Variant report

Variant	rs12196702
Chromosome Location	chr6:25325611-25325612
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr6:25316945..25319715-chr6:25323364..25325803,2	MCF-7	breast:

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

rSNPs within LD-proxies of this variant (count:23)

rs_ID	r²[population]
rs12055533	0.81[ASN][1000 genomes]
rs1989206	0.83[ASN][1000 genomes]
rs2143022	0.83[ASN][1000 genomes]
rs2252012	0.83[ASN][1000 genomes]
rs2328878	0.81[ASN][1000 genomes]
rs2690109	0.81[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2690115	0.80[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2690120	0.83[ASN][1000 genomes]
rs2690123	0.82[ASN][1000 genomes]
rs2690125	0.81[ASN][1000 genomes]
rs2690129	0.81[ASN][1000 genomes]
rs2690131	0.80[ASN][1000 genomes]
rs2744296	0.82[ASN][1000 genomes]
rs2744299	0.83[ASN][1000 genomes]
rs2744302	0.81[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2744303	0.81[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4712908	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9348670	0.81[ASN][1000 genomes]
rs9356973	0.81[ASN][1000 genomes]
rs9358850	0.81[ASN][1000 genomes]
rs9358851	0.82[ASN][1000 genomes]
rs9379751	0.81[ASN][1000 genomes]
rs9467465	0.81[AFR][1000 genomes];0.83[ASN][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	nsv883485	chr6:25259137-25437986	Weak transcription Enhancers Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS Strong transcription Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
2	nsv883486	chr6:25260434-25422369	Weak transcription Enhancers Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats Strong transcription Bivalent/Poised TSS Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
3	nsv883487	chr6:25280119-25508868	Weak transcription Enhancers Flanking Active TSS Strong transcription Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:58 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:25306600-25331400	Weak transcription	Spleen	Spleen
2	chr6:25313400-25329800	Weak transcription	Primary T cells from cord blood	blood
3	chr6:25313800-25325800	Weak transcription	Monocytes-CD14+_RO01746	blood
4	chr6:25313800-25326800	Weak transcription	Sigmoid Colon	Sigmoid Colon
5	chr6:25313800-25331400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
6	chr6:25315400-25329600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
7	chr6:25316200-25326800	Weak transcription	Gastric	stomach
8	chr6:25316400-25326600	Weak transcription	Fetal Kidney	kidney
9	chr6:25321000-25329400	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
10	chr6:25321000-25329600	Weak transcription	H9 Cell Line	embryonic stem cell
11	chr6:25321000-25331400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
12	chr6:25321200-25326000	Weak transcription	HUES48 Cell Line	embryonic stem cell
13	chr6:25321200-25329200	Weak transcription	iPS-18 Cell Line	embryonic stem cell
14	chr6:25321200-25329400	Weak transcription	HUES6 Cell Line	embryonic stem cell
15	chr6:25321200-25329400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
16	chr6:25321600-25329200	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
17	chr6:25321600-25329400	Weak transcription	iPS-20b Cell Line	embryonic stem cell
18	chr6:25321600-25329600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
19	chr6:25321600-25329800	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
20	chr6:25321600-25341200	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
21	chr6:25323000-25333200	Weak transcription	Rectal Mucosa Donor 29	rectum
22	chr6:25324000-25326000	Enhancers	Fetal Lung	lung
23	chr6:25324400-25327200	Weak transcription	Stomach Mucosa	stomach
24	chr6:25324600-25326600	Weak transcription	Small Intestine	intestine
25	chr6:25324600-25326800	Weak transcription	Brain Anterior Caudate	brain
26	chr6:25324600-25327000	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
27	chr6:25324600-25328000	Weak transcription	Brain Germinal Matrix	brain
28	chr6:25324600-25329200	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
29	chr6:25324600-25329600	Weak transcription	Brain Substantia Nigra	brain
30	chr6:25324600-25330400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
31	chr6:25324600-25331600	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
32	chr6:25324800-25327000	Weak transcription	Duodenum Mucosa	Duodenum
33	chr6:25325000-25327400	Weak transcription	HUES64 Cell Line	embryonic stem cell
34	chr6:25325000-25329400	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
35	chr6:25325000-25331600	Weak transcription	Adipose Nuclei	Adipose
36	chr6:25325200-25326200	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
37	chr6:25325200-25326600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
38	chr6:25325200-25326600	Weak transcription	Aorta	Aorta
39	chr6:25325200-25326600	Weak transcription	Left Ventricle	heart
40	chr6:25325200-25327200	Weak transcription	Fetal Intestine Large	intestine
41	chr6:25325200-25327200	Weak transcription	Ovary	ovary
42	chr6:25325200-25327200	Weak transcription	Right Atrium	heart
43	chr6:25325200-25327400	Weak transcription	Fetal Intestine Small	intestine
44	chr6:25325200-25327600	Enhancers	iPS-15b Cell Line	embryonic stem cell
45	chr6:25325200-25328800	Enhancers	Fetal Heart	heart
46	chr6:25325200-25329400	Weak transcription	Breast Myoepithelial Primary Cells	Breast
47	chr6:25325200-25330200	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
48	chr6:25325200-25330200	Weak transcription	Esophagus	oesophagus
49	chr6:25325200-25331400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
50	chr6:25325200-25331400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell

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