Variant report

Variant	rs3908968
Chromosome Location	chr13:52180568-52180569
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr13:52175306..52178787-chr13:52179968..52182908,3	K562	blood:
2	chr13:52156968..52159936-chr13:52177201..52181102,3	MCF-7	breast:
3	chr13:52025637..52029103-chr13:52175975..52180992,5	MCF-7	breast:

Variant related genes	Relation type
ENSG00000139668	Chromatin interaction
ENSG00000224892	Chromatin interaction
ENSG00000236778	Chromatin interaction
ENSG00000102786	Chromatin interaction

Extended variants
information (count: 59 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:58)

rs_ID	r²[population]
rs1060562	0.91[ASN][1000 genomes]
rs12146894	1.00[CHD][hapmap];0.94[JPT][hapmap];0.91[ASN][1000 genomes]
rs12427748	1.00[CEU][hapmap];1.00[CHD][hapmap];0.81[JPT][hapmap];1.00[TSI][hapmap];0.86[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs1475195	1.00[CEU][hapmap];0.94[JPT][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs17075907	1.00[AFR][1000 genomes];0.81[EUR][1000 genomes]
rs17532412	1.00[CEU][hapmap];1.00[CHD][hapmap];0.94[JPT][hapmap];1.00[TSI][hapmap];0.85[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs17532524	1.00[AFR][1000 genomes];0.86[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs17532936	1.00[AFR][1000 genomes];0.85[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs17597215	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs17597531	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.94[JPT][hapmap];1.00[TSI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1885854	1.00[ASW][hapmap];1.00[CEU][hapmap];0.94[JPT][hapmap];1.00[TSI][hapmap];1.00[AFR][1000 genomes];0.82[EUR][1000 genomes]
rs2296028	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHD][hapmap];0.94[JPT][hapmap];0.88[TSI][hapmap];1.00[AFR][1000 genomes];0.82[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2296029	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHD][hapmap];0.94[JPT][hapmap];1.00[TSI][hapmap];1.00[AFR][1000 genomes];0.83[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2780461	1.00[CEU][hapmap];0.80[JPT][hapmap];0.84[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs2897944	1.00[CHD][hapmap];0.94[JPT][hapmap];0.90[ASN][1000 genomes]
rs41292776	1.00[AFR][1000 genomes];0.85[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs4555048	1.00[ASW][hapmap];1.00[CEU][hapmap];0.95[CHD][hapmap];1.00[GIH][hapmap];0.94[JPT][hapmap];1.00[TSI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs481133	1.00[ASW][hapmap]
rs483879	0.94[CEU][hapmap];0.81[JPT][hapmap];1.00[AFR][1000 genomes];0.84[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs488261	1.00[AFR][1000 genomes];0.88[EUR][1000 genomes]
rs491103	0.87[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs4943003	1.00[ASW][hapmap]
rs60757273	1.00[AFR][1000 genomes];0.86[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs6561638	1.00[ASW][hapmap]
rs73199734	1.00[AFR][1000 genomes];0.85[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs73199746	1.00[AFR][1000 genomes];0.86[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs9526783	1.00[CEU][hapmap];0.94[JPT][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs9526786	1.00[ASW][hapmap];1.00[CEU][hapmap];0.95[CHD][hapmap];1.00[GIH][hapmap];0.94[JPT][hapmap];1.00[TSI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs9526788	1.00[ASW][hapmap];1.00[CEU][hapmap];0.84[GIH][hapmap];0.94[JPT][hapmap];1.00[TSI][hapmap];1.00[AFR][1000 genomes];0.82[AMR][1000 genomes];0.90[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs9526793	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHD][hapmap];0.94[JPT][hapmap];1.00[TSI][hapmap];1.00[AFR][1000 genomes];0.86[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs9526794	1.00[AFR][1000 genomes];0.85[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs9535661	1.00[ASW][hapmap]
rs9535663	1.00[ASW][hapmap]
rs9535665	1.00[ASW][hapmap]
rs9535699	1.00[ASW][hapmap]
rs9535714	1.00[CEU][hapmap];0.93[JPT][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9535715	1.00[CEU][hapmap];0.94[JPT][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9535717	1.00[ASW][hapmap];1.00[CEU][hapmap];0.93[GIH][hapmap];0.93[JPT][hapmap];1.00[TSI][hapmap];1.00[AFR][1000 genomes];0.92[AMR][1000 genomes];0.94[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs9535722	1.00[ASW][hapmap];1.00[CEU][hapmap];0.93[GIH][hapmap];0.94[JPT][hapmap];1.00[TSI][hapmap];1.00[AFR][1000 genomes];0.92[AMR][1000 genomes];0.94[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs9535734	0.91[ASN][1000 genomes]
rs9535735	0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs9535737	1.00[AFR][1000 genomes];0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs9535738	0.88[CHB][hapmap];0.84[JPT][hapmap];1.00[AFR][1000 genomes];0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs9535739	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHD][hapmap];0.90[GIH][hapmap];0.94[JPT][hapmap];1.00[TSI][hapmap];1.00[AFR][1000 genomes];0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs9535741	1.00[AFR][1000 genomes];0.92[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs9535743	1.00[AFR][1000 genomes];0.86[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs9535744	1.00[CEU][hapmap];1.00[CHD][hapmap];0.94[JPT][hapmap];1.00[TSI][hapmap];0.85[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs9535745	1.00[AFR][1000 genomes];0.86[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs9535746	1.00[ASW][hapmap];1.00[CEU][hapmap];0.94[JPT][hapmap];1.00[TSI][hapmap];1.00[AFR][1000 genomes];0.82[EUR][1000 genomes]
rs9535747	1.00[CEU][hapmap];0.94[JPT][hapmap];1.00[AFR][1000 genomes];0.86[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs9535748	1.00[CHD][hapmap];0.94[JPT][hapmap];0.90[ASN][1000 genomes]
rs9535749	1.00[CEU][hapmap];0.84[JPT][hapmap];0.85[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs9535750	0.94[CEU][hapmap];0.93[JPT][hapmap];1.00[AFR][1000 genomes];0.85[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs9535751	1.00[AFR][1000 genomes];0.85[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs9535752	1.00[AFR][1000 genomes];0.85[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs9535753	1.00[CEU][hapmap];0.94[JPT][hapmap];0.85[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs9535755	1.00[AFR][1000 genomes];0.85[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs9535756	1.00[CEU][hapmap];0.87[JPT][hapmap];1.00[AFR][1000 genomes];0.85[EUR][1000 genomes];0.90[ASN][1000 genomes]

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

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv832612	chr13:52176983-52362525	Weak transcription Enhancers Genic enhancers Strong transcription Flanking Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Active TSS Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:87 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr13:52160200-52181400	Weak transcription	Thymus	Thymus
2	chr13:52163200-52182600	Weak transcription	Ovary	ovary
3	chr13:52165600-52188600	Weak transcription	Fetal Stomach	stomach
4	chr13:52166000-52181200	Weak transcription	NH-A	brain
5	chr13:52166200-52181200	Weak transcription	NHLF	lung
6	chr13:52166400-52181200	Weak transcription	Hela-S3	cervix
7	chr13:52168400-52194400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
8	chr13:52169800-52187000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
9	chr13:52169800-52188600	Weak transcription	Esophagus	oesophagus
10	chr13:52169800-52188600	Weak transcription	Gastric	stomach
11	chr13:52173600-52190400	Weak transcription	Fetal Heart	heart
12	chr13:52174200-52183000	Weak transcription	iPS-18 Cell Line	embryonic stem cell
13	chr13:52174200-52188200	Weak transcription	Primary T cells fromperipheralblood	blood
14	chr13:52174400-52188400	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
15	chr13:52174600-52183000	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
16	chr13:52174800-52181200	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
17	chr13:52174800-52181400	Weak transcription	GM12878-XiMat	blood
18	chr13:52175000-52181200	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
19	chr13:52175000-52181400	Weak transcription	Aorta	Aorta
20	chr13:52175000-52183000	Weak transcription	HUES48 Cell Line	embryonic stem cell
21	chr13:52175000-52183000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
22	chr13:52175000-52187200	Weak transcription	Spleen	Spleen
23	chr13:52175000-52188600	Weak transcription	Fetal Muscle Leg	muscle
24	chr13:52176000-52188600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
25	chr13:52176200-52181400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
26	chr13:52176200-52184000	Weak transcription	Primary T helper cells fromperipheralblood	blood
27	chr13:52176600-52183000	Weak transcription	Primary hematopoietic stem cells short term culture	blood
28	chr13:52176600-52188400	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
29	chr13:52176600-52188400	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
30	chr13:52176800-52181200	Weak transcription	Stomach Mucosa	stomach
31	chr13:52176800-52181800	Weak transcription	Pancreatic Islets	Pancreatic Islet
32	chr13:52177000-52181400	Weak transcription	HSMM	muscle
33	chr13:52177000-52182600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
34	chr13:52177000-52182600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
35	chr13:52177000-52188400	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
36	chr13:52177200-52181400	Weak transcription	Primary B cells from peripheral blood	blood
37	chr13:52177600-52180600	Enhancers	NHEK	skin
38	chr13:52177600-52182400	Weak transcription	Right Ventricle	heart
39	chr13:52177600-52182600	Weak transcription	Primary monocytes fromperipheralblood	blood
40	chr13:52177600-52183000	Weak transcription	Monocytes-CD14+_RO01746	blood
41	chr13:52177800-52181400	Enhancers	HepG2	liver
42	chr13:52178000-52181400	Weak transcription	Primary B cells from cord blood	blood
43	chr13:52178000-52182000	Weak transcription	Primary T cells from cord blood	blood
44	chr13:52178200-52188600	Weak transcription	Left Ventricle	heart
45	chr13:52178200-52188600	Weak transcription	Lung	lung
46	chr13:52178800-52181600	Enhancers	NHDF-Ad	bronchial
47	chr13:52179000-52180600	Enhancers	Brain Cingulate Gyrus	brain
48	chr13:52179200-52180600	Enhancers	Brain Angular Gyrus	brain
49	chr13:52179400-52180600	Enhancers	Cortex derived primary cultured neurospheres	brain
50	chr13:52179400-52180600	Enhancers	Brain Hippocampus Middle	brain

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