Variant report

Variant	rs2078022
Chromosome Location	chr13:37559306-37559307
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr13:37541480..37544414-chr13:37558914..37561167,2	MCF-7	breast:
2	chr13:37557592..37563683-chr13:37571842..37575220,9	MCF-7	breast:
3	chr13:37559041..37561976-chr13:37572718..37575249,3	MCF-7	breast:
4	chr13:37558525..37560139-chr13:37564523..37566978,2	K562	blood:

Variant related genes	Relation type
ENSG00000120697	Chromatin interaction
ENSG00000120699	Chromatin interaction

Extended variants
information (count: 47 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:44)

rs_ID	r²[population]
rs11147624	0.86[JPT][hapmap]
rs11147625	0.86[JPT][hapmap]
rs11147626	0.86[JPT][hapmap]
rs11147627	0.86[JPT][hapmap]
rs1127446	0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2243710	0.94[CHB][hapmap];0.97[CHD][hapmap];1.00[JPT][hapmap];0.98[ASN][1000 genomes]
rs2323396	0.86[JPT][hapmap]
rs3818380	0.94[CHB][hapmap];0.97[CHD][hapmap];1.00[JPT][hapmap];0.93[ASN][1000 genomes]
rs3852618	0.86[JPT][hapmap]
rs3852619	0.91[JPT][hapmap]
rs3864999	0.86[JPT][hapmap]
rs4054546	0.89[JPT][hapmap]
rs4943438	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4943439	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4943440	0.84[ASW][hapmap];0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.90[LWK][hapmap];0.96[MEX][hapmap];0.83[MKK][hapmap];1.00[TSI][hapmap];0.86[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7336575	0.98[ASN][1000 genomes]
rs7989745	0.85[ASN][1000 genomes]
rs8000946	0.84[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.98[MKK][hapmap];0.97[TSI][hapmap];1.00[YRI][hapmap];0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9315455	0.82[CHD][hapmap];0.86[JPT][hapmap]
rs9469	0.96[CEU][hapmap];1.00[CHB][hapmap];0.93[CHD][hapmap];0.98[GIH][hapmap];0.93[JPT][hapmap];0.96[MEX][hapmap];0.87[MKK][hapmap];1.00[TSI][hapmap];0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs9532003	0.97[ASN][1000 genomes]
rs954370	1.00[JPT][hapmap]
rs9547708	0.98[ASN][1000 genomes]
rs9547709	0.96[ASN][1000 genomes]
rs9547711	0.94[CHB][hapmap];0.97[CHD][hapmap];1.00[JPT][hapmap];0.98[ASN][1000 genomes]
rs9547713	0.94[CHB][hapmap];0.95[CHD][hapmap];1.00[JPT][hapmap];0.98[ASN][1000 genomes]
rs9566172	0.96[AMR][1000 genomes];0.92[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs9566177	0.86[JPT][hapmap]
rs9566178	0.84[JPT][hapmap]
rs9576144	0.96[CEU][hapmap];0.80[CHB][hapmap];0.88[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs9576145	0.96[AMR][1000 genomes];0.92[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs9576146	1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9576147	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9576149	0.84[AFR][1000 genomes];0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9576150	0.85[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9576151	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.82[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];0.84[YRI][hapmap];0.82[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9576156	1.00[CHB][hapmap];0.93[CHD][hapmap];1.00[GIH][hapmap];0.93[JPT][hapmap];0.83[MEX][hapmap];0.85[MKK][hapmap];0.82[ASN][1000 genomes]
rs9576161	0.94[CHB][hapmap]
rs9576167	0.84[ASW][hapmap];1.00[CHB][hapmap];0.87[CHD][hapmap];1.00[JPT][hapmap];0.85[MKK][hapmap]
rs9576176	0.86[JPT][hapmap]
rs9576177	0.86[JPT][hapmap]
rs9576178	0.86[JPT][hapmap]
rs9576181	0.86[JPT][hapmap]
rs9603126	0.94[CHB][hapmap];0.95[CHD][hapmap];1.00[JPT][hapmap];0.95[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv948975	chr13:37281203-38280430	Enhancers Flanking Active TSS Weak transcription Strong transcription Active TSS Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	50 gene(s)	inside rSNPs	diseases
2	nsv522336	chr13:37305641-37584838	Weak transcription Flanking Active TSS Enhancers Strong transcription Bivalent/Poised TSS Active TSS Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	40 gene(s)	inside rSNPs	diseases
3	esv3450972	chr13:37559009-37559416	Strong transcription Weak transcription	Chromatin interactive region	2 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs2078022	ALG5	cis	parietal	SCAN
rs2078022	EXOSC8	cis	parietal	SCAN

Chromatin state (count:124 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr13:37519600-37561400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
2	chr13:37520600-37560800	Weak transcription	Small Intestine	intestine
3	chr13:37524000-37563800	Weak transcription	Psoas Muscle	Psoas
4	chr13:37524600-37572400	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
5	chr13:37525000-37560800	Weak transcription	Fetal Heart	heart
6	chr13:37526800-37559400	Weak transcription	Hela-S3	cervix
7	chr13:37531800-37570000	Strong transcription	Dnd41	blood
8	chr13:37539000-37561000	Weak transcription	Aorta	Aorta
9	chr13:37539400-37561000	Weak transcription	Right Ventricle	heart
10	chr13:37539400-37562400	Weak transcription	Primary T killer memory cells from peripheral blood	blood
11	chr13:37539600-37562400	Weak transcription	Fetal Brain Male	brain
12	chr13:37540200-37561400	Weak transcription	Esophagus	oesophagus
13	chr13:37540200-37562200	Weak transcription	K562	blood
14	chr13:37545600-37561200	Weak transcription	Skeletal Muscle Male	skeletal muscle
15	chr13:37547400-37570000	Strong transcription	Fetal Thymus	thymus
16	chr13:37547800-37559800	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
17	chr13:37547800-37570200	Strong transcription	Primary T helper cells PMA-I stimulated	--
18	chr13:37549000-37569400	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
19	chr13:37549600-37559400	Strong transcription	Fetal Intestine Large	intestine
20	chr13:37550000-37561200	Weak transcription	A549	lung
21	chr13:37550000-37563800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
22	chr13:37550000-37565400	Weak transcription	Pancreatic Islets	Pancreatic Islet
23	chr13:37550400-37570200	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
24	chr13:37550600-37570400	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
25	chr13:37551600-37565000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
26	chr13:37552200-37570000	Strong transcription	Fetal Muscle Trunk	muscle
27	chr13:37552400-37570000	Strong transcription	Primary T cells from cord blood	blood
28	chr13:37552600-37570200	Strong transcription	Primary hematopoietic stem cells short term culture	blood
29	chr13:37553200-37569600	Strong transcription	Placenta	Placenta
30	chr13:37553200-37569800	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
31	chr13:37553200-37570000	Strong transcription	Primary T cells fromperipheralblood	blood
32	chr13:37554200-37561600	Weak transcription	HSMMtube	muscle
33	chr13:37554200-37569800	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
34	chr13:37554400-37560200	Strong transcription	HUVEC	blood vessel
35	chr13:37554400-37569400	Strong transcription	Primary T helper naive cells fromperipheralblood	blood
36	chr13:37554600-37569800	Strong transcription	HUES64 Cell Line	embryonic stem cell
37	chr13:37555200-37570200	Strong transcription	HUES6 Cell Line	embryonic stem cell
38	chr13:37555200-37571200	Strong transcription	iPS-20b Cell Line	embryonic stem cell
39	chr13:37555600-37560200	Strong transcription	NH-A	brain
40	chr13:37555600-37569200	Strong transcription	Rectal Mucosa Donor 31	rectum
41	chr13:37555600-37570200	Strong transcription	Liver	Liver
42	chr13:37555600-37570200	Strong transcription	Rectal Mucosa Donor 29	rectum
43	chr13:37555600-37570400	Strong transcription	Skeletal Muscle Female	skeletal muscle
44	chr13:37555600-37570400	Strong transcription	Monocytes-CD14+_RO01746	blood
45	chr13:37555800-37567200	Weak transcription	Stomach Mucosa	stomach
46	chr13:37555800-37569400	Strong transcription	Adipose Nuclei	Adipose
47	chr13:37555800-37570000	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
48	chr13:37555800-37570200	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
49	chr13:37556000-37566600	Strong transcription	Fetal Muscle Leg	muscle
50	chr13:37556200-37559400	Strong transcription	Placenta Amnion	Placenta Amnion

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