Variant report

Variant	rs1454378
Chromosome Location	chr2:33440222-33440223
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	chr2:33440018..33441970-chr2:33445005..33447288,2	K562	blood:
2	chr2:33433433..33434972-chr2:33439448..33441761,2	MCF-7	breast:

Extended variants
information (count: 67 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:61)

rs_ID	r²[population]
rs10495784	0.89[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs1065324	0.83[EUR][1000 genomes]
rs11124310	0.84[AFR][1000 genomes];0.93[AMR][1000 genomes];0.93[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12611549	0.83[EUR][1000 genomes]
rs12617948	0.83[EUR][1000 genomes]
rs12617970	0.83[EUR][1000 genomes]
rs13021881	0.83[AMR][1000 genomes];0.88[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs1377946	0.85[ASN][1000 genomes]
rs1454376	0.81[AMR][1000 genomes];0.88[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs1454379	0.84[AMR][1000 genomes];0.93[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs17566780	0.83[EUR][1000 genomes]
rs17567417	0.82[AMR][1000 genomes];0.87[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs17568051	0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs17641062	0.84[EUR][1000 genomes]
rs17641180	0.88[AMR][1000 genomes];0.87[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs17641906	0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs17642074	0.83[AFR][1000 genomes];0.97[AMR][1000 genomes];0.92[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2061026	0.84[EUR][1000 genomes]
rs2061027	0.86[AMR][1000 genomes];0.87[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2290448	0.83[AFR][1000 genomes];0.97[AMR][1000 genomes];0.92[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2290449	0.83[ASN][1000 genomes]
rs2367508	0.81[AMR][1000 genomes]
rs2367623	0.86[AMR][1000 genomes];0.87[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs4630744	0.88[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs4670245	0.83[EUR][1000 genomes]
rs4670251	0.83[EUR][1000 genomes]
rs4670313	0.82[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs4670778	0.82[EUR][1000 genomes]
rs4670828	0.83[EUR][1000 genomes]
rs4670836	0.81[EUR][1000 genomes]
rs4670849	0.83[EUR][1000 genomes]
rs4670928	0.84[EUR][1000 genomes]
rs4671010	0.86[AMR][1000 genomes];0.87[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs4671016	0.87[ASN][1000 genomes]
rs4671024	0.83[AFR][1000 genomes];0.97[AMR][1000 genomes];0.93[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4671035	0.83[AFR][1000 genomes];0.97[AMR][1000 genomes];0.91[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs5006126	0.83[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs56163907	0.83[AFR][1000 genomes];0.98[AMR][1000 genomes];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs58774073	0.86[ASN][1000 genomes]
rs58920936	0.84[ASN][1000 genomes]
rs60000782	0.86[AMR][1000 genomes];0.87[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs60558455	0.85[AMR][1000 genomes];0.87[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs62146677	0.82[EUR][1000 genomes]
rs62146678	0.82[EUR][1000 genomes]
rs62146726	0.81[AMR][1000 genomes];0.87[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs62146732	0.82[AFR][1000 genomes];0.97[AMR][1000 genomes];0.91[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs62146734	0.89[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs6543699	0.83[EUR][1000 genomes]
rs6705772	0.86[AMR][1000 genomes];0.87[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs6707904	0.82[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs6720405	0.83[EUR][1000 genomes]
rs726429	0.83[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs72797893	0.84[ASN][1000 genomes]
rs7580348	0.85[AMR][1000 genomes];0.89[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs7581446	0.81[ASN][1000 genomes]
rs7584473	0.83[AMR][1000 genomes];0.84[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs7590965	0.84[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs7595240	0.82[EUR][1000 genomes]
rs7608222	0.83[AFR][1000 genomes];0.97[AMR][1000 genomes];0.92[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7608535	0.84[AFR][1000 genomes];0.98[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs996103	0.86[AMR][1000 genomes];0.87[EUR][1000 genomes];0.87[ASN][1000 genomes]

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	nsv998167	chr2:33074313-33541100	Strong transcription Enhancers Weak transcription ZNF genes & repeats Genic enhancers Active TSS Flanking Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	24 gene(s)	inside rSNPs	diseases
2	nsv535623	chr2:33074313-33541100	Genic enhancers Enhancers Weak transcription Strong transcription Active TSS Bivalent Enhancer Flanking Active TSS Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	24 gene(s)	inside rSNPs	diseases
3	nsv1005435	chr2:33136117-33747159	Weak transcription Strong transcription Enhancers Flanking Active TSS Transcr. at gene 5' and 3' Active TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA	22 gene(s)	inside rSNPs	diseases
4	nsv535624	chr2:33136117-33747159	Weak transcription Enhancers Genic enhancers Flanking Active TSS Bivalent Enhancer Strong transcription ZNF genes & repeats Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA	22 gene(s)	inside rSNPs	diseases
5	esv33628	chr2:33257484-33455355	Enhancers Weak transcription Flanking Active TSS Bivalent Enhancer Genic enhancers Strong transcription Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region	3 gene(s)	inside rSNPs	diseases
6	nsv873790	chr2:33369582-33466483	Enhancers Strong transcription Weak transcription Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Active TSS ZNF genes & repeats Active TSS	TF binding region CpG island Chromatin interactive region	1 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:57 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:33403800-33489800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
2	chr2:33409200-33441600	Weak transcription	Psoas Muscle	Psoas
3	chr2:33414600-33455400	Weak transcription	Fetal Stomach	stomach
4	chr2:33415200-33441600	Weak transcription	Fetal Muscle Trunk	muscle
5	chr2:33415400-33441600	Weak transcription	Fetal Muscle Leg	muscle
6	chr2:33434200-33442200	Enhancers	HUVEC	blood vessel
7	chr2:33435800-33444400	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
8	chr2:33436000-33441000	Enhancers	Stomach Smooth Muscle	stomach
9	chr2:33436400-33442200	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
10	chr2:33436600-33441600	Weak transcription	Breast Myoepithelial Primary Cells	Breast
11	chr2:33436600-33444200	Weak transcription	Brain Hippocampus Middle	brain
12	chr2:33436800-33440400	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
13	chr2:33436800-33443800	Genic enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
14	chr2:33436800-33455000	Weak transcription	Duodenum Smooth Muscle	Duodenum
15	chr2:33437200-33443400	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
16	chr2:33437400-33444200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
17	chr2:33437600-33441200	Weak transcription	HSMMtube	muscle
18	chr2:33437600-33441600	Weak transcription	Liver	Liver
19	chr2:33437800-33442200	Enhancers	NH-A	brain
20	chr2:33437800-33444400	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
21	chr2:33437800-33444600	Weak transcription	Hela-S3	cervix
22	chr2:33437800-33445200	Weak transcription	Fetal Kidney	kidney
23	chr2:33438000-33443000	Enhancers	A549	lung
24	chr2:33438200-33441600	Weak transcription	Esophagus	oesophagus
25	chr2:33438600-33440400	Enhancers	Rectal Smooth Muscle	rectum
26	chr2:33438800-33440600	Enhancers	NHLF	lung
27	chr2:33439000-33442000	Genic enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
28	chr2:33439200-33440800	Enhancers	Right Atrium	heart
29	chr2:33439200-33442800	Enhancers	Left Ventricle	heart
30	chr2:33439400-33442200	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
31	chr2:33439400-33442400	Enhancers	HMEC	breast
32	chr2:33439600-33440400	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
33	chr2:33439600-33440600	Weak transcription	Aorta	Aorta
34	chr2:33439600-33441000	Weak transcription	Gastric	stomach
35	chr2:33439600-33442400	Enhancers	NHDF-Ad	bronchial
36	chr2:33439600-33442800	Enhancers	Muscle Satellite Cultured Cells	--
37	chr2:33439800-33441600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
38	chr2:33439800-33441600	Weak transcription	Pancreas	Pancrea
39	chr2:33439800-33441600	Weak transcription	Right Ventricle	heart
40	chr2:33439800-33441800	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
41	chr2:33439800-33442200	Enhancers	Fetal Heart	heart
42	chr2:33439800-33442800	Enhancers	Osteobl	bone
43	chr2:33439800-33444400	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
44	chr2:33440000-33440400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
45	chr2:33440000-33440400	Weak transcription	Lung	lung
46	chr2:33440000-33440600	Weak transcription	Ovary	ovary
47	chr2:33440000-33440800	Strong transcription	Cortex derived primary cultured neurospheres	brain
48	chr2:33440000-33441000	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
49	chr2:33440000-33441400	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
50	chr2:33440000-33441400	Weak transcription	Colon Smooth Muscle	Colon

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