Variant report

Variant	rs5753434
Chromosome Location	chr22:31446233-31446234
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr22:31437736..31441147-chr22:31443914..31447179,4	K562	blood:
2	chr22:31445377..31447360-chr22:31483123..31485957,2	MCF-7	breast:
3	chr22:31445325..31447022-chr22:31475452..31477796,2	MCF-7	breast:
4	chr22:31445856..31448467-chr22:31451849..31454142,3	K562	blood:

Variant related genes	Relation type
ENSG00000183963	Chromatin interaction

Extended variants
information (count: 20 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:17)

rs_ID	r²[population]
rs12157450	0.84[CEU][hapmap]
rs12168052	0.83[GIH][hapmap]
rs2006301	0.84[CEU][hapmap]
rs5749209	0.90[AFR][1000 genomes];0.98[AMR][1000 genomes];0.92[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs5749210	0.94[JPT][hapmap];0.88[AMR][1000 genomes];0.90[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs5749211	0.82[CHB][hapmap]
rs5753433	1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs5753435	0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs5753436	0.93[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];0.81[GIH][hapmap];0.90[JPT][hapmap];0.84[LWK][hapmap];0.94[MEX][hapmap];0.84[MKK][hapmap];1.00[TSI][hapmap];0.96[YRI][hapmap];0.88[AFR][1000 genomes];0.92[AMR][1000 genomes];0.92[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs5753438	0.88[AMR][1000 genomes];0.90[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs5753441	0.82[CHB][hapmap]
rs5753444	0.82[CHB][hapmap]
rs5994365	0.87[EUR][1000 genomes]
rs7287178	0.82[ASN][1000 genomes]
rs7290780	0.91[AFR][1000 genomes];0.97[EUR][1000 genomes]
rs7291565	0.91[CEU][hapmap];0.82[TSI][hapmap];0.80[EUR][1000 genomes]
rs736901	0.84[CEU][hapmap]

Variant overlapped rSNPs/rCNVs (count:3 , 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	nsv966103	chr22:31410201-31452981	Enhancers Weak transcription Bivalent Enhancer Flanking Active TSS Flanking Bivalent TSS/Enh Active TSS ZNF genes & repeats Bivalent/Poised TSS	TF binding region Chromatin interactive region	5 gene(s)	inside rSNPs	diseases
3	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

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs5753434	LACTB2	trans	parietal	SCAN
rs5753434	SEZ6L	cis	cerebellum	SCAN
rs5753434	SEC14L4	cis	cerebellum	SCAN

Chromatin state (count:34 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr22:31440000-31453200	Enhancers	Fetal Adrenal Gland	Adrenal Gland
2	chr22:31440200-31447400	Enhancers	Adipose Nuclei	Adipose
3	chr22:31440600-31451000	Weak transcription	Osteobl	bone
4	chr22:31441600-31455000	Enhancers	Fetal Stomach	stomach
5	chr22:31443000-31449800	Weak transcription	Brain Inferior Temporal Lobe	brain
6	chr22:31443000-31450000	Weak transcription	Stomach Smooth Muscle	stomach
7	chr22:31443000-31450200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
8	chr22:31443000-31450800	Weak transcription	Breast Myoepithelial Primary Cells	Breast
9	chr22:31443000-31450800	Weak transcription	Colon Smooth Muscle	Colon
10	chr22:31443000-31451000	Weak transcription	A549	lung
11	chr22:31443200-31450800	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
12	chr22:31443200-31451000	Weak transcription	Rectal Mucosa Donor 31	rectum
13	chr22:31443200-31451000	Weak transcription	Hela-S3	cervix
14	chr22:31443400-31451200	Weak transcription	Right Ventricle	heart
15	chr22:31443600-31451000	Weak transcription	Ovary	ovary
16	chr22:31443600-31455400	Weak transcription	K562	blood
17	chr22:31444200-31446400	Enhancers	Left Ventricle	heart
18	chr22:31444400-31446400	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
19	chr22:31444600-31447400	Enhancers	Fetal Muscle Leg	muscle
20	chr22:31444800-31447000	Enhancers	Fetal Muscle Trunk	muscle
21	chr22:31445000-31446400	Enhancers	HUVEC	blood vessel
22	chr22:31445000-31451000	Weak transcription	Right Atrium	heart
23	chr22:31445200-31447200	Enhancers	Placenta	Placenta
24	chr22:31445600-31446400	Enhancers	HepG2	liver
25	chr22:31445600-31446600	Enhancers	Spleen	Spleen
26	chr22:31446000-31446400	Enhancers	Skeletal Muscle Female	skeletal muscle
27	chr22:31446200-31446800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
28	chr22:31446200-31446800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
29	chr22:31446200-31447000	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
30	chr22:31446200-31447000	Weak transcription	Primary hematopoietic stem cells short term culture	blood
31	chr22:31446200-31448800	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
32	chr22:31446200-31449800	Weak transcription	Fetal Lung	lung
33	chr22:31446200-31450200	Weak transcription	Skeletal Muscle Male	skeletal muscle
34	chr22:31446200-31450800	Weak transcription	Lung	lung

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