Variant report

Variant	rs16929830
Chromosome Location	chr12:26139058-26139059
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr12:26110616..26112920-chr12:26135351..26139719,3	MCF-7	breast:

Variant related genes	Relation type
ENSG00000123094	Chromatin interaction
ENSG00000246695	Chromatin interaction

Extended variants
information (count: 72 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:68)

rs_ID	r²[population]
rs10505990	0.82[JPT][hapmap]
rs10842643	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10842644	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10842653	1.00[CEU][hapmap];0.88[CHB][hapmap];0.90[JPT][hapmap];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs11048360	1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11048372	0.89[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs11048378	1.00[CEU][hapmap];0.94[CHB][hapmap];0.91[JPT][hapmap];0.83[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs11048379	1.00[CEU][hapmap];0.94[CHB][hapmap];0.91[JPT][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs11048380	1.00[CEU][hapmap];0.94[CHB][hapmap];0.91[JPT][hapmap];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs11048381	0.97[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs11048382	0.97[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs11048383	0.98[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs11048384	0.98[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs11048389	0.93[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs11048390	0.94[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs1120064	1.00[CEU][hapmap];1.00[CHB][hapmap];0.90[JPT][hapmap];0.97[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs1149804	0.88[CHB][hapmap];1.00[JPT][hapmap];0.84[AMR][1000 genomes];0.98[ASN][1000 genomes]
rs11561207	0.97[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs12227689	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12578169	0.81[CHB][hapmap];0.90[JPT][hapmap];0.84[AMR][1000 genomes]
rs12579489	0.82[AMR][1000 genomes]
rs12581361	0.81[AMR][1000 genomes]
rs12812200	0.81[CHB][hapmap];0.94[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs12812752	0.94[CHB][hapmap];0.91[JPT][hapmap];0.98[AMR][1000 genomes];0.93[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs12813641	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs12818478	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12831248	0.89[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs1390326	0.82[CHB][hapmap];0.90[JPT][hapmap];0.82[AMR][1000 genomes]
rs1495660	0.82[AMR][1000 genomes]
rs1691889	0.84[AMR][1000 genomes];0.98[ASN][1000 genomes]
rs16929784	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs16929817	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs16929846	0.87[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs16929940	0.82[CHB][hapmap];0.91[JPT][hapmap];0.85[AMR][1000 genomes]
rs16929945	0.82[CHB][hapmap];0.91[JPT][hapmap];0.84[AMR][1000 genomes]
rs16929950	0.82[CHB][hapmap];0.91[JPT][hapmap];0.85[AMR][1000 genomes]
rs16929958	0.81[CHB][hapmap];0.90[JPT][hapmap];0.85[AMR][1000 genomes]
rs2055180	1.00[CEU][hapmap];0.94[CHB][hapmap];0.90[JPT][hapmap];0.94[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs2132317	1.00[CEU][hapmap];0.94[CHB][hapmap];0.95[JPT][hapmap];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2279680	1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs2343201	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2643941	1.00[CEU][hapmap];0.81[CHB][hapmap];0.90[JPT][hapmap];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs34294573	0.95[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs34595529	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs35924984	0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs3741546	0.82[AMR][1000 genomes]
rs3741547	0.81[AMR][1000 genomes]
rs3803009	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs58299475	0.82[AMR][1000 genomes]
rs59757232	0.82[AMR][1000 genomes]
rs60335536	0.84[AMR][1000 genomes]
rs61622173	0.98[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs6487525	1.00[CEU][hapmap];0.94[CHB][hapmap];0.90[JPT][hapmap];0.94[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs706524	0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs706526	0.84[AMR][1000 genomes];0.98[ASN][1000 genomes]
rs706531	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs706532	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs706533	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs706538	1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[AMR][1000 genomes];0.98[ASN][1000 genomes]
rs7132590	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7134721	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7298162	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7953171	0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7963603	1.00[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7963856	0.95[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs829837	0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs829987	0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs853656	0.82[AMR][1000 genomes];0.98[ASN][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	esv2758300	chr12:25992331-26161116	Enhancers Weak transcription Active TSS Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent Enhancer Strong transcription Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	38 gene(s)	inside rSNPs	diseases
2	esv2759886	chr12:25992331-26161116	Enhancers Strong transcription Bivalent Enhancer Weak transcription Flanking Active TSS ZNF genes & repeats Active TSS Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA	38 gene(s)	inside rSNPs	diseases
3	nsv898931	chr12:26123345-26192936	Weak transcription Enhancers Flanking Active TSS ZNF genes & repeats Active TSS Genic enhancers Strong transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
4	nsv522351	chr12:26127230-26149703	Weak transcription Enhancers Active TSS Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:70 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:26117600-26150000	Weak transcription	Hela-S3	cervix
2	chr12:26129400-26139400	Weak transcription	Right Ventricle	heart
3	chr12:26129800-26143000	Enhancers	Colon Smooth Muscle	Colon
4	chr12:26131000-26139200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
5	chr12:26131000-26145400	Weak transcription	Lung	lung
6	chr12:26131000-26146000	Weak transcription	Muscle Satellite Cultured Cells	--
7	chr12:26131000-26146200	Weak transcription	HSMM	muscle
8	chr12:26132400-26141600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
9	chr12:26132400-26146800	Weak transcription	Brain Inferior Temporal Lobe	brain
10	chr12:26133000-26139200	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
11	chr12:26133000-26144600	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
12	chr12:26133000-26144600	Weak transcription	HMEC	breast
13	chr12:26133000-26144600	Weak transcription	NHEK	skin
14	chr12:26133000-26145200	Weak transcription	NH-A	brain
15	chr12:26133000-26145200	Weak transcription	Osteobl	bone
16	chr12:26134200-26148000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
17	chr12:26134400-26141600	Weak transcription	NHDF-Ad	bronchial
18	chr12:26134400-26145400	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
19	chr12:26134400-26145400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
20	chr12:26134400-26147800	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
21	chr12:26135600-26139400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
22	chr12:26135800-26139400	Weak transcription	Small Intestine	intestine
23	chr12:26136000-26141400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
24	chr12:26136400-26139800	Enhancers	Rectal Smooth Muscle	rectum
25	chr12:26136800-26142000	Enhancers	Breast Myoepithelial Primary Cells	Breast
26	chr12:26137200-26140200	Enhancers	Ovary	ovary
27	chr12:26137200-26140200	Enhancers	Psoas Muscle	Psoas
28	chr12:26137200-26143200	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
29	chr12:26137400-26139200	Enhancers	Duodenum Smooth Muscle	Duodenum
30	chr12:26137400-26139400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
31	chr12:26137400-26139400	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
32	chr12:26137400-26139800	Enhancers	HUES6 Cell Line	embryonic stem cell
33	chr12:26137600-26139400	Enhancers	HUES64 Cell Line	embryonic stem cell
34	chr12:26137600-26139600	Enhancers	iPS-18 Cell Line	embryonic stem cell
35	chr12:26137600-26139800	Enhancers	iPS-15b Cell Line	embryonic stem cell
36	chr12:26137800-26139400	Enhancers	Brain Angular Gyrus	brain
37	chr12:26137800-26139400	Enhancers	Brain Hippocampus Middle	brain
38	chr12:26137800-26139600	Enhancers	HUES48 Cell Line	embryonic stem cell
39	chr12:26137800-26139600	Enhancers	iPS-20b Cell Line	embryonic stem cell
40	chr12:26137800-26139800	Enhancers	ES-I3 Cell Line	embryonic stem cell
41	chr12:26137800-26139800	Enhancers	Foreskin Melanocyte Primary Cells skin01	Skin
42	chr12:26138000-26139200	Enhancers	ES-WA7 Cell Line	embryonic stem cell
43	chr12:26138000-26139400	Enhancers	H1 Cell Line	embryonic stem cell
44	chr12:26138000-26139600	Enhancers	Brain Substantia Nigra	brain
45	chr12:26138000-26139800	Enhancers	H9 Cell Line	embryonic stem cell
46	chr12:26138000-26139800	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
47	chr12:26138000-26139800	Enhancers	Skeletal Muscle Female	skeletal muscle
48	chr12:26138000-26140400	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
49	chr12:26138000-26140400	Enhancers	Fetal Intestine Large	intestine
50	chr12:26138000-26140400	Enhancers	Fetal Intestine Small	intestine

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