Variant report

Variant	rs34890962
Chromosome Location	chr16:70559666-70559667
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:12)
CpG islands
(count:0)
Chromatin interactive
region (count:10)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:12 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	YY1	chr16:70559530-70559941	K562	blood:	n/a	chr16:70559811-70559823
2	POLR2A	chr16:70555921-70559826	GM12878	blood:	n/a	n/a
3	POLR2A	chr16:70559505-70559674	H1-hESC	embryonic stem cell:	n/a	n/a
4	HEY1	chr16:70558780-70559724	K562	blood:	n/a	n/a
5	POLR2A	chr16:70558701-70559735	GM12878	blood:	n/a	n/a
6	POLR2A	chr16:70559440-70559904	K562	blood:	n/a	n/a
7	POLR2A	chr16:70559435-70559731	H1-hESC	embryonic stem cell:	n/a	n/a
8	POLR2A	chr16:70556018-70559879	GM12892	blood:	n/a	n/a
9	YY1	chr16:70559624-70560026	K562	blood:	n/a	chr16:70559811-70559823
10	POLR2A	chr16:70556030-70559733	GM12892	blood:	n/a	n/a
11	POLR2A	chr16:70558659-70559684	SK-N-MC	brain:	n/a	n/a
12	POLR2A	chr16:70559569-70559863	HepG2	liver:	n/a	n/a

No data

(count:10 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr16:70471134..70474092-chr16:70555921..70560516,5	K562	blood:
2	chr16:70321887..70324896-chr16:70556007..70561529,9	K562	blood:
3	chr16:70555634..70562342-chr16:70718026..70723686,6	MCF-7	breast:
4	chr16:70469000..70470691-chr16:70558563..70560602,2	K562	blood:
5	chr16:70540803..70547043-chr16:70555255..70559706,8	MCF-7	breast:
6	chr16:70558865..70562951-chr16:70591784..70595478,3	MCF-7	breast:
7	chr16:70559458..70561590-chr16:70562032..70564631,5	K562	blood:
8	chr16:70379447..70384942-chr16:70556059..70561583,7	K562	blood:
9	chr16:70413215..70416772-chr16:70556199..70563150,13	MCF-7	breast:
10	chr16:70413177..70417869-chr16:70554702..70561133,15	MCF-7	breast:

No data

Variant related genes	Relation type
COG4	TF binding region
SF3B3	TF binding region
SNORD111B	TF binding region
ENSG00000189091	Chromatin interaction
ENSG00000261777	Chromatin interaction
ENSG00000132613	Chromatin interaction
ENSG00000260111	Chromatin interaction
ENSG00000157350	Chromatin interaction
ENSG00000090861	Chromatin interaction
ENSG00000157349	Chromatin interaction
ENSG00000168872	Chromatin interaction
ENSG00000221514	Chromatin interaction
ENSG00000103051	Chromatin interaction

Extended variants
information (count: 67 )
Associated
traits (count: 12 )

rSNPs within LD-proxies of this variant (count:66)

rs_ID	r²[population]
rs10852465	0.89[AFR][1000 genomes];0.81[AMR][1000 genomes];0.82[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs11075767	0.98[AFR][1000 genomes];0.94[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11075768	0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11075769	0.84[AMR][1000 genomes];0.87[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs11075770	0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11640374	0.87[EUR][1000 genomes]
rs11641683	0.86[AFR][1000 genomes];0.88[AMR][1000 genomes];0.90[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs11643344	0.95[AFR][1000 genomes];0.82[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs11643373	0.87[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs11643823	0.87[EUR][1000 genomes]
rs11645092	0.87[EUR][1000 genomes]
rs11645214	0.91[EUR][1000 genomes]
rs11645287	0.87[EUR][1000 genomes]
rs11645437	0.98[AFR][1000 genomes];0.94[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11645585	0.88[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs11648402	0.81[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11649624	0.95[AFR][1000 genomes];0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11865527	0.92[AFR][1000 genomes];0.81[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs11866400	0.98[AFR][1000 genomes];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12597401	0.92[AFR][1000 genomes];0.94[AMR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12909	0.91[AMR][1000 genomes];0.91[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12925729	0.98[AFR][1000 genomes];0.94[AMR][1000 genomes];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12931402	0.85[EUR][1000 genomes]
rs12933634	0.81[AFR][1000 genomes];0.88[AMR][1000 genomes];0.87[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2168606	0.81[AMR][1000 genomes];0.90[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2288491	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2303792	0.89[AFR][1000 genomes];0.90[ASN][1000 genomes]
rs2303793	0.89[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs33910368	0.98[AFR][1000 genomes];0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs34567847	0.92[AFR][1000 genomes];0.94[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs3762171	0.96[AFR][1000 genomes];0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4277334	0.84[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs4284632	0.91[AMR][1000 genomes];0.92[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4324119	0.98[AFR][1000 genomes];0.93[AMR][1000 genomes];0.93[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4436771	0.96[AFR][1000 genomes];0.94[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4513092	0.92[AFR][1000 genomes];0.94[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4592653	0.88[AFR][1000 genomes];0.92[EUR][1000 genomes]
rs58963621	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6499320	0.81[AMR][1000 genomes];0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6499321	0.80[AMR][1000 genomes];0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs71401814	0.81[AMR][1000 genomes];0.91[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7194521	0.84[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7195030	0.86[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7197262	0.92[AFR][1000 genomes];0.94[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7197840	0.91[EUR][1000 genomes]
rs7198317	0.90[EUR][1000 genomes]
rs7199859	0.85[AFR][1000 genomes];0.88[AMR][1000 genomes];0.86[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7200430	0.86[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7201750	0.81[AMR][1000 genomes];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7204583	0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs722579	0.86[AFR][1000 genomes];0.88[AMR][1000 genomes];0.90[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs8045651	0.88[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs8046881	0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs8049641	0.85[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs8049786	0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs8051506	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs8052031	0.90[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs8052125	0.88[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs8053436	0.91[AFR][1000 genomes];0.97[ASN][1000 genomes]
rs8057610	0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs8062178	0.88[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs8063990	0.89[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs8064013	0.86[AFR][1000 genomes];0.89[AMR][1000 genomes];0.90[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs9635522	0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9929904	0.86[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs9936225	0.87[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	nsv833272	chr16:70369769-70569723	Enhancers Strong transcription Weak transcription Genic enhancers Active TSS Flanking Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	58 gene(s)	inside rSNPs	diseases

mRNA abundance (count:12)

SNP	Gene	Cis/trans	Tissue	Source
rs34890962	CLEC18A	cis	Whole Blood	GTEx
rs34890962	LOC440348	Cis_chr	lymphoblastoid	RTeQTL
rs34890962	IL34	cis	Nerve Tibial	GTEx
rs34890962	RP11-296I10.6	cis	Thyroid	GTEx
rs34890962	COG4	cis	Whole Blood	GTEx
rs34890962	RP11-419C5.2	cis	Skin Sun Exposed Lower leg	GTEx
rs34890962	RP11-296I10.6	cis	Skin Sun Exposed Lower leg	GTEx
rs34890962	RP11-296I10.6	cis	Muscle Skeletal	GTEx
rs34890962	RP11-296I10.6	cis	Nerve Tibial	GTEx
rs34890962	RP11-296I10.6	cis	Artery Tibial	GTEx
rs34890962	PDXDC2P	cis	Skin Sun Exposed Lower leg	GTEx
rs34890962	RP11-296I10.6	cis	Esophagus Muscularis	GTEx

Chromatin state (count:127 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr16:70556000-70560200	Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
2	chr16:70556400-70560400	Active TSS	ES-I3 Cell Line	embryonic stem cell
3	chr16:70556600-70559800	Active TSS	H1 Cell Line	embryonic stem cell
4	chr16:70556600-70560200	Active TSS	GM12878-XiMat	blood
5	chr16:70556600-70560400	Active TSS	K562	blood
6	chr16:70558200-70561200	Transcr. at gene 5' and 3'	Primary hematopoietic stem cells short term culture	blood
7	chr16:70558800-70559800	Flanking Active TSS	Primary T cells fromperipheralblood	blood
8	chr16:70558800-70559800	Enhancers	Spleen	Spleen
9	chr16:70558800-70560200	Flanking Active TSS	Primary T helper cells fromperipheralblood	blood
10	chr16:70558800-70561600	Transcr. at gene 5' and 3'	Foreskin Keratinocyte Primary Cells skin02	Skin
11	chr16:70558800-70565200	Weak transcription	Aorta	Aorta
12	chr16:70559000-70559800	Flanking Active TSS	Foreskin Melanocyte Primary Cells skin03	Skin
13	chr16:70559000-70559800	Flanking Active TSS	HUVEC	blood vessel
14	chr16:70559000-70561000	Transcr. at gene 5' and 3'	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
15	chr16:70559000-70561400	Transcr. at gene 5' and 3'	iPS-20b Cell Line	embryonic stem cell
16	chr16:70559000-70561600	Transcr. at gene 5' and 3'	HUES64 Cell Line	embryonic stem cell
17	chr16:70559000-70561600	Transcr. at gene 5' and 3'	Dnd41	blood
18	chr16:70559200-70559800	Transcr. at gene 5' and 3'	H9 Derived Neuron Cultured Cells	ES cell derived
19	chr16:70559200-70559800	Enhancers	Primary monocytes fromperipheralblood	blood
20	chr16:70559200-70559800	Transcr. at gene 5' and 3'	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
21	chr16:70559200-70559800	Flanking Active TSS	HSMM	muscle
22	chr16:70559200-70559800	Transcr. at gene 5' and 3'	Osteobl	bone
23	chr16:70559200-70560000	Enhancers	Pancreas	Pancrea
24	chr16:70559200-70560400	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
25	chr16:70559200-70561000	Enhancers	Gastric	stomach
26	chr16:70559200-70561600	Genic enhancers	Primary B cells from peripheral blood	blood
27	chr16:70559200-70561600	Transcr. at gene 5' and 3'	Foreskin Keratinocyte Primary Cells skin03	Skin
28	chr16:70559400-70559800	Enhancers	Primary T cells from cord blood	blood
29	chr16:70559400-70559800	Transcr. at gene 5' and 3'	Muscle Satellite Cultured Cells	--
30	chr16:70559400-70559800	Enhancers	Liver	Liver
31	chr16:70559400-70559800	Enhancers	Lung	lung
32	chr16:70559400-70559800	Enhancers	Psoas Muscle	Psoas
33	chr16:70559400-70559800	Enhancers	Skeletal Muscle Male	skeletal muscle
34	chr16:70559400-70559800	Enhancers	Stomach Smooth Muscle	stomach
35	chr16:70559400-70559800	Flanking Active TSS	HepG2	liver
36	chr16:70559400-70560000	Active TSS	HUES6 Cell Line	embryonic stem cell
37	chr16:70559400-70560000	Enhancers	Primary B cells from cord blood	blood
38	chr16:70559400-70560200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
39	chr16:70559400-70560200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
40	chr16:70559400-70560200	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
41	chr16:70559400-70560200	Weak transcription	Brain Cingulate Gyrus	brain
42	chr16:70559400-70560200	Weak transcription	Left Ventricle	heart
43	chr16:70559400-70560400	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
44	chr16:70559400-70560400	Enhancers	Primary hematopoietic stem cells	blood
45	chr16:70559400-70560400	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
46	chr16:70559400-70560400	Enhancers	Adipose Nuclei	Adipose
47	chr16:70559400-70560400	Weak transcription	Brain Anterior Caudate	brain
48	chr16:70559400-70560400	Weak transcription	Brain Inferior Temporal Lobe	brain
49	chr16:70559400-70560400	Enhancers	Fetal Heart	heart
50	chr16:70559400-70560400	Genic enhancers	Fetal Muscle Trunk	muscle

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