Variant report

Variant	rs7291565
Chromosome Location	chr22:31453321-31453322
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:1)
CpG islands
(count:0)
Chromatin interactive
region (count:10)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

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

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	RCOR1	chr22:31453077-31453580	IMR90	lung:	n/a	n/a

No data

(count:10 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr22:31445856..31448467-chr22:31451849..31454142,3	K562	blood:
2	chr22:31450684..31454190-chr22:31458624..31461519,3	K562	blood:
3	chr22:31449984..31454484-chr22:31456787..31462654,7	K562	blood:
4	chr22:31452690..31454726-chr22:31460173..31463712,3	MCF-7	breast:
5	chr22:31451720..31453462-chr22:31457824..31459739,2	MCF-7	breast:
6	chr22:31363469..31366268-chr22:31450278..31456884,6	MCF-7	breast:
7	chr22:31448944..31454267-chr22:31475725..31482456,15	MCF-7	breast:
8	chr22:31450722..31454659-chr22:31476861..31481048,4	K562	blood:
9	chr22:31362787..31366384-chr22:31450123..31453347,3	MCF-7	breast:
10	chr22:31449294..31454779-chr22:31475265..31480255,11	MCF-7	breast:

No data

Variant related genes	Relation type
RN7SL633P	TF binding region
ENSG00000133422	Chromatin interaction
ENSG00000183963	Chromatin interaction
ENSG00000273387	Chromatin interaction

Extended variants
information (count: 44 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:40)

rs_ID	r²[population]
rs10427701	0.85[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs10854603	0.85[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs11705177	0.92[ASN][1000 genomes]
rs11705250	0.92[ASN][1000 genomes]
rs11705313	0.92[ASN][1000 genomes]
rs11705396	0.82[ASN][1000 genomes]
rs12157450	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.86[MEX][hapmap];0.83[TSI][hapmap];0.85[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs12165471	0.95[ASN][1000 genomes]
rs12168052	0.81[CHD][hapmap];1.00[JPT][hapmap]
rs12170984	0.97[ASN][1000 genomes]
rs12330058	1.00[JPT][hapmap];0.95[ASN][1000 genomes]
rs13057068	0.92[ASN][1000 genomes]
rs2006301	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.86[MEX][hapmap];0.82[TSI][hapmap];0.81[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2240430	0.84[CHD][hapmap]
rs35060453	0.95[ASN][1000 genomes]
rs5749209	0.88[EUR][1000 genomes]
rs5749210	0.90[EUR][1000 genomes]
rs5753433	0.91[CEU][hapmap];0.80[EUR][1000 genomes]
rs5753434	0.91[CEU][hapmap];0.82[TSI][hapmap];0.80[EUR][1000 genomes]
rs5753435	0.80[EUR][1000 genomes]
rs5753436	0.91[CEU][hapmap];0.83[TSI][hapmap];0.88[EUR][1000 genomes]
rs5753438	0.90[EUR][1000 genomes]
rs5994365	0.88[AMR][1000 genomes];0.92[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs5994366	1.00[JPT][hapmap]
rs5994368	0.95[ASN][1000 genomes]
rs5994370	1.00[JPT][hapmap];0.95[ASN][1000 genomes]
rs5997863	0.92[ASN][1000 genomes]
rs5997864	0.85[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs5997866	0.85[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs5997871	0.85[ASN][1000 genomes]
rs5997872	0.84[CHD][hapmap];0.81[ASN][1000 genomes]
rs715297	1.00[JPT][hapmap]
rs7284593	1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.97[ASN][1000 genomes]
rs7285683	1.00[JPT][hapmap]
rs7290780	0.83[EUR][1000 genomes]
rs7292038	0.92[ASN][1000 genomes]
rs736901	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.86[MEX][hapmap];0.83[TSI][hapmap]
rs9619166	0.85[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs9619167	1.00[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];0.97[ASN][1000 genomes]
rs9621175	0.95[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv9896	chr22:31369204-31513933	Strong transcription Enhancers Genic enhancers Flanking Active TSS Active TSS Weak transcription ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	35 gene(s)	inside rSNPs	diseases
2	nsv524366	chr22:31440703-31480069	Flanking Active TSS Enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Weak transcription Active TSS Strong transcription Bivalent Enhancer Genic enhancers ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	18 gene(s)	inside rSNPs	diseases
3	nsv829173	chr22:31450043-31543956	Enhancers Weak transcription Flanking Active TSS Strong transcription Transcr. at gene 5' and 3' Active TSS Genic enhancers Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	30 gene(s)	inside rSNPs	diseases
4	nsv964620	chr22:31452981-31465140	Enhancers Weak transcription Active TSS Flanking Active TSS ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs7291565	SEZ6L	cis	cerebellum	SCAN
rs7291565	SEC14L4	cis	cerebellum	SCAN
rs7291565	HORMAD2	cis	cerebellum	SCAN

Chromatin state (count:37 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr22:31441600-31455000	Enhancers	Fetal Stomach	stomach
2	chr22:31443600-31455400	Weak transcription	K562	blood
3	chr22:31449200-31453400	Enhancers	Fetal Muscle Leg	muscle
4	chr22:31450200-31454400	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
5	chr22:31450800-31453600	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
6	chr22:31450800-31454600	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
7	chr22:31451000-31453400	Enhancers	ES-I3 Cell Line	embryonic stem cell
8	chr22:31451000-31453400	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
9	chr22:31451400-31455400	Weak transcription	Right Ventricle	heart
10	chr22:31451600-31453400	Enhancers	Rectal Smooth Muscle	rectum
11	chr22:31451600-31453600	Enhancers	Colon Smooth Muscle	Colon
12	chr22:31451600-31453600	Enhancers	A549	lung
13	chr22:31452000-31458000	Weak transcription	Adipose Nuclei	Adipose
14	chr22:31452200-31453400	Enhancers	Stomach Smooth Muscle	stomach
15	chr22:31452200-31453400	Enhancers	HepG2	liver
16	chr22:31452200-31455600	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
17	chr22:31452200-31455600	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
18	chr22:31452200-31455600	Weak transcription	Ovary	ovary
19	chr22:31452200-31455800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
20	chr22:31452200-31455800	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
21	chr22:31452200-31456000	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
22	chr22:31452200-31456000	Weak transcription	NHEK	skin
23	chr22:31452800-31453800	Weak transcription	Placenta Amnion	Placenta Amnion
24	chr22:31452800-31455600	Weak transcription	HMEC	breast
25	chr22:31452800-31456800	Weak transcription	Hela-S3	cervix
26	chr22:31452800-31458200	Weak transcription	Breast Myoepithelial Primary Cells	Breast
27	chr22:31453000-31453400	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
28	chr22:31453000-31455600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
29	chr22:31453000-31455600	Weak transcription	Fetal Muscle Trunk	muscle
30	chr22:31453000-31455600	Weak transcription	Placenta	Placenta
31	chr22:31453200-31453400	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
32	chr22:31453200-31453600	Enhancers	Foreskin Melanocyte Primary Cells skin01	Skin
33	chr22:31453200-31455400	Weak transcription	Fetal Lung	lung
34	chr22:31453200-31455600	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
35	chr22:31453200-31455600	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
36	chr22:31453200-31455600	Weak transcription	Fetal Intestine Large	intestine
37	chr22:31453200-31455600	Weak transcription	Fetal Intestine Small	intestine

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