Variant report

Variant	rs4946962
Chromosome Location	chr6:109646840-109646841
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr6:109641011..109643072-chr6:109645120..109647555,2	K562	blood:
2	chr6:109638384..109640553-chr6:109645179..109647068,2	K562	blood:
3	chr6:109645286..109648549-chr6:109701457..109703772,3	K562	blood:
4	chr6:109630124..109632200-chr6:109645326..109646848,2	K562	blood:
5	chr6:109644113..109647625-chr6:109647816..109651076,4	K562	blood:

Variant related genes	Relation type
ENSG00000203799	Chromatin interaction
ENSG00000135535	Chromatin interaction
ENSG00000218632	Chromatin interaction

Extended variants
information (count: 26 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:24)

rs_ID	r²[population]
rs1006081	0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs11153164	0.80[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs11153169	0.91[AMR][1000 genomes];0.85[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs11759230	0.91[AMR][1000 genomes];0.85[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs11759269	0.91[AMR][1000 genomes];0.85[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs12191774	0.92[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12200757	0.80[AMR][1000 genomes]
rs3941888	0.88[EUR][1000 genomes]
rs4945826	0.80[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs4945829	0.86[AMR][1000 genomes];0.84[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs4946953	0.80[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs4946954	0.91[AMR][1000 genomes];0.84[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs4946955	0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4946956	0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4946957	0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4946959	0.91[AMR][1000 genomes];0.85[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs4946960	0.91[AMR][1000 genomes];0.85[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs57749539	0.91[AMR][1000 genomes];0.85[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs60248809	0.91[AMR][1000 genomes];0.85[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs6903519	0.92[AMR][1000 genomes];0.94[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs884366	0.89[EUR][1000 genomes]
rs9374083	0.91[AMR][1000 genomes];0.85[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs9386798	0.91[AMR][1000 genomes];0.85[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs9400274	0.91[AMR][1000 genomes];0.85[EUR][1000 genomes];0.91[ASN][1000 genomes]

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	nsv5435	chr6:109633035-109669127	Weak transcription Flanking Active TSS Enhancers Bivalent Enhancer Strong transcription Active TSS Genic enhancers	TF binding region Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
2	nsv969434	chr6:109645476-109649777	Weak transcription Enhancers Flanking Active TSS	TF binding region Chromatin interactive region	3 gene(s)	inside rSNPs	n/a

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs4946962	CD164	cis	Muscle Skeletal	GTEx

Chromatin state (count:23 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:109629600-109654000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
2	chr6:109637400-109649800	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
3	chr6:109640600-109648800	Weak transcription	Skeletal Muscle Female	skeletal muscle
4	chr6:109640800-109648600	Weak transcription	Skeletal Muscle Male	skeletal muscle
5	chr6:109641000-109653600	Weak transcription	Small Intestine	intestine
6	chr6:109641800-109647200	Weak transcription	Fetal Intestine Large	intestine
7	chr6:109642000-109647400	Weak transcription	Fetal Intestine Small	intestine
8	chr6:109643800-109647800	Enhancers	Primary monocytes fromperipheralblood	blood
9	chr6:109644600-109675200	Weak transcription	Primary T cells from cord blood	blood
10	chr6:109644800-109657400	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
11	chr6:109645200-109647200	Enhancers	Primary hematopoietic stem cells short term culture	blood
12	chr6:109645400-109647600	Weak transcription	K562	blood
13	chr6:109645400-109653600	Weak transcription	Spleen	Spleen
14	chr6:109645400-109662400	Weak transcription	Aorta	Aorta
15	chr6:109646000-109647000	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
16	chr6:109646200-109647000	Enhancers	Fetal Muscle Leg	muscle
17	chr6:109646600-109647000	Flanking Active TSS	Primary neutrophils fromperipheralblood	blood
18	chr6:109646600-109647000	Enhancers	HSMMtube	muscle
19	chr6:109646600-109647800	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
20	chr6:109646800-109647000	Enhancers	Primary B cells from cord blood	blood
21	chr6:109646800-109647000	Enhancers	Brain Dorsolateral Prefrontal Cortex	brain
22	chr6:109646800-109647200	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
23	chr6:109646800-109647400	Weak transcription	Adipose Nuclei	Adipose

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