Variant report

Variant	rs10842509
Chromosome Location	chr12:25375946-25375947
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr12:25374667..25376275-chr12:25538589..25540510,2	MCF-7	breast:

Extended variants
information (count: 41 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:34)

rs_ID	r²[population]
rs10842507	1.00[AFR][1000 genomes];0.97[EUR][1000 genomes]
rs10842508	0.92[CHB][hapmap];0.92[ASN][1000 genomes]
rs10842511	0.97[ASN][1000 genomes]
rs11047877	1.00[AFR][1000 genomes];0.93[EUR][1000 genomes]
rs11047880	0.90[CHB][hapmap];1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];0.93[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs11047882	0.92[CHB][hapmap];0.86[ASN][1000 genomes]
rs11047892	1.00[AFR][1000 genomes];0.97[EUR][1000 genomes]
rs11047893	1.00[AFR][1000 genomes];0.96[EUR][1000 genomes]
rs11047911	0.86[EUR][1000 genomes]
rs11047918	0.92[CHB][hapmap];0.87[EUR][1000 genomes]
rs12228277	0.84[CHB][hapmap];0.94[AMR][1000 genomes];0.87[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs12230737	0.92[CHB][hapmap];0.94[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs12230955	1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs12423011	0.82[EUR][1000 genomes]
rs12423489	0.92[CHB][hapmap];1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];0.94[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs12424283	0.92[CHB][hapmap]
rs12427141	0.92[CHB][hapmap];1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs17329424	0.88[EUR][1000 genomes]
rs2970532	0.84[CHB][hapmap];0.87[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs3924649	0.92[CHB][hapmap]
rs4356326	0.83[AMR][1000 genomes]
rs4623993	0.92[CHB][hapmap];0.83[EUR][1000 genomes]
rs4963857	1.00[AFR][1000 genomes]
rs61016093	0.85[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs61761101	0.94[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs61763584	1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs73071272	0.88[AMR][1000 genomes];0.85[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs73073207	1.00[AFR][1000 genomes];0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs73077316	0.82[AMR][1000 genomes]
rs73077322	0.82[AMR][1000 genomes]
rs7309862	0.86[EUR][1000 genomes]
rs7312175	0.92[CHB][hapmap];0.83[AMR][1000 genomes]
rs7973746	0.92[CHB][hapmap];0.86[EUR][1000 genomes]
rs7979296	0.92[CHB][hapmap];0.83[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:7 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv898922	chr12:25274593-25408047	Genic enhancers Flanking Active TSS Enhancers Active TSS Flanking Bivalent TSS/Enh Weak transcription Strong transcription Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	15 gene(s)	inside rSNPs	diseases
2	nsv1048631	chr12:25353517-25378661	Weak transcription Strong transcription Enhancers Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region miRNA target site	4 gene(s)	inside rSNPs	diseases
3	nsv898923	chr12:25357680-25397282	Strong transcription Weak transcription Enhancers Genic enhancers Transcr. at gene 5' and 3' Flanking Active TSS ZNF genes & repeats Active TSS	TF binding region CpG island Chromatin interactive region miRNA target site	5 gene(s)	inside rSNPs	diseases
4	nsv898924	chr12:25357680-25398972	Weak transcription Strong transcription Enhancers Genic enhancers Active TSS Transcr. at gene 5' and 3' Flanking Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region miRNA target site	5 gene(s)	inside rSNPs	diseases
5	nsv557798	chr12:25359841-25397282	Strong transcription Weak transcription Enhancers Genic enhancers Flanking Active TSS Active TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region miRNA target site	5 gene(s)	inside rSNPs	diseases
6	nsv898925	chr12:25367669-25398972	Strong transcription Weak transcription Enhancers Genic enhancers Flanking Active TSS ZNF genes & repeats Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region miRNA target site	5 gene(s)	inside rSNPs	diseases
7	nsv898926	chr12:25367669-25408047	Weak transcription Bivalent/Poised TSS Genic enhancers Enhancers Flanking Active TSS Strong transcription Transcr. at gene 5' and 3' Active TSS Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region miRNA target site	10 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:114 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:25348600-25402200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
2	chr12:25348600-25403200	Weak transcription	Spleen	Spleen
3	chr12:25349000-25386000	Weak transcription	Left Ventricle	heart
4	chr12:25349000-25402400	Weak transcription	Right Ventricle	heart
5	chr12:25349400-25388200	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
6	chr12:25349400-25388600	Weak transcription	NHLF	lung
7	chr12:25349400-25393800	Weak transcription	Brain Inferior Temporal Lobe	brain
8	chr12:25349400-25396000	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
9	chr12:25349400-25401800	Weak transcription	Fetal Brain Male	brain
10	chr12:25349400-25402600	Weak transcription	Brain Germinal Matrix	brain
11	chr12:25349600-25389000	Weak transcription	Brain Angular Gyrus	brain
12	chr12:25349600-25394600	Weak transcription	Rectal Smooth Muscle	rectum
13	chr12:25349600-25402600	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
14	chr12:25349600-25402600	Weak transcription	Brain Cingulate Gyrus	brain
15	chr12:25349600-25402600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
16	chr12:25349600-25402600	Weak transcription	Stomach Smooth Muscle	stomach
17	chr12:25349800-25379200	Weak transcription	Brain Anterior Caudate	brain
18	chr12:25349800-25386200	Weak transcription	Hela-S3	cervix
19	chr12:25349800-25390200	Weak transcription	K562	blood
20	chr12:25350000-25402800	Weak transcription	Ovary	ovary
21	chr12:25353200-25378800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
22	chr12:25354000-25402400	Weak transcription	Skeletal Muscle Male	skeletal muscle
23	chr12:25354400-25378400	Weak transcription	HMEC	breast
24	chr12:25354400-25402200	Weak transcription	Pancreas	Pancrea
25	chr12:25354600-25389000	Weak transcription	HSMMtube	muscle
26	chr12:25355800-25396000	Weak transcription	Small Intestine	intestine
27	chr12:25356600-25377600	Weak transcription	Gastric	stomach
28	chr12:25356600-25402600	Weak transcription	Fetal Heart	heart
29	chr12:25360200-25379200	Weak transcription	Muscle Satellite Cultured Cells	--
30	chr12:25360200-25380200	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
31	chr12:25360400-25377000	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
32	chr12:25360800-25388600	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
33	chr12:25360800-25389200	Weak transcription	Primary T helper naive cells from peripheral blood	blood
34	chr12:25360800-25402200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
35	chr12:25361000-25376800	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
36	chr12:25361000-25378600	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
37	chr12:25361000-25379800	Weak transcription	Fetal Muscle Leg	muscle
38	chr12:25361000-25383800	Weak transcription	NHEK	skin
39	chr12:25361000-25388000	Weak transcription	A549	lung
40	chr12:25361000-25388600	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
41	chr12:25361000-25388800	Weak transcription	Esophagus	oesophagus
42	chr12:25361000-25395800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
43	chr12:25361000-25402600	Weak transcription	Cortex derived primary cultured neurospheres	brain
44	chr12:25361000-25402600	Weak transcription	Fetal Brain Female	brain
45	chr12:25361200-25388400	Weak transcription	Sigmoid Colon	Sigmoid Colon
46	chr12:25361200-25389200	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
47	chr12:25361800-25376800	Weak transcription	Skeletal Muscle Female	skeletal muscle
48	chr12:25361800-25380000	Weak transcription	Fetal Muscle Trunk	muscle
49	chr12:25362000-25376800	Weak transcription	Breast Myoepithelial Primary Cells	Breast
50	chr12:25362000-25402400	Weak transcription	HepG2	liver

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