Variant report

Variant	rs922642
Chromosome Location	chr3:43558356-43558357
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	chr3:43551814..43556670-chr3:43557433..43560190,5	K562	blood:
2	chr3:43558298..43560862-chr3:43561297..43563047,3	K562	blood:

Extended variants
information (count: 27 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:25)

rs_ID	r²[population]
rs1026888	0.89[ASW][hapmap];1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.92[YRI][hapmap];0.88[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs10510737	1.00[CEU][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs17075754	1.00[CEU][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs1842805	1.00[CEU][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs1905181	0.96[AFR][1000 genomes]
rs2372435	0.88[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs6441778	1.00[CEU][hapmap];0.88[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs6769241	0.86[AFR][1000 genomes]
rs6772068	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[GIH][hapmap];0.97[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs6795944	0.82[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs6800306	0.89[ASW][hapmap];0.84[LWK][hapmap];0.92[MKK][hapmap];1.00[YRI][hapmap];0.87[AFR][1000 genomes]
rs6802567	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[GIH][hapmap];0.84[LWK][hapmap];1.00[MEX][hapmap];0.81[MKK][hapmap];1.00[TSI][hapmap];0.96[YRI][hapmap];0.89[AFR][1000 genomes];0.94[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs72865005	0.89[AFR][1000 genomes];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs72865013	0.88[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs72865025	0.82[AFR][1000 genomes];0.88[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs72865027	0.99[AFR][1000 genomes];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs72865029	0.99[AFR][1000 genomes];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs72865102	0.96[AFR][1000 genomes]
rs72866821	0.94[AFR][1000 genomes]
rs72866845	0.88[AFR][1000 genomes]
rs7628239	0.91[AFR][1000 genomes]
rs7636753	1.00[CEU][hapmap];0.96[AFR][1000 genomes];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs7651078	1.00[CEU][hapmap];0.90[AFR][1000 genomes];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs9758468	0.94[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs9758483	0.94[AMR][1000 genomes];0.93[EUR][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	nsv428738	chr3:43491435-43651168	Strong transcription Bivalent Enhancer Weak transcription Enhancers ZNF genes & repeats Flanking Active TSS Genic enhancers Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region	4 gene(s)	inside rSNPs	diseases
2	esv2763720	chr3:43551038-43575884	Enhancers Weak transcription ZNF genes & repeats Strong transcription Genic enhancers Active TSS Flanking Active TSS	Chromatin interactive region	2 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs922642	SNRK	cis	cerebellum	SCAN
rs922642	CPB1	trans	parietal	SCAN
rs922642	PTH1R	cis	parietal	SCAN

Chromatin state (count:63 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:43526000-43560800	Weak transcription	Rectal Mucosa Donor 31	rectum
2	chr3:43527200-43560200	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
3	chr3:43539200-43575000	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
4	chr3:43539600-43558800	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
5	chr3:43540000-43582000	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
6	chr3:43540200-43559000	Weak transcription	HUES6 Cell Line	embryonic stem cell
7	chr3:43540200-43564600	Weak transcription	NHEK	skin
8	chr3:43540200-43602200	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
9	chr3:43540600-43560800	Weak transcription	Skeletal Muscle Female	skeletal muscle
10	chr3:43540800-43559200	Weak transcription	Fetal Muscle Leg	muscle
11	chr3:43541600-43559000	Weak transcription	Adipose Nuclei	Adipose
12	chr3:43541800-43558600	Weak transcription	Aorta	Aorta
13	chr3:43542000-43559000	Weak transcription	Monocytes-CD14+_RO01746	blood
14	chr3:43542800-43588800	Weak transcription	Left Ventricle	heart
15	chr3:43544000-43617600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
16	chr3:43544200-43558600	Weak transcription	Primary hematopoietic stem cells short term culture	blood
17	chr3:43544400-43560200	Weak transcription	Primary neutrophils fromperipheralblood	blood
18	chr3:43545200-43559200	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
19	chr3:43545200-43560200	Weak transcription	iPS-18 Cell Line	embryonic stem cell
20	chr3:43546400-43561000	Weak transcription	Stomach Smooth Muscle	stomach
21	chr3:43547200-43567200	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
22	chr3:43547400-43560800	Weak transcription	Breast Myoepithelial Primary Cells	Breast
23	chr3:43547600-43595800	Weak transcription	Fetal Stomach	stomach
24	chr3:43548400-43559000	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
25	chr3:43548400-43559000	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
26	chr3:43548400-43559200	Weak transcription	Primary hematopoietic stem cells	blood
27	chr3:43549000-43561200	Weak transcription	Right Ventricle	heart
28	chr3:43551000-43562600	Weak transcription	HUVEC	blood vessel
29	chr3:43551000-43577800	Weak transcription	H1 Cell Line	embryonic stem cell
30	chr3:43551200-43560800	Weak transcription	Fetal Heart	heart
31	chr3:43552000-43564200	Weak transcription	Gastric	stomach
32	chr3:43553000-43601600	Weak transcription	Colon Smooth Muscle	Colon
33	chr3:43553600-43595800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
34	chr3:43553800-43560600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
35	chr3:43554000-43579000	Weak transcription	Fetal Brain Male	brain
36	chr3:43554600-43561000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
37	chr3:43554600-43561000	Weak transcription	Rectal Mucosa Donor 29	rectum
38	chr3:43554800-43560600	Weak transcription	Fetal Muscle Trunk	muscle
39	chr3:43554800-43561000	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
40	chr3:43554800-43561200	Weak transcription	HSMM	muscle
41	chr3:43554800-43564400	Weak transcription	Osteobl	bone
42	chr3:43554800-43564600	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
43	chr3:43554800-43564600	Weak transcription	Muscle Satellite Cultured Cells	--
44	chr3:43554800-43565200	Weak transcription	NHDF-Ad	bronchial
45	chr3:43554800-43565400	Weak transcription	NHLF	lung
46	chr3:43554800-43573400	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
47	chr3:43554800-43589400	Weak transcription	HSMMtube	muscle
48	chr3:43555400-43567800	Weak transcription	Sigmoid Colon	Sigmoid Colon
49	chr3:43556000-43560600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
50	chr3:43556200-43624800	Weak transcription	Rectal Smooth Muscle	rectum

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