Variant report

Variant	rs5753622
Chromosome Location	chr22:31848944-31848945
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr22:31848766-31848957	MCF-7	breast:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr22:31847213..31849082-chr22:31849317..31851160,2	K562	blood:
2	chr22:31844458..31846488-chr22:31846838..31850631,3	K562	blood:

Variant related genes	Relation type
EIF4ENIF1	TF binding region
ENSG00000240591	TF binding region
ENSG00000240591	Chromatin interaction
ENSG00000184708	Chromatin interaction

Extended variants
information (count: 40 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:35)

rs_ID	r²[population]
rs1044085	1.00[ASW][hapmap];0.80[CHD][hapmap];1.00[MKK][hapmap];0.91[TSI][hapmap]
rs11089512	1.00[ASW][hapmap];0.90[CHB][hapmap];0.90[CHD][hapmap];1.00[LWK][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];0.81[AFR][1000 genomes];0.86[AMR][1000 genomes]
rs11089514	0.81[AFR][1000 genomes];0.86[AMR][1000 genomes]
rs11089515	0.82[AMR][1000 genomes]
rs12170867	0.90[AFR][1000 genomes]
rs12485048	1.00[CEU][hapmap];0.85[JPT][hapmap];0.92[TSI][hapmap];0.88[EUR][1000 genomes]
rs12628465	1.00[MKK][hapmap]
rs17821102	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.91[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2024747	1.00[ASW][hapmap];0.86[CHB][hapmap];0.85[CHD][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];0.90[AFR][1000 genomes]
rs3818134	0.82[CHB][hapmap];0.81[CHD][hapmap]
rs4820979	0.86[CHB][hapmap];0.81[CHD][hapmap]
rs4820980	0.86[CHB][hapmap]
rs5749278	1.00[CEU][hapmap];0.94[CHB][hapmap];0.94[JPT][hapmap];1.00[AFR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs5749280	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[AFR][1000 genomes];0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs5749293	1.00[ASW][hapmap];0.82[CHB][hapmap];0.88[CHD][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];0.90[AFR][1000 genomes]
rs5749301	0.86[AMR][1000 genomes]
rs5749303	1.00[ASW][hapmap];0.88[CEU][hapmap];0.85[CHD][hapmap];1.00[MKK][hapmap];0.91[TSI][hapmap];0.90[AFR][1000 genomes]
rs5753559	1.00[MKK][hapmap]
rs5753620	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.96[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.91[AMR][1000 genomes];0.91[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs5753627	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[AFR][1000 genomes];0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs5753631	0.80[JPT][hapmap]
rs5753633	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.93[GIH][hapmap];0.94[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.81[AFR][1000 genomes];0.91[AMR][1000 genomes];0.91[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs5753635	0.81[AFR][1000 genomes];0.91[AMR][1000 genomes];0.91[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs5753647	0.86[AMR][1000 genomes];0.81[ASN][1000 genomes]
rs5753650	0.81[AFR][1000 genomes];0.86[AMR][1000 genomes];0.81[ASN][1000 genomes]
rs5753657	0.81[AFR][1000 genomes];0.86[AMR][1000 genomes]
rs5753667	0.90[CHB][hapmap];0.81[CHD][hapmap]
rs5753677	0.90[AFR][1000 genomes];0.86[AMR][1000 genomes]
rs5753681	1.00[ASW][hapmap];0.82[CHB][hapmap];0.88[CHD][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];0.82[AMR][1000 genomes]
rs59285943	0.81[AFR][1000 genomes];0.86[AMR][1000 genomes]
rs61675151	0.91[EUR][1000 genomes]
rs738656	0.82[CHB][hapmap];0.81[CHD][hapmap]
rs738702	1.00[ASW][hapmap];0.81[CHD][hapmap];0.91[TSI][hapmap]
rs9306268	1.00[MKK][hapmap]
rs9621269	1.00[CEU][hapmap];0.95[CHB][hapmap];0.85[JPT][hapmap];0.81[AFR][1000 genomes];0.91[AMR][1000 genomes];0.91[EUR][1000 genomes];0.91[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	nsv834176	chr22:31682426-31864701	Weak transcription Enhancers Genic enhancers Active TSS Strong transcription Bivalent/Poised TSS Flanking Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	52 gene(s)	inside rSNPs	diseases
2	nsv1063634	chr22:31797004-31921254	Strong transcription Weak transcription Enhancers Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' Genic enhancers Flanking Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	41 gene(s)	inside rSNPs	diseases
3	nsv459872	chr22:31833759-31977594	Strong transcription Weak transcription Flanking Active TSS Active TSS ZNF genes & repeats Genic enhancers Enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	47 gene(s)	inside rSNPs	diseases
4	nsv588894	chr22:31833759-31977594	Weak transcription Flanking Active TSS Active TSS Strong transcription Enhancers Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	47 gene(s)	inside rSNPs	diseases
5	esv1791934	chr22:31846234-31874194	Weak transcription Strong transcription Genic enhancers Transcr. at gene 5' and 3' Enhancers Flanking Active TSS	TF binding region Chromatin interactive region	18 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs5753622	PATZ1	cis	lymphoblastoid	seeQTL

Chromatin state (count:125 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr22:31797000-31884400	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
2	chr22:31797000-31884400	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
3	chr22:31797200-31860600	Strong transcription	Fetal Stomach	stomach
4	chr22:31815000-31868200	Strong transcription	Dnd41	blood
5	chr22:31815000-31883400	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
6	chr22:31822400-31859800	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
7	chr22:31823600-31884600	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
8	chr22:31829600-31852000	Strong transcription	Stomach Smooth Muscle	stomach
9	chr22:31831200-31850000	Weak transcription	Pancreatic Islets	Pancreatic Islet
10	chr22:31832600-31867800	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
11	chr22:31836200-31873600	Weak transcription	Stomach Mucosa	stomach
12	chr22:31836800-31853000	Weak transcription	Primary T killer memory cells from peripheral blood	blood
13	chr22:31838200-31859000	Weak transcription	Hela-S3	cervix
14	chr22:31838400-31849800	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
15	chr22:31838600-31854400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
16	chr22:31839200-31850000	Weak transcription	H1 Cell Line	embryonic stem cell
17	chr22:31840800-31857200	Weak transcription	iPS-15b Cell Line	embryonic stem cell
18	chr22:31841200-31849800	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
19	chr22:31841400-31850200	Weak transcription	Primary T helper naive cells from peripheral blood	blood
20	chr22:31843000-31850000	Weak transcription	HepG2	liver
21	chr22:31843000-31851800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
22	chr22:31843400-31849000	Weak transcription	HMEC	breast
23	chr22:31843600-31849600	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
24	chr22:31843600-31850000	Weak transcription	Small Intestine	intestine
25	chr22:31843800-31849200	Weak transcription	Colon Smooth Muscle	Colon
26	chr22:31844000-31849400	Weak transcription	Placenta Amnion	Placenta Amnion
27	chr22:31844200-31849800	Weak transcription	iPS-18 Cell Line	embryonic stem cell
28	chr22:31844400-31849800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
29	chr22:31844400-31850000	Weak transcription	H9 Cell Line	embryonic stem cell
30	chr22:31844400-31850000	Weak transcription	Brain Angular Gyrus	brain
31	chr22:31844400-31850000	Weak transcription	Esophagus	oesophagus
32	chr22:31844400-31850000	Weak transcription	Pancreas	Pancrea
33	chr22:31844600-31849400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
34	chr22:31844600-31849400	Weak transcription	Fetal Lung	lung
35	chr22:31844600-31849400	Weak transcription	Gastric	stomach
36	chr22:31844600-31849600	Weak transcription	NHEK	skin
37	chr22:31844600-31849800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
38	chr22:31844600-31854400	Weak transcription	Psoas Muscle	Psoas
39	chr22:31844600-31857800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
40	chr22:31844800-31849400	Weak transcription	Lung	lung
41	chr22:31845000-31854400	Weak transcription	NHLF	lung
42	chr22:31845800-31849000	Weak transcription	iPS-20b Cell Line	embryonic stem cell
43	chr22:31845800-31849200	Weak transcription	Skeletal Muscle Male	skeletal muscle
44	chr22:31845800-31853000	Strong transcription	Fetal Muscle Leg	muscle
45	chr22:31845800-31860400	Strong transcription	Primary T cells from cord blood	blood
46	chr22:31846000-31849200	Weak transcription	Colonic Mucosa	Colon
47	chr22:31846000-31849200	Weak transcription	Fetal Intestine Small	intestine
48	chr22:31846000-31853400	Strong transcription	Fetal Muscle Trunk	muscle
49	chr22:31846000-31865800	Strong transcription	Rectal Mucosa Donor 31	rectum
50	chr22:31846400-31849000	Strong transcription	GM12878-XiMat	blood

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