Variant report

Variant	rs11940758
Chromosome Location	chr4:175239318-175239319
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 21 )
Associated
traits (count: 3 )

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

rs_ID	r²[population]
rs10565	0.88[ASN][1000 genomes]
rs11929798	0.80[AFR][1000 genomes];0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs11933187	0.96[AMR][1000 genomes];0.93[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs11940726	0.97[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11942947	0.92[AMR][1000 genomes];0.85[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs11947136	0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs13101580	0.82[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs13130276	0.88[ASN][1000 genomes]
rs2332836	0.85[EUR][1000 genomes]
rs34407356	0.96[AMR][1000 genomes];0.94[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs34888351	0.93[AMR][1000 genomes];0.85[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs35332594	0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs4287982	0.88[ASN][1000 genomes]
rs4695919	0.87[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4695921	0.84[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs4695922	0.88[ASN][1000 genomes]
rs7678305	0.84[AMR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1016910	chr4:174952788-175349057	Bivalent Enhancer Flanking Active TSS Active TSS Enhancers Weak transcription ZNF genes & repeats Flanking Bivalent TSS/Enh Strong transcription Bivalent/Poised TSS Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	22 gene(s)	inside rSNPs	diseases
2	nsv537363	chr4:174952788-175349057	Active TSS Bivalent Enhancer Weak transcription Enhancers Strong transcription ZNF genes & repeats Bivalent/Poised TSS Flanking Active TSS Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	22 gene(s)	inside rSNPs	diseases
3	nsv596234	chr4:175053051-175361437	Weak transcription Bivalent Enhancer Enhancers Active TSS Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent/Poised TSS Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	17 gene(s)	inside rSNPs	diseases
4	nsv869116	chr4:175231090-175801761	Flanking Active TSS Enhancers Genic enhancers Weak transcription Bivalent/Poised TSS Active TSS Strong transcription Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA	13 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs11940758	CEP44	cis	Thyroid	GTEx
rs11940758	CEP44	cis	Nerve Tibial	GTEx
rs11940758	KIAA1712	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:95 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:175205600-175241600	Weak transcription	Small Intestine	intestine
2	chr4:175206200-175241000	Weak transcription	Right Ventricle	heart
3	chr4:175206800-175241800	Weak transcription	Primary T killer memory cells from peripheral blood	blood
4	chr4:175207000-175240000	Weak transcription	Rectal Smooth Muscle	rectum
5	chr4:175207000-175242000	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
6	chr4:175214600-175240000	Weak transcription	Colon Smooth Muscle	Colon
7	chr4:175214600-175240200	Weak transcription	Brain Angular Gyrus	brain
8	chr4:175214600-175240600	Weak transcription	Fetal Stomach	stomach
9	chr4:175214600-175241600	Weak transcription	Lung	lung
10	chr4:175214600-175241600	Weak transcription	Thymus	Thymus
11	chr4:175214600-175241800	Weak transcription	Pancreas	Pancrea
12	chr4:175214600-175242000	Weak transcription	Brain Substantia Nigra	brain
13	chr4:175214600-175243200	Weak transcription	Ovary	ovary
14	chr4:175214600-175244800	Weak transcription	Psoas Muscle	Psoas
15	chr4:175214600-175245400	Weak transcription	HSMM	muscle
16	chr4:175214600-175254800	Weak transcription	Esophagus	oesophagus
17	chr4:175214800-175240000	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
18	chr4:175214800-175241200	Weak transcription	Brain Anterior Caudate	brain
19	chr4:175215200-175241600	Weak transcription	Primary hematopoietic stem cells short term culture	blood
20	chr4:175215200-175242600	Weak transcription	GM12878-XiMat	blood
21	chr4:175217600-175241600	Weak transcription	Fetal Muscle Trunk	muscle
22	chr4:175217800-175240600	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
23	chr4:175218600-175242000	Weak transcription	iPS-18 Cell Line	embryonic stem cell
24	chr4:175219000-175239600	Weak transcription	Fetal Brain Female	brain
25	chr4:175219000-175242800	Weak transcription	Cortex derived primary cultured neurospheres	brain
26	chr4:175221600-175240600	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
27	chr4:175222400-175242000	Weak transcription	Fetal Intestine Small	intestine
28	chr4:175222600-175241400	Weak transcription	Spleen	Spleen
29	chr4:175225400-175241800	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
30	chr4:175225800-175240800	Weak transcription	Brain Hippocampus Middle	brain
31	chr4:175225800-175241600	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
32	chr4:175230000-175245800	Weak transcription	Fetal Muscle Leg	muscle
33	chr4:175230400-175239400	Weak transcription	Fetal Kidney	kidney
34	chr4:175230400-175240000	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
35	chr4:175230600-175241600	Weak transcription	Duodenum Smooth Muscle	Duodenum
36	chr4:175230600-175242800	Weak transcription	Primary B cells from peripheral blood	blood
37	chr4:175230800-175246200	Weak transcription	Duodenum Mucosa	Duodenum
38	chr4:175231200-175240000	Weak transcription	Primary T cells fromperipheralblood	blood
39	chr4:175231200-175240200	Weak transcription	NHLF	lung
40	chr4:175231800-175240000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
41	chr4:175231800-175243200	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
42	chr4:175232400-175247000	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
43	chr4:175233800-175252600	Weak transcription	Left Ventricle	heart
44	chr4:175233800-175255800	Weak transcription	Fetal Intestine Large	intestine
45	chr4:175234000-175241800	Weak transcription	Stomach Smooth Muscle	stomach
46	chr4:175234200-175241200	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
47	chr4:175234600-175241600	Weak transcription	Fetal Lung	lung
48	chr4:175236200-175242800	Weak transcription	Sigmoid Colon	Sigmoid Colon
49	chr4:175236200-175258400	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
50	chr4:175236400-175245400	Weak transcription	NHDF-Ad	bronchial

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