Variant report

Variant	rs535994
Chromosome Location	chr3:43130201-43130202
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 16 )
Associated
traits (count: 10 )

rSNPs within LD-proxies of this variant (count:14)

rs_ID	r²[population]
rs10865926	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs11129985	1.00[ASW][hapmap]
rs4683359	0.92[AFR][1000 genomes]
rs483765	1.00[ASW][hapmap]
rs491970	1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs503100	0.89[MKK][hapmap]
rs513065	1.00[ASW][hapmap]
rs552472	1.00[ASW][hapmap];0.92[LWK][hapmap];1.00[MKK][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs614993	1.00[YRI][hapmap]
rs632013	1.00[YRI][hapmap];0.92[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs664197	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs674118	1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs939436	0.95[AFR][1000 genomes]
rs9828191	0.92[AFR][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	nsv460522	chr3:42967597-43175207	Weak transcription Active TSS Enhancers Flanking Active TSS ZNF genes & repeats Strong transcription Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh Genic enhancers Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
2	nsv590149	chr3:42967597-43175207	Flanking Active TSS ZNF genes & repeats Enhancers Weak transcription Bivalent/Poised TSS Strong transcription Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases

mRNA abundance (count:10)

SNP	Gene	Cis/trans	Tissue	Source
rs535994	BANK1	trans	lymphoblastoid	seeQTL
rs535994	PLEKHF2	trans	lymphoblastoid	seeQTL
rs535994	UBASH3B	trans	lymphoblastoid	seeQTL
rs535994	ARHGAP25	trans	lymphoblastoid	seeQTL
rs535994	CA8	trans	lymphoblastoid	seeQTL
rs535994	HHEX	trans	lymphoblastoid	seeQTL
rs535994	PTK2	trans	lymphoblastoid	seeQTL
rs535994	OSBPL10	trans	lymphoblastoid	seeQTL
rs535994	ITGAX	trans	lymphoblastoid	seeQTL
rs535994	CD4	trans	lymphoblastoid	seeQTL

Chromatin state (count:65 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:43119600-43130400	Weak transcription	Hela-S3	cervix
2	chr3:43119600-43135000	Weak transcription	Psoas Muscle	Psoas
3	chr3:43119800-43143800	Weak transcription	Fetal Heart	heart
4	chr3:43122400-43134400	Weak transcription	HepG2	liver
5	chr3:43122400-43145800	Weak transcription	Primary T helper cells PMA-I stimulated	--
6	chr3:43122600-43145200	Weak transcription	Primary T helper cells fromperipheralblood	blood
7	chr3:43122800-43132200	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
8	chr3:43122800-43132200	Weak transcription	Fetal Lung	lung
9	chr3:43122800-43133000	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
10	chr3:43122800-43134800	Weak transcription	Brain Substantia Nigra	brain
11	chr3:43122800-43136000	Weak transcription	Pancreas	Pancrea
12	chr3:43122800-43136400	Weak transcription	HSMMtube	muscle
13	chr3:43122800-43145600	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
14	chr3:43123000-43132200	Weak transcription	Rectal Smooth Muscle	rectum
15	chr3:43123000-43132600	Weak transcription	Sigmoid Colon	Sigmoid Colon
16	chr3:43123000-43135200	Weak transcription	Brain Angular Gyrus	brain
17	chr3:43123000-43136000	Weak transcription	Right Ventricle	heart
18	chr3:43123000-43144400	Weak transcription	Fetal Intestine Large	intestine
19	chr3:43123000-43146400	Weak transcription	Duodenum Mucosa	Duodenum
20	chr3:43123000-43146600	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
21	chr3:43123200-43132000	Weak transcription	Colon Smooth Muscle	Colon
22	chr3:43123200-43140400	Weak transcription	Gastric	stomach
23	chr3:43123200-43144400	Weak transcription	Spleen	Spleen
24	chr3:43123200-43145000	Weak transcription	Adipose Nuclei	Adipose
25	chr3:43123400-43146400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
26	chr3:43123600-43135000	Weak transcription	Cortex derived primary cultured neurospheres	brain
27	chr3:43123600-43135400	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
28	chr3:43123600-43143600	Weak transcription	Lung	lung
29	chr3:43123600-43146600	Weak transcription	Fetal Intestine Small	intestine
30	chr3:43123800-43132400	Weak transcription	Duodenum Smooth Muscle	Duodenum
31	chr3:43123800-43136400	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
32	chr3:43124000-43133400	Weak transcription	Fetal Brain Male	brain
33	chr3:43124000-43134600	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
34	chr3:43124200-43131400	Weak transcription	Ovary	ovary
35	chr3:43124200-43135600	Weak transcription	Fetal Brain Female	brain
36	chr3:43124200-43145000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
37	chr3:43124400-43132000	Weak transcription	Skeletal Muscle Male	skeletal muscle
38	chr3:43124400-43135600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
39	chr3:43124400-43136200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
40	chr3:43124400-43136200	Weak transcription	Breast Myoepithelial Primary Cells	Breast
41	chr3:43124400-43144200	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
42	chr3:43124400-43146000	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
43	chr3:43124400-43146600	Weak transcription	Aorta	Aorta
44	chr3:43124600-43131800	Weak transcription	Brain Inferior Temporal Lobe	brain
45	chr3:43124600-43132000	Weak transcription	Stomach Smooth Muscle	stomach
46	chr3:43124600-43138600	Weak transcription	Thymus	Thymus
47	chr3:43124600-43144800	Weak transcription	Primary T cells fromperipheralblood	blood
48	chr3:43124600-43146800	Weak transcription	Primary hematopoietic stem cells	blood
49	chr3:43127000-43144400	Weak transcription	Dnd41	blood
50	chr3:43128000-43131200	Strong transcription	Fetal Muscle Trunk	muscle

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