Variant report

Variant	rs4943440
Chromosome Location	chr13:37555882-37555883
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:0)
CpG islands
(count:0)
Chromatin interactive
region (count:9)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:9 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr13:37553008..37556678-chr13:37572383..37575003,3	K562	blood:
2	chr13:37554957..37556941-chr13:37564099..37565843,2	K562	blood:
3	chr13:37432034..37432832-chr13:37555384..37555960,2	K562	blood:
4	chr13:37432072..37432992-chr13:37554939..37555977,8	MCF-7	breast:
5	chr13:37555396..37557070-chr13:37570309..37573495,3	MCF-7	breast:
6	chr13:37555502..37557441-chr13:37560771..37563958,3	K562	blood:
7	chr13:37429778..37432394-chr13:37555605..37558202,2	MCF-7	breast:
8	chr13:37553008..37556678-chr13:37572814..37575003,3	K562	blood:
9	chr13:37555533..37557211-chr13:37565179..37569543,3	MCF-7	breast:

No data

Variant related genes	Relation type
ENSG00000120699	Chromatin interaction
ENSG00000120697	Chromatin interaction

Extended variants
information (count: 46 )
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	0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2078022	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]
rs2243710	0.94[CHB][hapmap];0.97[CHD][hapmap];1.00[JPT][hapmap];0.99[ASN][1000 genomes]
rs2323396	0.86[JPT][hapmap]
rs3818380	0.94[CHB][hapmap];0.97[CHD][hapmap];1.00[JPT][hapmap];0.94[ASN][1000 genomes]
rs3852618	0.86[JPT][hapmap]
rs3852619	0.91[JPT][hapmap]
rs3864999	0.86[JPT][hapmap]
rs4054546	0.89[JPT][hapmap]
rs4943438	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4943439	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.80[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7336575	0.99[ASN][1000 genomes]
rs7989745	0.86[ASN][1000 genomes]
rs8000946	0.96[CEU][hapmap];1.00[CHB][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.90[LWK][hapmap];0.81[MKK][hapmap];0.97[TSI][hapmap];0.80[AFR][1000 genomes];0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9315455	0.81[CHD][hapmap];0.86[JPT][hapmap]
rs9469	0.96[CEU][hapmap];1.00[CHB][hapmap];0.92[CHD][hapmap];0.97[GIH][hapmap];0.93[JPT][hapmap];0.91[MEX][hapmap];1.00[TSI][hapmap];0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs9532003	0.97[ASN][1000 genomes]
rs954370	1.00[JPT][hapmap]
rs9547708	0.99[ASN][1000 genomes]
rs9547709	0.97[ASN][1000 genomes]
rs9547711	0.94[CHB][hapmap];0.97[CHD][hapmap];1.00[JPT][hapmap];0.99[ASN][1000 genomes]
rs9547713	0.94[CHB][hapmap];0.95[CHD][hapmap];1.00[JPT][hapmap];0.99[ASN][1000 genomes]
rs9566172	0.89[AFR][1000 genomes];0.94[AMR][1000 genomes];0.93[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs9566177	0.86[JPT][hapmap]
rs9566178	0.84[JPT][hapmap]
rs9576144	0.92[CEU][hapmap];0.80[CHB][hapmap];0.87[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs9576145	0.89[AFR][1000 genomes];0.94[AMR][1000 genomes];0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs9576146	0.90[AFR][1000 genomes];0.99[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9576147	0.80[AFR][1000 genomes];0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9576149	0.99[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9576150	0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9576151	0.84[ASW][hapmap];0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.96[MEX][hapmap];0.83[MKK][hapmap];1.00[TSI][hapmap];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9576156	1.00[CHB][hapmap];0.92[CHD][hapmap];1.00[GIH][hapmap];0.93[JPT][hapmap];0.83[ASN][1000 genomes]
rs9576161	0.94[CHB][hapmap]
rs9576167	1.00[CHB][hapmap];0.89[CHD][hapmap];1.00[JPT][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];0.94[CHD][hapmap];1.00[JPT][hapmap];0.96[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 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

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs4943440	ALG5	cis	parietal	SCAN
rs4943440	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	chr13:37523200-37558200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
4	chr13:37524000-37563800	Weak transcription	Psoas Muscle	Psoas
5	chr13:37524600-37572400	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
6	chr13:37525000-37560800	Weak transcription	Fetal Heart	heart
7	chr13:37526600-37556200	Weak transcription	Brain Angular Gyrus	brain
8	chr13:37526800-37559400	Weak transcription	Hela-S3	cervix
9	chr13:37529400-37558200	Weak transcription	Gastric	stomach
10	chr13:37531800-37570000	Strong transcription	Dnd41	blood
11	chr13:37539000-37558400	Weak transcription	Colonic Mucosa	Colon
12	chr13:37539000-37561000	Weak transcription	Aorta	Aorta
13	chr13:37539200-37558000	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
14	chr13:37539400-37561000	Weak transcription	Right Ventricle	heart
15	chr13:37539400-37562400	Weak transcription	Primary T killer memory cells from peripheral blood	blood
16	chr13:37539600-37558200	Weak transcription	Brain Germinal Matrix	brain
17	chr13:37539600-37562400	Weak transcription	Fetal Brain Male	brain
18	chr13:37539800-37557600	Weak transcription	H9 Cell Line	embryonic stem cell
19	chr13:37540200-37558800	Weak transcription	Fetal Kidney	kidney
20	chr13:37540200-37561400	Weak transcription	Esophagus	oesophagus
21	chr13:37540200-37562200	Weak transcription	K562	blood
22	chr13:37540400-37558400	Weak transcription	Brain Substantia Nigra	brain
23	chr13:37540800-37556200	Weak transcription	Primary neutrophils fromperipheralblood	blood
24	chr13:37541000-37558600	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
25	chr13:37542400-37556400	Weak transcription	Colon Smooth Muscle	Colon
26	chr13:37543200-37558400	Weak transcription	Rectal Smooth Muscle	rectum
27	chr13:37543600-37556400	Weak transcription	HSMM	muscle
28	chr13:37545600-37561200	Weak transcription	Skeletal Muscle Male	skeletal muscle
29	chr13:37545800-37557000	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
30	chr13:37545800-37558400	Weak transcription	Spleen	Spleen
31	chr13:37546200-37556200	Weak transcription	Placenta Amnion	Placenta Amnion
32	chr13:37547400-37570000	Strong transcription	Fetal Thymus	thymus
33	chr13:37547800-37559800	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
34	chr13:37547800-37570200	Strong transcription	Primary T helper cells PMA-I stimulated	--
35	chr13:37548400-37556400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
36	chr13:37548400-37556400	Weak transcription	Primary B cells from cord blood	blood
37	chr13:37549000-37569400	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
38	chr13:37549400-37558400	Weak transcription	Pancreas	Pancrea
39	chr13:37549600-37559400	Strong transcription	Fetal Intestine Large	intestine
40	chr13:37549800-37558400	Weak transcription	Brain Inferior Temporal Lobe	brain
41	chr13:37550000-37557000	Weak transcription	Primary T helper naive cells from peripheral blood	blood
42	chr13:37550000-37561200	Weak transcription	A549	lung
43	chr13:37550000-37563800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
44	chr13:37550000-37565400	Weak transcription	Pancreatic Islets	Pancreatic Islet
45	chr13:37550200-37556200	Weak transcription	HMEC	breast
46	chr13:37550200-37557200	Weak transcription	Primary hematopoietic stem cells	blood
47	chr13:37550200-37557200	Weak transcription	Brain Anterior Caudate	brain
48	chr13:37550400-37557600	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
49	chr13:37550400-37557800	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
50	chr13:37550400-37570200	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived

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