genomes];0.97[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs1797647	1.00[CEU][hapmap];0.85[CHB][hapmap];0.90[JPT][hapmap];0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs1797662	0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2111166	0.86[CHB][hapmap];0.80[JPT][hapmap];0.92[ASN][1000 genomes]
rs2160523	0.86[CHB][hapmap];0.81[JPT][hapmap];0.92[ASN][1000 genomes]
rs2430611	1.00[CEU][hapmap];0.85[CHB][hapmap];0.90[JPT][hapmap];0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2430612	1.00[CEU][hapmap];0.90[CHB][hapmap];0.90[JPT][hapmap];0.89[AMR][1000 genomes];0.97[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2448029	0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2448030	1.00[CEU][hapmap];0.86[CHB][hapmap];0.90[JPT][hapmap];0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2448031	1.00[CEU][hapmap];0.85[CHB][hapmap];0.90[JPT][hapmap];0.89[AMR][1000 genomes];0.97[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2448048	1.00[CEU][hapmap];0.90[CHB][hapmap];0.90[JPT][hapmap];0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2448049	0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2448052	0.81[JPT][hapmap]
rs2961550	0.85[AMR][1000 genomes];0.93[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2961551	0.90[AMR][1000 genomes];0.93[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2961552	0.90[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs2961553	0.92[AMR][1000 genomes];0.88[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2961554	0.96[CEU][hapmap];0.86[CHB][hapmap];0.90[JPT][hapmap];0.93[AMR][1000 genomes];0.92[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs3851594	0.93[ASN][1000 genomes]
rs885636	0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];0.90[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv949003	chr12:11938229-12618690	Weak transcription Enhancers Strong transcription Flanking Active TSS Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	36 gene(s)	inside rSNPs	diseases
2	nsv557583	chr12:12238317-12253591	Enhancers Weak transcription Strong transcription Bivalent Enhancer ZNF genes & repeats Active TSS Flanking Active TSS Genic enhancers	Chromatin interactive region	1 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	chr12:12225000-12255000	Weak transcription	Small Intestine	intestine
2	chr12:12232800-12257000	Weak transcription	HSMMtube	muscle
3	chr12:12234800-12259600	Weak transcription	Aorta	Aorta
4	chr12:12235400-12260200	Weak transcription	Gastric	stomach
5	chr12:12235400-12260800	Weak transcription	Stomach Smooth Muscle	stomach
6	chr12:12235400-12278800	Weak transcription	Muscle Satellite Cultured Cells	--
7	chr12:12237400-12259800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
8	chr12:12239600-12249200	Strong transcription	Fetal Intestine Small	intestine
9	chr12:12240400-12254200	Weak transcription	Stomach Mucosa	stomach
10	chr12:12240600-12245400	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
11	chr12:12240600-12245400	Weak transcription	Brain Germinal Matrix	brain
12	chr12:12240600-12256800	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
13	chr12:12241000-12250200	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
14	chr12:12241000-12260600	Weak transcription	HUES48 Cell Line	embryonic stem cell
15	chr12:12241000-12273400	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
16	chr12:12241200-12245600	Weak transcription	HUES64 Cell Line	embryonic stem cell
17	chr12:12241200-12245600	Weak transcription	iPS-20b Cell Line	embryonic stem cell
18	chr12:12241200-12256800	Weak transcription	H1 Cell Line	embryonic stem cell
19	chr12:12241200-12261000	Weak transcription	iPS-15b Cell Line	embryonic stem cell
20	chr12:12241400-12252000	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
21	chr12:12241400-12272600	Weak transcription	iPS-18 Cell Line	embryonic stem cell
22	chr12:12241800-12245400	Weak transcription	Fetal Stomach	stomach
23	chr12:12241800-12247400	Weak transcription	Sigmoid Colon	Sigmoid Colon
24	chr12:12241800-12260400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
25	chr12:12242000-12245800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
26	chr12:12242000-12251000	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
27	chr12:12242000-12257000	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
28	chr12:12242800-12249000	Strong transcription	Fetal Intestine Large	intestine
29	chr12:12243600-12246200	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
30	chr12:12243800-12245800	Enhancers	NHLF	lung
31	chr12:12243800-12246200	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
32	chr12:12244000-12246400	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
33	chr12:12244200-12245400	Enhancers	HepG2	liver
34	chr12:12244200-12245800	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
35	chr12:12244200-12245800	Enhancers	Fetal Muscle Leg	muscle
36	chr12:12244200-12245800	Enhancers	Lung	lung
37	chr12:12244200-12246200	Enhancers	Fetal Lung	lung
38	chr12:12244400-12247200	Weak transcription	Rectal Mucosa Donor 29	rectum
39	chr12:12244600-12245600	Strong transcription	Colonic Mucosa	Colon
40	chr12:12244800-12245400	Bivalent Enhancer	Adipose Nuclei	Adipose
41	chr12:12244800-12245800	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
42	chr12:12245000-12245600	Enhancers	HUES6 Cell Line	embryonic stem cell
43	chr12:12245000-12245600	Enhancers	Brain Inferior Temporal Lobe	brain
44	chr12:12245000-12245600	Enhancers	Fetal Brain Male	brain
45	chr12:12245000-12245600	Enhancers	Placenta	Placenta
46	chr12:12245000-12245800	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
47	chr12:12245000-12245800	ZNF genes & repeats	IMR90 fetal lung fibroblasts Cell Line	lung
48	chr12:12245000-12245800	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
49	chr12:12245000-12245800	Enhancers	Brain Substantia Nigra	brain
50	chr12:12245000-12246200	Enhancers	Cortex derived primary cultured neurospheres	brain

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