Variant report

Variant	rs4944038
Chromosome Location	chr11:73783478-73783479
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	BATF	chr11:73783363-73783712	GM12878	blood:	n/a	n/a
2	USF2	chr11:73783360-73783620	GM12878	blood:	n/a	n/a
3	PAX5	chr11:73783419-73783655	GM12878	blood:	n/a	chr11:73783555-73783572 chr11:73783556-73783574
4	BATF	chr11:73783408-73783619	GM12878	blood:	n/a	n/a
5	PAX5	chr11:73783436-73783643	GM12878	blood:	n/a	chr11:73783555-73783572 chr11:73783556-73783574
6	PAX5	chr11:73783396-73783778	GM12891	blood:	n/a	chr11:73783555-73783572 chr11:73783556-73783574
7	PAX5	chr11:73783346-73783663	GM12892	blood:	n/a	chr11:73783555-73783572 chr11:73783556-73783574

No.	Distal block	Cell Line	Cell type
1	chr11:73691754..73696567-chr11:73778152..73784121,11	MCF-7	breast:
2	chr11:73756986..73758915-chr11:73782265..73784783,2	MCF-7	breast:
3	chr11:73780866..73784002-chr11:73798180..73802078,6	MCF-7	breast:
4	chr11:73691101..73695528-chr11:73777647..73786599,14	MCF-7	breast:
5	chr11:73782168..73784901-chr11:73790303..73791833,2	K562	blood:
6	chr11:73779701..73782835-chr11:73783436..73786743,4	K562	blood:

Variant related genes	Relation type
C2CD3	TF binding region
ENSG00000175567	Chromatin interaction
ENSG00000168014	Chromatin interaction

Extended variants
information (count: 30 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:29)

rs_ID	r²[population]
rs10898954	1.00[AMR][1000 genomes];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1614299	0.92[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1615115	0.92[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs1685326	0.82[ASN][1000 genomes]
rs1726735	0.83[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1726744	0.92[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs1726746	0.87[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs1726752	0.92[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1726764	0.83[ASN][1000 genomes]
rs1790381	0.92[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1790398	0.82[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1790399	0.86[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1790404	0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2007567	0.83[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs3018184	0.81[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs4453265	0.81[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs474835	0.80[EUR][1000 genomes]
rs4944036	0.98[AFR][1000 genomes];0.97[AMR][1000 genomes];0.91[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4944878	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs575096	0.86[EUR][1000 genomes]
rs6592545	0.82[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7121868	0.99[AMR][1000 genomes];0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7483884	1.00[AMR][1000 genomes];0.92[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs826033	0.82[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs826039	0.88[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs826056	0.83[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs826061	0.89[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs826062	0.87[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs826066	0.97[EUR][1000 genomes];0.89[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	nsv492091	chr11:73285970-73844424	Weak transcription Strong transcription Flanking Active TSS Genic enhancers Enhancers ZNF genes & repeats Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	85 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs4944038	P4HA3	cis	Thyroid	GTEx

Chromatin state (count:121 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:73730800-73800800	Weak transcription	Fetal Heart	heart
2	chr11:73750800-73783600	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
3	chr11:73750800-73800400	Weak transcription	HMEC	breast
4	chr11:73753200-73796400	Weak transcription	Small Intestine	intestine
5	chr11:73753200-73804600	Weak transcription	Colonic Mucosa	Colon
6	chr11:73753400-73784800	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
7	chr11:73759200-73783600	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
8	chr11:73759400-73783600	Weak transcription	Colon Smooth Muscle	Colon
9	chr11:73760000-73802600	Weak transcription	Primary T helper naive cells from peripheral blood	blood
10	chr11:73760600-73785200	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
11	chr11:73765400-73784000	Weak transcription	Fetal Intestine Small	intestine
12	chr11:73767600-73783800	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
13	chr11:73768800-73798200	Weak transcription	NHEK	skin
14	chr11:73769000-73788600	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
15	chr11:73771000-73783800	Weak transcription	Rectal Smooth Muscle	rectum
16	chr11:73771000-73784800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
17	chr11:73771200-73783800	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
18	chr11:73771200-73784000	Weak transcription	Fetal Stomach	stomach
19	chr11:73771200-73785200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
20	chr11:73771200-73785200	Weak transcription	Esophagus	oesophagus
21	chr11:73771200-73789000	Weak transcription	H9 Cell Line	embryonic stem cell
22	chr11:73777000-73788400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
23	chr11:73777600-73788600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
24	chr11:73777600-73818600	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
25	chr11:73778000-73790600	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
26	chr11:73778200-73786000	Strong transcription	Left Ventricle	heart
27	chr11:73778200-73789800	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
28	chr11:73778200-73791000	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
29	chr11:73778400-73786000	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
30	chr11:73778400-73786000	Strong transcription	HSMMtube	muscle
31	chr11:73778400-73790000	Strong transcription	Fetal Thymus	thymus
32	chr11:73778800-73785600	Strong transcription	Primary hematopoietic stem cells	blood
33	chr11:73778800-73786000	Strong transcription	Primary hematopoietic stem cells short term culture	blood
34	chr11:73778800-73790200	Strong transcription	Primary monocytes fromperipheralblood	blood
35	chr11:73778800-73790400	Strong transcription	Fetal Muscle Leg	muscle
36	chr11:73778800-73790400	Strong transcription	Rectal Mucosa Donor 29	rectum
37	chr11:73778800-73792800	Strong transcription	Primary B cells from cord blood	blood
38	chr11:73779000-73783800	Weak transcription	NHLF	lung
39	chr11:73779000-73785600	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
40	chr11:73779000-73785600	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
41	chr11:73779000-73785800	Strong transcription	Primary T cells fromperipheralblood	blood
42	chr11:73779000-73790200	Strong transcription	Primary T helper cells fromperipheralblood	blood
43	chr11:73779000-73792600	Strong transcription	Monocytes-CD14+_RO01746	blood
44	chr11:73779200-73791000	Strong transcription	Fetal Muscle Trunk	muscle
45	chr11:73779400-73784000	Enhancers	Skeletal Muscle Male	skeletal muscle
46	chr11:73779400-73785800	Strong transcription	Primary neutrophils fromperipheralblood	blood
47	chr11:73779600-73790800	Strong transcription	Primary T cells from cord blood	blood
48	chr11:73779800-73789000	Weak transcription	HepG2	liver
49	chr11:73780200-73785400	Strong transcription	iPS-20b Cell Line	embryonic stem cell
50	chr11:73780200-73785800	Strong transcription	HSMM	muscle

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