Variant report

Variant	rs2554369
Chromosome Location	chr8:131314047-131314048
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr8:131313445..131319102-chr8:131321325..131324984,6	MCF-7	breast:
2	chr8:131305468..131307636-chr8:131313126..131315652,2	K562	blood:
3	chr8:131305468..131308042-chr8:131311655..131315652,3	K562	blood:
4	chr8:131278240..131280307-chr8:131313127..131315525,2	K562	blood:

Extended variants
information (count: 44 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:38)

rs_ID	r²[population]
rs10085959	1.00[YRI][hapmap];0.84[AFR][1000 genomes]
rs10089819	0.82[ASW][hapmap];0.83[CEU][hapmap];0.93[CHB][hapmap];0.83[CHD][hapmap];0.88[GIH][hapmap];0.94[JPT][hapmap];1.00[MEX][hapmap];0.83[TSI][hapmap];0.85[YRI][hapmap]
rs10091450	1.00[ASW][hapmap];0.95[CEU][hapmap];1.00[CHB][hapmap];0.82[CHD][hapmap];1.00[GIH][hapmap];0.94[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.97[MKK][hapmap];0.86[TSI][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];0.82[AMR][1000 genomes];0.82[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs10097893	0.90[LWK][hapmap];0.96[YRI][hapmap];0.81[AFR][1000 genomes]
rs10100892	0.83[ASW][hapmap];0.91[CEU][hapmap];1.00[CHB][hapmap];0.85[CHD][hapmap];1.00[GIH][hapmap];0.94[JPT][hapmap];0.95[MEX][hapmap];0.91[TSI][hapmap];0.81[AMR][1000 genomes];0.80[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs10103280	1.00[CHB][hapmap]
rs10956512	0.86[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[YRI][hapmap];0.87[AFR][1000 genomes];0.81[ASN][1000 genomes]
rs1158570	0.82[CHD][hapmap];0.80[MEX][hapmap]
rs11774947	0.81[CHD][hapmap]
rs12546206	0.81[CHD][hapmap]
rs12679149	0.82[AFR][1000 genomes]
rs13258946	0.81[CHD][hapmap]
rs1340022	0.88[CHD][hapmap]
rs1426101	0.91[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];0.82[AFR][1000 genomes];0.80[AMR][1000 genomes]
rs16904259	0.82[CEU][hapmap];1.00[CHB][hapmap];0.84[CHD][hapmap];0.83[MEX][hapmap]
rs2554372	0.82[CHB][hapmap];0.82[TSI][hapmap]
rs2670885	0.91[CEU][hapmap];0.93[CHB][hapmap];1.00[JPT][hapmap];0.84[AMR][1000 genomes];0.88[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2670888	0.91[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[AFR][1000 genomes];0.87[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs2670890	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[YRI][hapmap];0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2670891	0.82[AMR][1000 genomes];0.86[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2791338	0.91[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[AFR][1000 genomes];0.86[AMR][1000 genomes];0.86[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2791342	1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.96[MEX][hapmap];1.00[TSI][hapmap];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2791343	0.91[CEU][hapmap];0.81[AMR][1000 genomes];0.87[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2791350	0.91[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];0.88[AMR][1000 genomes];0.88[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs28491737	0.81[AFR][1000 genomes]
rs28495072	0.92[AFR][1000 genomes];0.83[ASN][1000 genomes]
rs2943086	0.94[ASW][hapmap];0.91[CEU][hapmap];1.00[CHB][hapmap];0.91[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.93[LWK][hapmap];1.00[MEX][hapmap];0.92[MKK][hapmap];0.94[TSI][hapmap];0.89[YRI][hapmap];0.95[AFR][1000 genomes];0.99[AMR][1000 genomes];0.91[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs3057	0.84[MEX][hapmap]
rs6415510	0.87[CEU][hapmap];0.82[ASN][1000 genomes]
rs6470801	0.88[ASW][hapmap];1.00[CHB][hapmap];0.88[CHD][hapmap];0.94[GIH][hapmap];0.94[JPT][hapmap];0.90[LWK][hapmap];1.00[MEX][hapmap];0.85[MKK][hapmap];0.88[TSI][hapmap]
rs6470804	1.00[CHB][hapmap];0.94[JPT][hapmap];0.86[AFR][1000 genomes]
rs7004884	0.87[ASW][hapmap];0.82[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];0.90[LWK][hapmap];0.87[MEX][hapmap];0.87[MKK][hapmap];0.91[TSI][hapmap];0.81[YRI][hapmap]
rs7460225	0.84[MEX][hapmap]
rs7817803	0.84[MEX][hapmap]
rs7839523	0.84[MEX][hapmap]
rs7846376	0.83[ASW][hapmap];0.87[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.96[MEX][hapmap];0.88[TSI][hapmap]
rs9297805	0.88[ASW][hapmap];0.95[CEU][hapmap];1.00[CHB][hapmap];0.91[CHD][hapmap];1.00[GIH][hapmap];0.93[JPT][hapmap];0.95[MEX][hapmap];0.82[YRI][hapmap];0.80[AMR][1000 genomes];0.82[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs966185	0.83[CHD][hapmap]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv869334	chr8:131025093-131651487	Weak transcription Enhancers Genic enhancers Flanking Active TSS Strong transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	15 gene(s)	inside rSNPs	diseases
2	nsv915580	chr8:131025093-131667578	Weak transcription Genic enhancers Enhancers Flanking Active TSS Strong transcription Flanking Bivalent TSS/Enh Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	15 gene(s)	inside rSNPs	diseases
3	nsv465810	chr8:131039109-131331012	Weak transcription Strong transcription Enhancers Flanking Active TSS Genic enhancers Active TSS ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	6 gene(s)	inside rSNPs	diseases
4	nsv612234	chr8:131039109-131331012	Weak transcription Strong transcription Enhancers Genic enhancers Flanking Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats Active TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	6 gene(s)	inside rSNPs	diseases
5	nsv533085	chr8:131042781-131755007	Strong transcription Weak transcription Enhancers Transcr. at gene 5' and 3' Flanking Active TSS Genic enhancers Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	15 gene(s)	inside rSNPs	diseases
6	nsv870148	chr8:131206342-131373989	Strong transcription Enhancers Weak transcription Active TSS Genic enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:121 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr8:131282400-131314800	Weak transcription	Gastric	stomach
2	chr8:131300400-131314800	Weak transcription	Fetal Muscle Trunk	muscle
3	chr8:131302600-131317400	Enhancers	Cortex derived primary cultured neurospheres	brain
4	chr8:131302800-131315400	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
5	chr8:131304400-131315600	Enhancers	Brain Hippocampus Middle	brain
6	chr8:131305200-131315400	Enhancers	Brain Cingulate Gyrus	brain
7	chr8:131305800-131315400	Enhancers	Stomach Smooth Muscle	stomach
8	chr8:131306000-131314600	Weak transcription	Placenta	Placenta
9	chr8:131306000-131314800	Weak transcription	Fetal Brain Female	brain
10	chr8:131306000-131321200	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
11	chr8:131306000-131321600	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
12	chr8:131306200-131314600	Weak transcription	Duodenum Mucosa	Duodenum
13	chr8:131306200-131314600	Weak transcription	Fetal Thymus	thymus
14	chr8:131306200-131315000	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
15	chr8:131306800-131314800	Weak transcription	Primary T killer memory cells from peripheral blood	blood
16	chr8:131307000-131314400	Weak transcription	Rectal Mucosa Donor 31	rectum
17	chr8:131307000-131329600	Weak transcription	Aorta	Aorta
18	chr8:131308400-131314600	Weak transcription	Fetal Intestine Small	intestine
19	chr8:131308400-131315600	Enhancers	Adipose Nuclei	Adipose
20	chr8:131308800-131314200	Weak transcription	Breast Myoepithelial Primary Cells	Breast
21	chr8:131308800-131314600	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
22	chr8:131309400-131314600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
23	chr8:131309400-131315400	Enhancers	Brain Dorsolateral Prefrontal Cortex	brain
24	chr8:131309400-131315400	Enhancers	Brain Substantia Nigra	brain
25	chr8:131309600-131314200	Weak transcription	Primary hematopoietic stem cells	blood
26	chr8:131309800-131315400	Enhancers	Ovary	ovary
27	chr8:131309800-131315800	Enhancers	Fetal Heart	heart
28	chr8:131310000-131314800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
29	chr8:131310000-131315400	Enhancers	Brain Inferior Temporal Lobe	brain
30	chr8:131310000-131316000	Enhancers	HUES6 Cell Line	embryonic stem cell
31	chr8:131310200-131314600	Weak transcription	H1 Cell Line	embryonic stem cell
32	chr8:131310200-131314600	Weak transcription	Thymus	Thymus
33	chr8:131310200-131314800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
34	chr8:131310400-131314600	Weak transcription	K562	blood
35	chr8:131310600-131314200	Weak transcription	HepG2	liver
36	chr8:131310600-131316400	Enhancers	Pancreatic Islets	Pancreatic Islet
37	chr8:131310800-131317200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
38	chr8:131310800-131328200	Weak transcription	Lung	lung
39	chr8:131311000-131314200	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
40	chr8:131311200-131314600	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
41	chr8:131311400-131314600	Weak transcription	NHEK	skin
42	chr8:131311600-131316000	Enhancers	Primary neutrophils fromperipheralblood	blood
43	chr8:131311600-131317400	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
44	chr8:131311600-131319200	Enhancers	NHDF-Ad	bronchial
45	chr8:131311600-131321600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
46	chr8:131311800-131314200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
47	chr8:131311800-131315200	Enhancers	Brain Germinal Matrix	brain
48	chr8:131312000-131314400	Weak transcription	HUVEC	blood vessel
49	chr8:131312000-131315600	Enhancers	Skeletal Muscle Male	skeletal muscle
50	chr8:131312200-131315400	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived

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