Variant report

Variant	rs5997433
Chromosome Location	chr22:29429369-29429370
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr22:29428793..29430315-chr22:29546051..29548231,2	K562	blood:
2	chr22:29194663..29197354-chr22:29426484..29429608,3	K562	blood:
3	chr22:29193926..29196590-chr22:29426887..29431178,4	K562	blood:
4	chr22:29275977..29281461-chr22:29425203..29430435,9	MCF-7	breast:

Variant related genes	Relation type
ENSG00000183579	Chromatin interaction
ENSG00000100219	Chromatin interaction
ENSG00000226471	Chromatin interaction

Extended variants
information (count: 52 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:50)

rs_ID	r²[population]
rs12484832	0.91[CEU][hapmap];0.80[EUR][1000 genomes]
rs132565	0.83[EUR][1000 genomes]
rs17440734	0.96[CEU][hapmap]
rs1883197	0.81[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs1983553	1.00[CEU][hapmap];0.83[CHB][hapmap];0.82[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs2064084	1.00[CEU][hapmap]
rs2072774	0.89[EUR][1000 genomes]
rs2103544	0.82[EUR][1000 genomes]
rs2347790	0.96[CEU][hapmap]
rs28541979	0.89[EUR][1000 genomes]
rs3178915	0.81[CHB][hapmap];0.93[CHD][hapmap];0.94[JPT][hapmap];0.82[ASN][1000 genomes]
rs4140643	0.96[CEU][hapmap];0.85[TSI][hapmap]
rs469994	0.96[CEU][hapmap];0.83[EUR][1000 genomes]
rs4820794	0.96[CEU][hapmap];0.83[CHB][hapmap];0.89[EUR][1000 genomes]
rs4823002	0.93[CEU][hapmap];0.83[TSI][hapmap]
rs4823003	1.00[CEU][hapmap];0.82[CHD][hapmap];0.89[TSI][hapmap];0.82[EUR][1000 genomes]
rs4823005	1.00[CEU][hapmap];0.82[EUR][1000 genomes]
rs4823006	0.89[CHD][hapmap]
rs5997430	0.81[EUR][1000 genomes]
rs5997431	0.83[EUR][1000 genomes]
rs5997432	0.80[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs5997434	0.85[EUR][1000 genomes]
rs5997435	0.88[EUR][1000 genomes]
rs6005954	0.82[EUR][1000 genomes]
rs6005955	0.96[CEU][hapmap]
rs6005956	0.96[CEU][hapmap]
rs6005958	1.00[CEU][hapmap];0.86[EUR][1000 genomes]
rs6005959	0.83[EUR][1000 genomes]
rs6005964	0.96[CEU][hapmap];0.85[EUR][1000 genomes]
rs6005965	0.96[CEU][hapmap];0.91[EUR][1000 genomes]
rs6005967	0.93[CEU][hapmap]
rs6005975	0.81[ASN][1000 genomes]
rs6519770	0.81[ASN][1000 genomes]
rs713834	0.93[CEU][hapmap];0.83[CHB][hapmap];0.85[TSI][hapmap];0.88[EUR][1000 genomes]
rs727892	0.96[CEU][hapmap];0.81[EUR][1000 genomes]
rs7284304	0.83[EUR][1000 genomes]
rs7287517	0.82[EUR][1000 genomes]
rs7290304	1.00[CEU][hapmap];0.81[CHD][hapmap];0.89[TSI][hapmap];0.82[EUR][1000 genomes]
rs738246	0.92[CEU][hapmap];0.80[EUR][1000 genomes]
rs8137254	0.96[CEU][hapmap];0.87[TSI][hapmap];0.89[EUR][1000 genomes]
rs8137499	0.96[CEU][hapmap];0.83[EUR][1000 genomes]
rs8138950	0.84[ASN][1000 genomes]
rs874917	0.80[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs9608719	0.93[CEU][hapmap];0.81[EUR][1000 genomes]
rs9608721	0.88[EUR][1000 genomes]
rs9613776	0.96[CEU][hapmap];0.82[EUR][1000 genomes]
rs9613777	0.96[CEU][hapmap]
rs9613784	0.87[EUR][1000 genomes]
rs9613785	0.93[CEU][hapmap]
rs964589	0.93[CEU][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	nsv1064079	chr22:29065528-29456059	Weak transcription Strong transcription Genic enhancers Flanking Active TSS Active TSS Enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	92 gene(s)	inside rSNPs	diseases
2	nsv531586	chr22:29252132-29902266	Enhancers Weak transcription Active TSS Strong transcription Flanking Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	46 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs5997433	MN1	cis	cerebellum	SCAN
rs5997433	SEZ6L	cis	cerebellum	SCAN

Chromatin state (count:59 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr22:29426400-29430000	Enhancers	Lung	lung
2	chr22:29426800-29430000	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
3	chr22:29427200-29430200	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
4	chr22:29427200-29430600	Enhancers	Right Atrium	heart
5	chr22:29427400-29429800	Enhancers	Gastric	stomach
6	chr22:29427400-29448400	Weak transcription	Pancreatic Islets	Pancreatic Islet
7	chr22:29427600-29429600	Enhancers	Hela-S3	cervix
8	chr22:29427800-29429600	Enhancers	Pancreas	Pancrea
9	chr22:29427800-29430400	Enhancers	Fetal Adrenal Gland	Adrenal Gland
10	chr22:29427800-29431200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
11	chr22:29427800-29436600	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
12	chr22:29427800-29451400	Weak transcription	Psoas Muscle	Psoas
13	chr22:29428000-29441800	Weak transcription	Sigmoid Colon	Sigmoid Colon
14	chr22:29428200-29430400	Enhancers	Liver	Liver
15	chr22:29428200-29434600	Genic enhancers	HepG2	liver
16	chr22:29428200-29436400	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
17	chr22:29428400-29429400	Weak transcription	Skeletal Muscle Female	skeletal muscle
18	chr22:29428400-29436400	Weak transcription	NHEK	skin
19	chr22:29428400-29436600	Weak transcription	K562	blood
20	chr22:29428600-29429400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
21	chr22:29428600-29433200	Weak transcription	Duodenum Mucosa	Duodenum
22	chr22:29428600-29440400	Weak transcription	Esophagus	oesophagus
23	chr22:29428600-29440800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
24	chr22:29428800-29433000	Weak transcription	Fetal Intestine Large	intestine
25	chr22:29428800-29436400	Weak transcription	H1 Cell Line	embryonic stem cell
26	chr22:29428800-29436400	Weak transcription	Left Ventricle	heart
27	chr22:29428800-29436600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
28	chr22:29428800-29436600	Weak transcription	iPS-15b Cell Line	embryonic stem cell
29	chr22:29428800-29443600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
30	chr22:29429000-29430000	Enhancers	A549	lung
31	chr22:29429000-29430200	Strong transcription	Fetal Intestine Small	intestine
32	chr22:29429000-29432200	Weak transcription	Rectal Mucosa Donor 31	rectum
33	chr22:29429000-29433000	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
34	chr22:29429000-29433000	Weak transcription	Rectal Mucosa Donor 29	rectum
35	chr22:29429000-29433200	Weak transcription	HUES64 Cell Line	embryonic stem cell
36	chr22:29429000-29433200	Weak transcription	Brain Cingulate Gyrus	brain
37	chr22:29429000-29433600	Weak transcription	Placenta	Placenta
38	chr22:29429000-29435000	Weak transcription	Fetal Muscle Leg	muscle
39	chr22:29429000-29436400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
40	chr22:29429000-29436400	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
41	chr22:29429000-29436400	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
42	chr22:29429000-29436400	Weak transcription	Breast Myoepithelial Primary Cells	Breast
43	chr22:29429000-29436400	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
44	chr22:29429000-29436400	Weak transcription	Brain Anterior Caudate	brain
45	chr22:29429000-29436400	Weak transcription	Fetal Lung	lung
46	chr22:29429000-29436400	Weak transcription	Stomach Smooth Muscle	stomach
47	chr22:29429000-29436400	Weak transcription	HSMMtube	muscle
48	chr22:29429000-29436600	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
49	chr22:29429000-29436600	Weak transcription	HUES6 Cell Line	embryonic stem cell
50	chr22:29429000-29436600	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung

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