Variant report

Variant	rs309867
Chromosome Location	chr4:48331850-48331851
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr4:48322582..48327982-chr4:48329571..48333922,4	K562	blood:
2	chr4:48331436..48334148-chr4:48342438..48345400,3	MCF-7	breast:
3	chr4:48330630..48332591-chr4:48335471..48337148,2	K562	blood:
4	chr4:48329154..48338368-chr4:48340296..48348694,15	MCF-7	breast:
5	chr4:48322582..48325559-chr4:48331467..48333922,2	K562	blood:

Variant related genes	Relation type
ENSG00000109171	Chromatin interaction

Extended variants
information (count: 15 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:12)

rs_ID	r²[population]
rs11732338	0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs13110483	0.89[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs13133024	0.89[AMR][1000 genomes];0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1472972	0.81[CEU][hapmap]
rs192832	1.00[ASW][hapmap];0.92[CEU][hapmap];1.00[CHB][hapmap];0.89[CHD][hapmap];0.93[GIH][hapmap];0.94[JPT][hapmap];0.85[LWK][hapmap];0.85[MEX][hapmap];0.83[MKK][hapmap];0.83[TSI][hapmap];0.85[AMR][1000 genomes];0.92[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs309869	0.88[AFR][1000 genomes];0.85[AMR][1000 genomes];0.92[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs309874	0.96[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];0.88[YRI][hapmap];0.83[AFR][1000 genomes];0.85[AMR][1000 genomes];0.92[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs309876	0.90[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs309884	0.95[AFR][1000 genomes];0.91[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs454707	0.96[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];0.85[AFR][1000 genomes];0.85[AMR][1000 genomes];0.92[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4599384	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];0.85[TSI][hapmap];0.98[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs62309397	0.95[AFR][1000 genomes];0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]

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	nsv482316	chr4:48151953-48338746	Weak transcription ZNF genes & repeats Flanking Active TSS Genic enhancers Enhancers Active TSS Strong transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	22 gene(s)	inside rSNPs	diseases
2	nsv1006610	chr4:48209294-48415387	Weak transcription Enhancers Strong transcription Active TSS Flanking Active TSS Bivalent/Poised TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	28 gene(s)	inside rSNPs	diseases
3	nsv537085	chr4:48209294-48415387	Strong transcription Enhancers Flanking Active TSS Weak transcription Active TSS ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	28 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs309867	SLAIN2	Cis_1M	lymphoblastoid	RTeQTL

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:48325200-48334200	Weak transcription	Placenta	Placenta
2	chr4:48330000-48334200	Enhancers	HSMM	muscle
3	chr4:48330000-48336200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
4	chr4:48330000-48342400	Weak transcription	Esophagus	oesophagus
5	chr4:48330200-48335200	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
6	chr4:48330400-48333800	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
7	chr4:48330600-48332000	Enhancers	Rectal Mucosa Donor 31	rectum
8	chr4:48330800-48336000	Enhancers	NHDF-Ad	bronchial
9	chr4:48331000-48332200	Enhancers	Muscle Satellite Cultured Cells	--
10	chr4:48331000-48334200	Enhancers	NH-A	brain
11	chr4:48331000-48334200	Enhancers	NHLF	lung
12	chr4:48331000-48336400	Enhancers	NHEK	skin
13	chr4:48331000-48337400	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
14	chr4:48331200-48332200	Enhancers	A549	lung
15	chr4:48331200-48333000	Enhancers	Hela-S3	cervix
16	chr4:48331200-48334200	Enhancers	Osteobl	bone
17	chr4:48331200-48335000	Enhancers	HMEC	breast
18	chr4:48331200-48336400	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
19	chr4:48331400-48332800	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
20	chr4:48331400-48332800	Enhancers	HUVEC	blood vessel
21	chr4:48331400-48334200	Weak transcription	Psoas Muscle	Psoas
22	chr4:48331600-48332000	Flanking Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
23	chr4:48331600-48332200	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
24	chr4:48331600-48332800	Weak transcription	Skeletal Muscle Female	skeletal muscle
25	chr4:48331600-48335600	Weak transcription	K562	blood
26	chr4:48331600-48339400	Weak transcription	Breast Myoepithelial Primary Cells	Breast
27	chr4:48331600-48339600	Weak transcription	Stomach Mucosa	stomach
28	chr4:48331600-48340800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
29	chr4:48331800-48332000	Flanking Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
30	chr4:48331800-48332000	Flanking Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
31	chr4:48331800-48332200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
32	chr4:48331800-48332200	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
33	chr4:48331800-48332200	Weak transcription	HSMMtube	muscle
34	chr4:48331800-48333600	Weak transcription	Placenta Amnion	Placenta Amnion

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