Variant report

Variant	rs2296572
Chromosome Location	chr13:48660683-48660684
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr13:48660649..48663796-chr13:48667591..48670650,5	MCF-7	breast:
2	chr13:48653583..48656519-chr13:48659541..48662277,2	K562	blood:

Variant related genes	Relation type
ENSG00000136146	Chromatin interaction

Extended variants
information (count: 77 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:75)

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];1.00[YRI][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]
rs11838821	1.00[EUR][1000 genomes]
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	0.89[CHB][hapmap];1.00[JPT][hapmap];0.93[YRI][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];1.00[YRI][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[YRI][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]
rs12428098	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]
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];1.00[YRI][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];1.00[YRI][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]
rs35535367	1.00[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs3742108	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.87[AFR][1000 genomes];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3782979	0.90[CHB][hapmap];0.92[YRI][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]
rs57530384	1.00[EUR][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]
rs73485345	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	0.90[CHB][hapmap]
rs7990408	0.85[AFR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7997347	0.89[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	chr13:48640200-48661200	Strong transcription	Primary T cells fromperipheralblood	blood
2	chr13:48645200-48661000	Strong transcription	Primary T helper cells PMA-I stimulated	--
3	chr13:48645800-48661000	Strong transcription	HepG2	liver
4	chr13:48646200-48661000	Strong transcription	Primary T helper cells fromperipheralblood	blood
5	chr13:48647000-48660800	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
6	chr13:48647000-48662400	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
7	chr13:48647400-48663600	Weak transcription	Small Intestine	intestine
8	chr13:48648600-48660800	Strong transcription	HUES48 Cell Line	embryonic stem cell
9	chr13:48648600-48661000	Strong transcription	Primary hematopoietic stem cells short term culture	blood
10	chr13:48648600-48667400	Weak transcription	Pancreatic Islets	Pancreatic Islet
11	chr13:48648800-48660800	Strong transcription	Primary B cells from cord blood	blood
12	chr13:48649400-48661000	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
13	chr13:48649600-48663400	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
14	chr13:48649800-48661200	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
15	chr13:48649800-48661600	Strong transcription	Primary monocytes fromperipheralblood	blood
16	chr13:48649800-48662200	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
17	chr13:48650000-48661000	Strong transcription	HUES6 Cell Line	embryonic stem cell
18	chr13:48650000-48662400	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
19	chr13:48650200-48660800	Strong transcription	Dnd41	blood
20	chr13:48650200-48662400	Strong transcription	Monocytes-CD14+_RO01746	blood
21	chr13:48650400-48664800	Weak transcription	Fetal Heart	heart
22	chr13:48650800-48661000	Strong transcription	Primary T helper naive cells fromperipheralblood	blood
23	chr13:48651600-48661000	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
24	chr13:48652800-48663200	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
25	chr13:48652800-48668200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
26	chr13:48653000-48660800	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
27	chr13:48653000-48660800	Weak transcription	Psoas Muscle	Psoas
28	chr13:48653000-48661000	Strong transcription	Primary B cells from peripheral blood	blood
29	chr13:48653000-48667800	Weak transcription	Stomach Mucosa	stomach
30	chr13:48653000-48668200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
31	chr13:48653200-48668200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
32	chr13:48653800-48667600	Weak transcription	A549	lung
33	chr13:48654200-48666800	Weak transcription	Pancreas	Pancrea
34	chr13:48654200-48667600	Weak transcription	Right Ventricle	heart
35	chr13:48655400-48660800	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
36	chr13:48655400-48662200	Weak transcription	Hela-S3	cervix
37	chr13:48655400-48666000	Weak transcription	Esophagus	oesophagus
38	chr13:48655400-48666000	Weak transcription	Spleen	Spleen
39	chr13:48655400-48667000	Weak transcription	Gastric	stomach
40	chr13:48655400-48667600	Weak transcription	H9 Cell Line	embryonic stem cell
41	chr13:48655400-48668000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
42	chr13:48655400-48668200	Weak transcription	Aorta	Aorta
43	chr13:48655600-48666800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
44	chr13:48656200-48666000	Weak transcription	K562	blood
45	chr13:48656200-48667000	Weak transcription	HUVEC	blood vessel
46	chr13:48656200-48668000	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
47	chr13:48656800-48661000	Strong transcription	GM12878-XiMat	blood
48	chr13:48657000-48660800	Strong transcription	Primary T helper 17 cells PMA-I stimulated	--
49	chr13:48657400-48666800	Weak transcription	iPS-15b Cell Line	embryonic stem cell
50	chr13:48657400-48666800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain

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