Variant report

Variant	rs1384435
Chromosome Location	chr3:43559097-43559098
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr3:43551814..43556670-chr3:43557433..43560190,5	K562	blood:
2	chr3:43559073..43563510-chr3:43563874..43567670,4	K562	blood:
3	chr3:43558298..43560862-chr3:43561297..43563047,3	K562	blood:

Extended variants
information (count: 66 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:64)

rs_ID	r²[population]
rs1013758	0.92[CEU][hapmap];0.95[GIH][hapmap];0.98[TSI][hapmap];0.94[EUR][1000 genomes]
rs1038202	0.85[CEU][hapmap];0.81[TSI][hapmap];0.87[EUR][1000 genomes]
rs10461013	0.96[CEU][hapmap];0.94[EUR][1000 genomes]
rs10461015	0.89[EUR][1000 genomes]
rs11130004	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11130005	0.92[CEU][hapmap];0.96[EUR][1000 genomes]
rs11715896	0.85[CEU][hapmap]
rs12374079	0.86[EUR][1000 genomes]
rs12486736	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12492694	0.89[CEU][hapmap];0.82[EUR][1000 genomes]
rs12638282	1.00[ASW][hapmap];1.00[CEU][hapmap];0.93[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs13066902	0.83[EUR][1000 genomes]
rs13319147	0.91[EUR][1000 genomes]
rs1351631	0.93[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.90[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.86[AFR][1000 genomes];0.89[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1564434	0.85[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.96[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs17030517	0.85[CEU][hapmap];0.80[EUR][1000 genomes]
rs17408925	0.87[EUR][1000 genomes]
rs1842806	0.82[AFR][1000 genomes];0.84[AMR][1000 genomes];0.93[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1842807	0.92[CEU][hapmap];0.87[EUR][1000 genomes]
rs1975997	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.86[LWK][hapmap];1.00[MEX][hapmap];0.98[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.86[AFR][1000 genomes];0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2054553	0.86[EUR][1000 genomes]
rs2054554	0.85[CEU][hapmap];0.81[TSI][hapmap];0.86[EUR][1000 genomes]
rs2101064	1.00[ASW][hapmap];0.96[CEU][hapmap];1.00[CHB][hapmap];0.93[CHD][hapmap];0.88[GIH][hapmap];1.00[JPT][hapmap];0.96[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];0.98[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2127725	0.82[EUR][1000 genomes]
rs34279519	0.84[EUR][1000 genomes]
rs3772160	0.92[CEU][hapmap];0.95[GIH][hapmap];0.98[TSI][hapmap];0.96[EUR][1000 genomes]
rs3772165	0.85[CEU][hapmap];0.81[TSI][hapmap];0.86[EUR][1000 genomes]
rs3772167	0.85[CEU][hapmap]
rs3821381	0.85[CEU][hapmap];0.81[TSI][hapmap];0.86[EUR][1000 genomes]
rs3902207	0.88[EUR][1000 genomes]
rs4128530	0.88[CEU][hapmap]
rs4264704	0.90[AFR][1000 genomes];0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4407383	0.96[CEU][hapmap];1.00[CHB][hapmap];0.89[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.90[MEX][hapmap];0.89[TSI][hapmap];0.84[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs4505672	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.86[AFR][1000 genomes];0.85[AMR][1000 genomes];0.93[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4547674	0.96[CEU][hapmap];1.00[CHB][hapmap];0.89[CHD][hapmap];0.97[GIH][hapmap];0.89[TSI][hapmap];0.84[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4561805	0.84[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs4682690	0.85[CEU][hapmap];0.81[TSI][hapmap];0.86[EUR][1000 genomes]
rs61102363	0.94[EUR][1000 genomes]
rs6441786	0.85[CEU][hapmap];0.81[TSI][hapmap];0.83[EUR][1000 genomes]
rs6763321	0.86[EUR][1000 genomes]
rs6769576	0.92[CEU][hapmap];1.00[CHB][hapmap];0.89[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap];0.89[TSI][hapmap];0.84[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs737516	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[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];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7616708	0.85[CEU][hapmap];0.81[TSI][hapmap];0.86[EUR][1000 genomes]
rs7621271	0.85[CEU][hapmap];0.81[TSI][hapmap];0.86[EUR][1000 genomes]
rs7621298	0.90[GIH][hapmap]
rs9311340	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.90[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.86[AFR][1000 genomes];0.89[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs9311341	0.85[CEU][hapmap];0.86[EUR][1000 genomes]
rs9809643	0.92[CEU][hapmap];0.91[GIH][hapmap];0.98[TSI][hapmap];0.98[EUR][1000 genomes]
rs9814737	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9815196	0.93[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.90[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.86[AFR][1000 genomes];0.89[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs9824990	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs9826275	0.85[EUR][1000 genomes]
rs9829067	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9830697	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9834786	0.89[EUR][1000 genomes]
rs9835664	0.89[AFR][1000 genomes];0.85[AMR][1000 genomes];0.86[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs9835793	0.96[AFR][1000 genomes];0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9845142	0.84[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs9851894	0.82[EUR][1000 genomes]
rs9852783	0.91[GIH][hapmap];0.91[TSI][hapmap];0.81[EUR][1000 genomes]
rs9862259	0.89[CEU][hapmap];1.00[GIH][hapmap];0.84[TSI][hapmap];0.81[EUR][1000 genomes]
rs9873316	0.92[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9878330	0.86[EUR][1000 genomes]
rs9881028	0.84[AMR][1000 genomes];0.91[EUR][1000 genomes];0.96[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	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:4)

SNP	Gene	Cis/trans	Tissue	Source
rs1384435	SNRK	cis	cerebellum	SCAN
rs1384435	PTH1R	cis	parietal	SCAN
rs1384435	RPL14	cis	parietal	SCAN
rs1384435	MRPS18A	trans	cerebellum	SCAN

Chromatin state (count:59 , 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	chr3:43540000-43582000	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
5	chr3:43540200-43564600	Weak transcription	NHEK	skin
6	chr3:43540200-43602200	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
7	chr3:43540600-43560800	Weak transcription	Skeletal Muscle Female	skeletal muscle
8	chr3:43540800-43559200	Weak transcription	Fetal Muscle Leg	muscle
9	chr3:43542800-43588800	Weak transcription	Left Ventricle	heart
10	chr3:43544000-43617600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
11	chr3:43544400-43560200	Weak transcription	Primary neutrophils fromperipheralblood	blood
12	chr3:43545200-43559200	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
13	chr3:43545200-43560200	Weak transcription	iPS-18 Cell Line	embryonic stem cell
14	chr3:43546400-43561000	Weak transcription	Stomach Smooth Muscle	stomach
15	chr3:43547200-43567200	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
16	chr3:43547400-43560800	Weak transcription	Breast Myoepithelial Primary Cells	Breast
17	chr3:43547600-43595800	Weak transcription	Fetal Stomach	stomach
18	chr3:43548400-43559200	Weak transcription	Primary hematopoietic stem cells	blood
19	chr3:43549000-43561200	Weak transcription	Right Ventricle	heart
20	chr3:43551000-43562600	Weak transcription	HUVEC	blood vessel
21	chr3:43551000-43577800	Weak transcription	H1 Cell Line	embryonic stem cell
22	chr3:43551200-43560800	Weak transcription	Fetal Heart	heart
23	chr3:43552000-43564200	Weak transcription	Gastric	stomach
24	chr3:43553000-43601600	Weak transcription	Colon Smooth Muscle	Colon
25	chr3:43553600-43595800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
26	chr3:43553800-43560600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
27	chr3:43554000-43579000	Weak transcription	Fetal Brain Male	brain
28	chr3:43554600-43561000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
29	chr3:43554600-43561000	Weak transcription	Rectal Mucosa Donor 29	rectum
30	chr3:43554800-43560600	Weak transcription	Fetal Muscle Trunk	muscle
31	chr3:43554800-43561000	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
32	chr3:43554800-43561200	Weak transcription	HSMM	muscle
33	chr3:43554800-43564400	Weak transcription	Osteobl	bone
34	chr3:43554800-43564600	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
35	chr3:43554800-43564600	Weak transcription	Muscle Satellite Cultured Cells	--
36	chr3:43554800-43565200	Weak transcription	NHDF-Ad	bronchial
37	chr3:43554800-43565400	Weak transcription	NHLF	lung
38	chr3:43554800-43573400	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
39	chr3:43554800-43589400	Weak transcription	HSMMtube	muscle
40	chr3:43555400-43567800	Weak transcription	Sigmoid Colon	Sigmoid Colon
41	chr3:43556000-43560600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
42	chr3:43556200-43624800	Weak transcription	Rectal Smooth Muscle	rectum
43	chr3:43556600-43559200	Enhancers	Fetal Intestine Small	intestine
44	chr3:43556600-43559600	Enhancers	Fetal Intestine Large	intestine
45	chr3:43557000-43561000	Weak transcription	Pancreas	Pancrea
46	chr3:43557000-43561400	Weak transcription	Stomach Mucosa	stomach
47	chr3:43557000-43577200	Weak transcription	iPS-15b Cell Line	embryonic stem cell
48	chr3:43558400-43559200	Weak transcription	K562	blood
49	chr3:43558600-43559400	Strong transcription	Aorta	Aorta
50	chr3:43558600-43564200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived

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