Variant report

Variant	rs28382892
Chromosome Location	chr2:100053295-100053296
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr2:100047706..100049310-chr2:100051628..100054301,2	K562	blood:
2	chr2:100049389..100050894-chr2:100051918..100054292,2	K562	blood:
3	chr2:100049753..100054297-chr2:100054339..100060399,6	K562	blood:

Variant related genes	Relation type
ENSG00000135945	Chromatin interaction

Extended variants
information (count: 76 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:71)

rs_ID	r²[population]
rs1011633	0.80[CHB][hapmap];0.89[JPT][hapmap]
rs10207981	0.85[CHB][hapmap];0.89[CHD][hapmap];0.84[JPT][hapmap];0.86[ASN][1000 genomes]
rs1053544	0.84[CHB][hapmap];0.89[JPT][hapmap]
rs11123775	0.89[JPT][hapmap]
rs11123785	1.00[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];0.87[AMR][1000 genomes];0.95[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs11884686	0.85[CHB][hapmap];0.89[JPT][hapmap]
rs11892441	0.85[CHB][hapmap];0.89[JPT][hapmap]
rs11899745	0.80[CHB][hapmap];0.89[JPT][hapmap]
rs12053519	0.94[CHD][hapmap];1.00[JPT][hapmap]
rs12053566	0.85[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs12233086	1.00[CEU][hapmap];0.94[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.91[MKK][hapmap];1.00[TSI][hapmap];0.87[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs12233126	1.00[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];0.87[AMR][1000 genomes];0.91[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs12464785	0.85[CHB][hapmap];0.94[JPT][hapmap]
rs1451245	0.91[CEU][hapmap];0.89[CHB][hapmap];0.97[CHD][hapmap];1.00[JPT][hapmap];0.94[LWK][hapmap];0.94[MEX][hapmap];0.96[MKK][hapmap];0.86[TSI][hapmap];0.85[AMR][1000 genomes];0.88[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1584647	0.84[CHB][hapmap];0.89[JPT][hapmap]
rs1584648	0.85[CHB][hapmap];0.89[JPT][hapmap]
rs17022433	0.89[JPT][hapmap]
rs17022564	0.88[CHB][hapmap];0.94[JPT][hapmap]
rs17022629	0.85[CHB][hapmap];0.89[JPT][hapmap]
rs2200578	0.94[CHD][hapmap];1.00[JPT][hapmap]
rs2242036	1.00[CEU][hapmap];0.94[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.91[MKK][hapmap];1.00[TSI][hapmap];0.87[AMR][1000 genomes];0.95[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2290255	0.85[CHB][hapmap];0.89[JPT][hapmap]
rs2290257	0.85[CHB][hapmap];0.89[JPT][hapmap]
rs2290261	0.85[CHB][hapmap];0.88[JPT][hapmap]
rs2309617	0.85[CHB][hapmap];0.89[JPT][hapmap]
rs28369925	0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs28369944	0.83[EUR][1000 genomes]
rs28382949	0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs3087395	0.81[MEX][hapmap]
rs3749087	0.84[CHB][hapmap];0.89[JPT][hapmap]
rs3791212	0.85[CHB][hapmap];0.89[JPT][hapmap]
rs3791213	0.87[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs3792135	0.91[CEU][hapmap];0.82[CHB][hapmap];0.94[CHD][hapmap];1.00[JPT][hapmap];0.88[LWK][hapmap];0.86[MEX][hapmap];0.96[MKK][hapmap];0.86[TSI][hapmap];0.85[AMR][1000 genomes];0.88[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs3792136	1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];0.94[JPT][hapmap];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3792137	0.89[JPT][hapmap]
rs3792138	0.81[MEX][hapmap]
rs3792142	0.83[CHB][hapmap];0.88[JPT][hapmap]
rs4143760	0.80[CHB][hapmap];0.89[JPT][hapmap]
rs4851206	0.80[CHB][hapmap];0.89[JPT][hapmap]
rs57043099	0.90[AMR][1000 genomes]
rs58766196	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs59360884	0.81[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs60572342	0.93[AMR][1000 genomes]
rs60730619	0.83[EUR][1000 genomes]
rs61577246	0.85[AMR][1000 genomes];0.88[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs6715321	0.89[JPT][hapmap]
rs6722617	0.83[CHD][hapmap];0.84[JPT][hapmap]
rs6727483	1.00[CEU][hapmap];0.89[CHB][hapmap];1.00[JPT][hapmap];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6728175	0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6746320	0.87[AFR][1000 genomes]
rs717454	0.85[CHB][hapmap];0.89[JPT][hapmap]
rs72954262	0.81[EUR][1000 genomes]
rs72954283	0.83[EUR][1000 genomes]
rs72954284	0.83[EUR][1000 genomes]
rs72954287	0.83[EUR][1000 genomes]
rs72956308	0.84[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs72956312	0.87[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs72956317	0.87[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs72956346	0.85[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs72956387	0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs72958313	0.87[AFR][1000 genomes]
rs72958366	0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs72958380	0.89[AMR][1000 genomes]
rs7563462	0.84[CHB][hapmap];0.89[JPT][hapmap]
rs7585019	0.80[CHB][hapmap];0.89[JPT][hapmap]
rs7593274	0.85[CHB][hapmap];0.89[JPT][hapmap]
rs7597141	0.85[CHB][hapmap];0.89[JPT][hapmap]
rs769105	0.80[CHB][hapmap];0.89[JPT][hapmap]
rs896248	0.82[CHB][hapmap];0.87[JPT][hapmap]
rs896249	0.80[CHB][hapmap];0.89[JPT][hapmap]
rs9941566	1.00[CEU][hapmap];0.94[CHB][hapmap];0.94[CHD][hapmap];1.00[GIH][hapmap];0.88[JPT][hapmap];1.00[MEX][hapmap];0.96[MKK][hapmap];1.00[TSI][hapmap];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.86[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv431424	chr2:99652682-100494682	Flanking Active TSS Enhancers Strong transcription Weak transcription ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers Active TSS Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	49 gene(s)	inside rSNPs	diseases
2	nsv1014604	chr2:99980851-100097884	Strong transcription Weak transcription Genic enhancers Enhancers ZNF genes & repeats Flanking Active TSS Transcr. at gene 5' and 3' Active TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	5 gene(s)	inside rSNPs	diseases
3	nsv1006625	chr2:99984550-100096371	Strong transcription Weak transcription Genic enhancers ZNF genes & repeats Flanking Active TSS Enhancers Transcr. at gene 5' and 3' Active TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	5 gene(s)	inside rSNPs	diseases
4	nsv1014161	chr2:100021040-100063406	Strong transcription Weak transcription Enhancers Genic enhancers Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
5	nsv962113	chr2:100022168-100317461	Weak transcription Enhancers Strong transcription Genic enhancers Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs28382892	COX5B	cis	parietal	SCAN
rs28382892	TSGA10	cis	parietal	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:99999400-100056800	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
2	chr2:100005800-100062600	Strong transcription	Dnd41	blood
3	chr2:100005800-100066000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
4	chr2:100006000-100081200	Strong transcription	Monocytes-CD14+_RO01746	blood
5	chr2:100021200-100077800	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
6	chr2:100022000-100054800	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
7	chr2:100022200-100059000	Strong transcription	Liver	Liver
8	chr2:100032600-100078000	Weak transcription	Psoas Muscle	Psoas
9	chr2:100034000-100055200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
10	chr2:100034200-100055000	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
11	chr2:100034200-100088800	Weak transcription	Small Intestine	intestine
12	chr2:100036800-100074800	Weak transcription	Primary T killer memory cells from peripheral blood	blood
13	chr2:100038200-100055200	Weak transcription	Gastric	stomach
14	chr2:100038200-100063200	Weak transcription	Fetal Intestine Small	intestine
15	chr2:100038200-100073800	Weak transcription	Esophagus	oesophagus
16	chr2:100040000-100055200	Weak transcription	Colonic Mucosa	Colon
17	chr2:100041000-100055400	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
18	chr2:100041000-100056600	Weak transcription	Fetal Brain Male	brain
19	chr2:100041200-100055200	Weak transcription	Brain Angular Gyrus	brain
20	chr2:100041400-100055000	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
21	chr2:100041400-100055200	Weak transcription	Aorta	Aorta
22	chr2:100041400-100077800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
23	chr2:100041600-100083400	Weak transcription	Brain Substantia Nigra	brain
24	chr2:100042200-100055000	Weak transcription	Fetal Kidney	kidney
25	chr2:100042800-100065000	Weak transcription	Lung	lung
26	chr2:100044600-100054800	Weak transcription	Placenta Amnion	Placenta Amnion
27	chr2:100044800-100054600	Weak transcription	Hela-S3	cervix
28	chr2:100044800-100055200	Weak transcription	Right Ventricle	heart
29	chr2:100044800-100055400	Weak transcription	iPS-15b Cell Line	embryonic stem cell
30	chr2:100045000-100064200	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
31	chr2:100045400-100053600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
32	chr2:100045400-100068200	Weak transcription	Ovary	ovary
33	chr2:100045600-100054400	Weak transcription	Brain Anterior Caudate	brain
34	chr2:100047800-100063200	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
35	chr2:100048200-100054400	Weak transcription	Primary T cells fromperipheralblood	blood
36	chr2:100048200-100055200	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
37	chr2:100048200-100090600	Weak transcription	Stomach Mucosa	stomach
38	chr2:100048400-100053400	Weak transcription	Rectal Smooth Muscle	rectum
39	chr2:100048400-100054600	Weak transcription	NHDF-Ad	bronchial
40	chr2:100048400-100054800	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
41	chr2:100048400-100055000	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
42	chr2:100048400-100055000	Weak transcription	Brain Germinal Matrix	brain
43	chr2:100048400-100055000	Weak transcription	Brain Hippocampus Middle	brain
44	chr2:100048400-100055000	Weak transcription	Duodenum Smooth Muscle	Duodenum
45	chr2:100048400-100055000	Weak transcription	Skeletal Muscle Male	skeletal muscle
46	chr2:100048400-100055000	Weak transcription	HSMMtube	muscle
47	chr2:100048400-100055200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
48	chr2:100048400-100055200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
49	chr2:100048400-100055200	Weak transcription	H9 Cell Line	embryonic stem cell
50	chr2:100048400-100055200	Weak transcription	Left Ventricle	heart

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