Variant report

Variant	rs2624436
Chromosome Location	chr1:93952702-93952703
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr1:93952150..93954485-chr1:94031536..94034425,2	K562	blood:
2	chr1:93912994..93915026-chr1:93952273..93954304,2	K562	blood:

Variant related genes	Relation type
ENSG00000137936	Chromatin interaction
ENSG00000137942	Chromatin interaction

Extended variants
information (count: 33 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:32)

rs_ID	r²[population]
rs1055654	0.89[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs10874786	0.89[AMR][1000 genomes];0.98[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs10874790	0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs11164936	0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11164938	0.90[AMR][1000 genomes];0.98[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs11164939	1.00[JPT][hapmap];0.84[ASN][1000 genomes]
rs11164941	0.83[ASN][1000 genomes]
rs11164942	0.86[AMR][1000 genomes];0.90[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs11164943	0.87[AMR][1000 genomes];0.88[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs12034656	0.81[ASN][1000 genomes]
rs12042552	0.89[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs12123339	0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs12135266	0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs12742850	0.90[AMR][1000 genomes];0.98[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs17109958	1.00[JPT][hapmap];0.81[ASN][1000 genomes]
rs1812668	0.90[AMR][1000 genomes];0.98[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs237438	0.90[CHB][hapmap];0.93[JPT][hapmap];0.95[YRI][hapmap];0.85[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs237439	0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2433279	1.00[JPT][hapmap];0.81[ASN][1000 genomes]
rs2624439	0.88[AMR][1000 genomes];0.99[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs3767966	0.80[CHB][hapmap];1.00[JPT][hapmap]
rs3767967	0.89[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs4847245	0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs4847428	0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs4847429	0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs4847431	0.84[CHB][hapmap];0.93[JPT][hapmap];0.85[YRI][hapmap];0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs61780647	0.81[ASN][1000 genomes]
rs61784068	0.83[ASN][1000 genomes]
rs7543847	1.00[JPT][hapmap];0.81[ASN][1000 genomes]
rs7546702	0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs7551016	0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs8179368	0.83[AMR][1000 genomes];0.96[EUR][1000 genomes];0.82[ASN][1000 genomes]

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

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv871640	chr1:93807122-93953469	Flanking Active TSS Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Enhancers Weak transcription ZNF genes & repeats Active TSS Flanking Bivalent TSS/Enh Strong transcription Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	31 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs2624436	TMED5	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:22 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:93937600-93954800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
2	chr1:93943200-93974400	Weak transcription	Fetal Lung	lung
3	chr1:93944000-93974600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
4	chr1:93944200-93954800	Weak transcription	Cortex derived primary cultured neurospheres	brain
5	chr1:93944200-93971800	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
6	chr1:93944200-93974800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
7	chr1:93945200-93958000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
8	chr1:93946800-93958000	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
9	chr1:93946800-93973200	Weak transcription	Fetal Intestine Small	intestine
10	chr1:93950200-93959400	Weak transcription	iPS-20b Cell Line	embryonic stem cell
11	chr1:93950400-93974800	Weak transcription	HepG2	liver
12	chr1:93950600-93954000	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
13	chr1:93951000-93972800	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
14	chr1:93951600-93960000	Enhancers	Breast Myoepithelial Primary Cells	Breast
15	chr1:93951800-93954800	Weak transcription	HUVEC	blood vessel
16	chr1:93952000-93952800	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
17	chr1:93952200-93953200	Enhancers	HUES64 Cell Line	embryonic stem cell
18	chr1:93952400-93956600	Weak transcription	Small Intestine	intestine
19	chr1:93952400-93958600	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
20	chr1:93952600-93953600	Enhancers	Pancreatic Islets	Pancreatic Islet
21	chr1:93952600-93954200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
22	chr1:93952600-93973600	Weak transcription	Brain Germinal Matrix	brain

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