Variant report

Variant	rs9621371
Chromosome Location	chr22:32356150-32356151
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:4)
CpG islands
(count:0)
Chromatin interactive
region (count:11)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:4 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr22:32356133-32356478	HUVEC	blood vessel:	n/a	n/a
2	POLR2A	chr22:32356049-32356514	SK-N-SH	brain:	n/a	n/a
3	POLR2A	chr22:32353986-32356378	MCF-7	breast:	n/a	n/a
4	POLR2A	chr22:32351832-32356486	K562	blood:	n/a	n/a

No data

(count:11 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr22:32339237..32345444-chr22:32352616..32356758,7	K562	blood:
2	22:31864703-31891033..22:32354828-32357874	K562	blood:
3	22:32162110-32166713..22:32354828-32357874	GM12878	blood:
4	22:32012966-32043914..22:32354828-32357874	GM12878	blood:
5	22:32354828-32357874..22:32740683-32750950	K562	blood:
6	22:32102727-32109893..22:32354828-32357874	GM12878	blood:
7	22:32228866-32235273..22:32354828-32357874	K562	blood:
8	22:32170492-32188129..22:32354828-32357874	Hela-S3	cervix:
9	22:32096851-32100847..22:32354828-32357874	K562	blood:
10	22:32264718-32278135..22:32354828-32357874	K562	blood:
11	22:32053085-32061138..22:32354828-32357874	Hela-S3	cervix:

No data

Variant related genes	Relation type
ENSG00000227519	TF binding region
ENSG00000100150	Chromatin interaction
ENSG00000198089	Chromatin interaction
ENSG00000199248	Chromatin interaction
ENSG00000128245	Chromatin interaction
ENSG00000128276	Chromatin interaction
ENSG00000252909	Chromatin interaction
ENSG00000241878	Chromatin interaction
ENSG00000128254	Chromatin interaction
ENSG00000184708	Chromatin interaction
ENSG00000183530	Chromatin interaction

Extended variants
information (count: 31 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:29)

rs_ID	r²[population]
rs1049583	0.94[CEU][hapmap];0.88[CHB][hapmap];1.00[YRI][hapmap];0.80[ASN][1000 genomes]
rs12168840	0.95[CEU][hapmap];0.88[CHB][hapmap];0.81[CHD][hapmap];1.00[LWK][hapmap];1.00[YRI][hapmap]
rs130256	0.81[MEX][hapmap]
rs130264	0.81[MEX][hapmap]
rs2246704	0.88[CHB][hapmap];0.86[CHD][hapmap]
rs2301415	0.95[CEU][hapmap];0.88[CHB][hapmap];0.82[CHD][hapmap];1.00[LWK][hapmap];1.00[YRI][hapmap]
rs2853884	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[YRI][hapmap]
rs2853887	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[YRI][hapmap];0.80[ASN][1000 genomes]
rs2858750	0.95[CEU][hapmap];0.88[CHB][hapmap];0.86[CHD][hapmap];1.00[LWK][hapmap];1.00[YRI][hapmap]
rs2858752	0.88[CHB][hapmap]
rs4820059	0.88[CHB][hapmap];0.82[CHD][hapmap];1.00[YRI][hapmap]
rs6518758	0.81[MEX][hapmap]
rs71806276	0.89[AFR][1000 genomes];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7290696	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.92[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7291050	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.92[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7364274	0.90[CEU][hapmap];1.00[LWK][hapmap]
rs738181	1.00[ASW][hapmap];1.00[CHB][hapmap];1.00[LWK][hapmap];0.81[MEX][hapmap];0.88[AFR][1000 genomes];0.85[ASN][1000 genomes]
rs8141011	0.95[CEU][hapmap];0.88[CHB][hapmap];0.82[CHD][hapmap];1.00[LWK][hapmap];1.00[YRI][hapmap]
rs933226	1.00[CHB][hapmap];0.88[AFR][1000 genomes];0.85[ASN][1000 genomes]
rs9606887	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9606888	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9606893	0.81[MEX][hapmap]
rs9606907	0.81[MEX][hapmap]
rs9609389	1.00[ASW][hapmap]
rs9609394	0.95[CEU][hapmap];0.88[CHB][hapmap];1.00[YRI][hapmap];0.80[ASN][1000 genomes]
rs9609396	0.86[CHB][hapmap];0.81[MEX][hapmap]
rs9609397	1.00[YRI][hapmap]
rs9621373	0.84[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs9621386	0.81[MEX][hapmap]

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	nsv428046	chr22:32316302-32356963	Weak transcription Flanking Active TSS Strong transcription Enhancers Genic enhancers Active TSS ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	27 gene(s)	inside rSNPs	diseases
2	nsv1055450	chr22:32356150-32468832	Enhancers Flanking Bivalent TSS/Enh Weak transcription Active TSS Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' Strong transcription Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	30 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs9621371	CCDC117	cis	cerebellum	SCAN
rs9621371	TUG1	cis	cerebellum	SCAN
rs9621371	LIF	cis	cerebellum	SCAN

Chromatin state (count:113 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr22:32342400-32357600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
2	chr22:32346600-32356400	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
3	chr22:32351200-32366000	Weak transcription	Stomach Mucosa	stomach
4	chr22:32351400-32366400	Weak transcription	Right Atrium	heart
5	chr22:32352600-32358600	Weak transcription	Fetal Heart	heart
6	chr22:32353000-32357400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
7	chr22:32353000-32366000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
8	chr22:32353000-32366000	Weak transcription	Esophagus	oesophagus
9	chr22:32353000-32366000	Weak transcription	Gastric	stomach
10	chr22:32353000-32366200	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
11	chr22:32353200-32359400	Weak transcription	Primary T killer memory cells from peripheral blood	blood
12	chr22:32353200-32360400	Weak transcription	Rectal Smooth Muscle	rectum
13	chr22:32353200-32365800	Weak transcription	Pancreatic Islets	Pancreatic Islet
14	chr22:32353400-32366000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
15	chr22:32353400-32366400	Weak transcription	Psoas Muscle	Psoas
16	chr22:32353600-32356800	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
17	chr22:32353600-32357000	Weak transcription	H9 Cell Line	embryonic stem cell
18	chr22:32353600-32365400	Weak transcription	GM12878-XiMat	blood
19	chr22:32353800-32359000	Weak transcription	Small Intestine	intestine
20	chr22:32353800-32365600	Weak transcription	NHEK	skin
21	chr22:32354000-32356200	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
22	chr22:32354000-32357800	Weak transcription	Hela-S3	cervix
23	chr22:32354000-32358600	Weak transcription	Fetal Kidney	kidney
24	chr22:32354000-32366200	Weak transcription	Placenta Amnion	Placenta Amnion
25	chr22:32354200-32356400	Weak transcription	Skeletal Muscle Female	skeletal muscle
26	chr22:32354200-32356400	Weak transcription	HepG2	liver
27	chr22:32354200-32356600	Weak transcription	NHDF-Ad	bronchial
28	chr22:32354200-32356800	Weak transcription	HUES64 Cell Line	embryonic stem cell
29	chr22:32354200-32356800	Weak transcription	Brain Substantia Nigra	brain
30	chr22:32354200-32356800	Weak transcription	Stomach Smooth Muscle	stomach
31	chr22:32354200-32357000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
32	chr22:32354200-32357000	Weak transcription	HUES48 Cell Line	embryonic stem cell
33	chr22:32354200-32357000	Weak transcription	iPS-18 Cell Line	embryonic stem cell
34	chr22:32354200-32357000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
35	chr22:32354200-32357000	Weak transcription	A549	lung
36	chr22:32354200-32357000	Weak transcription	HSMMtube	muscle
37	chr22:32354200-32365600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
38	chr22:32354200-32365800	Weak transcription	K562	blood
39	chr22:32354200-32366000	Weak transcription	Primary B cells from cord blood	blood
40	chr22:32354400-32356800	Weak transcription	Adipose Nuclei	Adipose
41	chr22:32354400-32357000	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
42	chr22:32354400-32357000	Weak transcription	Breast Myoepithelial Primary Cells	Breast
43	chr22:32354400-32358600	Weak transcription	Right Ventricle	heart
44	chr22:32354400-32358800	Weak transcription	Duodenum Smooth Muscle	Duodenum
45	chr22:32354400-32359200	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
46	chr22:32354400-32365800	Weak transcription	Brain Anterior Caudate	brain
47	chr22:32354400-32366400	Weak transcription	Colonic Mucosa	Colon
48	chr22:32354600-32357200	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
49	chr22:32354600-32357400	Weak transcription	Primary neutrophils fromperipheralblood	blood
50	chr22:32354600-32357600	Enhancers	iPS-15b Cell Line	embryonic stem cell

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