Variant report

Variant	rs12428098
Chromosome Location	chr13:48663358-48663359
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	chr13:48662663..48666159-chr13:48666999..48670435,6	MCF-7	breast:
2	chr13:48660649..48663796-chr13:48667591..48670650,5	MCF-7	breast:

Variant related genes	Relation type
ENSG00000136146	Chromatin interaction

Extended variants
information (count: 74 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:72)

rs_ID	r²[population]
rs11148101	1.00[AFR][1000 genomes];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11148102	1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[AFR][1000 genomes];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11148103	1.00[AFR][1000 genomes];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11148104	0.91[AFR][1000 genomes];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11148105	1.00[AFR][1000 genomes];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11838539	1.00[CHB][hapmap]
rs11840013	1.00[AFR][1000 genomes];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11840146	1.00[EUR][1000 genomes]
rs11841025	1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[AFR][1000 genomes];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11841089	0.95[AFR][1000 genomes];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11841517	1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[AFR][1000 genomes];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11842190	1.00[EUR][1000 genomes]
rs11842654	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12427769	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12428738	0.95[AFR][1000 genomes];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs12428782	0.89[AFR][1000 genomes];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12428797	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12429895	0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12429926	0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12430608	1.00[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs12584124	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12584625	0.93[AFR][1000 genomes];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12584738	1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[AFR][1000 genomes];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12585232	1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[AFR][1000 genomes];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12585517	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12585766	0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1410116	1.00[CHB][hapmap];0.98[ASN][1000 genomes]
rs2148247	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2296572	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35535367	1.00[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs3742108	1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[AFR][1000 genomes];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3782979	0.88[CHB][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs56670154	0.93[AFR][1000 genomes];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs58080658	0.87[AFR][1000 genomes];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs59447207	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs59845585	1.00[EUR][1000 genomes]
rs59991172	1.00[EUR][1000 genomes]
rs60398625	1.00[EUR][1000 genomes]
rs60828855	0.93[AFR][1000 genomes];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61403342	0.89[AFR][1000 genomes];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73477042	1.00[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs73479175	0.89[AFR][1000 genomes];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73479183	0.89[AFR][1000 genomes];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73479186	0.91[AFR][1000 genomes];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73479195	0.93[AFR][1000 genomes];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73479199	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73479200	0.91[AFR][1000 genomes];0.91[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs73481207	0.93[AFR][1000 genomes];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73481212	1.00[ASN][1000 genomes]
rs73481217	1.00[AFR][1000 genomes];0.83[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73481223	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73481228	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73481239	0.93[AFR][1000 genomes];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73481250	0.93[AFR][1000 genomes];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73481261	0.91[AFR][1000 genomes];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73481266	0.91[AFR][1000 genomes];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73481271	0.91[AFR][1000 genomes];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73481288	0.86[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs73483108	1.00[EUR][1000 genomes]
rs73483122	0.84[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs73485349	1.00[EUR][1000 genomes]
rs73485356	1.00[EUR][1000 genomes]
rs73487241	1.00[EUR][1000 genomes]
rs73487264	1.00[EUR][1000 genomes]
rs73487269	1.00[EUR][1000 genomes]
rs73489207	1.00[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs73489232	1.00[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs73493331	1.00[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs73493345	1.00[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs7982479	0.88[CHB][hapmap]
rs7990408	0.85[AFR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7997347	1.00[CHB][hapmap]

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	nsv430556	chr13:48516799-48679099	ZNF genes & repeats Enhancers Weak transcription Strong transcription Flanking Active TSS Genic enhancers Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	40 gene(s)	inside rSNPs	diseases
2	nsv832601	chr13:48569952-48735939	Strong transcription Enhancers Weak transcription Flanking Active TSS Active TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	42 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:126 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr13:48647400-48663600	Weak transcription	Small Intestine	intestine
2	chr13:48648600-48667400	Weak transcription	Pancreatic Islets	Pancreatic Islet
3	chr13:48649600-48663400	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
4	chr13:48650400-48664800	Weak transcription	Fetal Heart	heart
5	chr13:48652800-48668200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
6	chr13:48653000-48667800	Weak transcription	Stomach Mucosa	stomach
7	chr13:48653000-48668200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
8	chr13:48653200-48668200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
9	chr13:48653800-48667600	Weak transcription	A549	lung
10	chr13:48654200-48666800	Weak transcription	Pancreas	Pancrea
11	chr13:48654200-48667600	Weak transcription	Right Ventricle	heart
12	chr13:48655400-48666000	Weak transcription	Esophagus	oesophagus
13	chr13:48655400-48666000	Weak transcription	Spleen	Spleen
14	chr13:48655400-48667000	Weak transcription	Gastric	stomach
15	chr13:48655400-48667600	Weak transcription	H9 Cell Line	embryonic stem cell
16	chr13:48655400-48668000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
17	chr13:48655400-48668200	Weak transcription	Aorta	Aorta
18	chr13:48655600-48666800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
19	chr13:48656200-48666000	Weak transcription	K562	blood
20	chr13:48656200-48667000	Weak transcription	HUVEC	blood vessel
21	chr13:48656200-48668000	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
22	chr13:48657400-48666800	Weak transcription	iPS-15b Cell Line	embryonic stem cell
23	chr13:48657400-48666800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
24	chr13:48657400-48667600	Weak transcription	Brain Angular Gyrus	brain
25	chr13:48657400-48668000	Weak transcription	HSMMtube	muscle
26	chr13:48657600-48664800	Weak transcription	Primary T helper naive cells from peripheral blood	blood
27	chr13:48657600-48667000	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
28	chr13:48657600-48667600	Weak transcription	Brain Substantia Nigra	brain
29	chr13:48657800-48667200	Weak transcription	Placenta Amnion	Placenta Amnion
30	chr13:48658000-48667000	Weak transcription	Cortex derived primary cultured neurospheres	brain
31	chr13:48658000-48667000	Weak transcription	Rectal Smooth Muscle	rectum
32	chr13:48658000-48667200	Weak transcription	NH-A	brain
33	chr13:48658000-48667600	Weak transcription	Colonic Mucosa	Colon
34	chr13:48658200-48663600	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
35	chr13:48658200-48667800	Weak transcription	Brain Cingulate Gyrus	brain
36	chr13:48658400-48666800	Weak transcription	Lung	lung
37	chr13:48658400-48667000	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
38	chr13:48658600-48666600	Weak transcription	Primary hematopoietic stem cells	blood
39	chr13:48658800-48667600	Weak transcription	Brain Hippocampus Middle	brain
40	chr13:48658800-48667600	Weak transcription	Fetal Brain Male	brain
41	chr13:48658800-48667600	Weak transcription	Fetal Lung	lung
42	chr13:48659000-48667800	Weak transcription	Fetal Kidney	kidney
43	chr13:48659400-48667800	Weak transcription	Brain Germinal Matrix	brain
44	chr13:48659600-48665800	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
45	chr13:48659600-48666000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
46	chr13:48659600-48667600	Weak transcription	H1 Cell Line	embryonic stem cell
47	chr13:48659600-48668000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
48	chr13:48659800-48663400	Weak transcription	Skeletal Muscle Male	skeletal muscle
49	chr13:48659800-48664400	Weak transcription	Stomach Smooth Muscle	stomach
50	chr13:48659800-48665000	Weak transcription	Colon Smooth Muscle	Colon

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