Variant report

Variant	rs9859556
Chromosome Location	chr3:49455986-49455987
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr3:49452993-49456018	HepG2	liver:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr3:49453314..49456247-chr3:49456435..49459274,2	MCF-7	breast:
2	chr3:49455358..49458192-chr3:49507443..49509538,2	MCF-7	breast:
3	chr3:49449761..49451817-chr3:49454782..49457438,2	MCF-7	breast:

Variant related genes	Relation type
NICN1-AS1	TF binding region
ENSG00000145020	Chromatin interaction
ENSG00000067560	Chromatin interaction
ENSG00000145022	Chromatin interaction
ENSG00000173402	Chromatin interaction

Extended variants
information (count: 81 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:80)

rs_ID	r²[population]
rs10212296	0.85[AMR][1000 genomes]
rs1050450	0.92[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs10640	0.84[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11130192	0.90[ASN][1000 genomes]
rs11706370	0.98[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11711485	0.97[AMR][1000 genomes];0.88[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs11711536	0.89[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs11712569	0.88[AMR][1000 genomes]
rs11713474	0.82[AMR][1000 genomes]
rs11715915	0.97[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11716974	0.98[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs11719996	0.91[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs11922013	0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11926781	0.83[AMR][1000 genomes]
rs12330269	0.91[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs13079082	0.86[AMR][1000 genomes]
rs13079643	0.82[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs13086611	0.86[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs13087851	0.80[AFR][1000 genomes];0.94[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs13090388	0.92[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs1464566	0.90[ASN][1000 genomes]
rs1464567	0.90[ASN][1000 genomes]
rs1464568	0.90[ASN][1000 genomes]
rs17080528	0.92[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs1800668	0.86[AFR][1000 genomes];0.94[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs1801143	0.86[AMR][1000 genomes]
rs1987628	0.86[AFR][1000 genomes];0.94[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs34196454	0.88[AMR][1000 genomes]
rs34293138	0.85[AMR][1000 genomes]
rs34363169	0.91[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs34427167	0.83[AMR][1000 genomes]
rs34588335	0.92[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs34937635	0.83[ASN][1000 genomes]
rs35115732	0.92[AFR][1000 genomes];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs35169793	0.92[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs35261698	0.89[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs35999162	0.82[AMR][1000 genomes]
rs3811697	0.82[AMR][1000 genomes]
rs3811699	0.92[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs3926569	0.89[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs4459909	0.90[ASN][1000 genomes]
rs4625	0.86[AMR][1000 genomes]
rs4855873	0.90[ASN][1000 genomes]
rs4855877	0.90[ASN][1000 genomes]
rs55957735	0.88[ASN][1000 genomes]
rs6446264	0.80[AFR][1000 genomes];0.94[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs6446272	0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6446274	0.83[ASN][1000 genomes]
rs6446277	0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs67216675	0.97[AMR][1000 genomes];0.88[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs67485053	0.94[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs6766131	0.89[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs6766581	0.91[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs6779524	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6784820	0.90[ASN][1000 genomes]
rs6792911	0.82[ASN][1000 genomes]
rs6793308	0.92[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs6797664	0.91[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs6809216	0.92[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs6997	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs71324962	0.95[AMR][1000 genomes];0.92[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs7622302	0.88[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs7623659	0.92[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs7630869	0.86[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs7633271	0.89[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs7643586	0.82[ASN][1000 genomes]
rs7646366	0.82[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs7648841	0.80[AFR][1000 genomes];0.94[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs9814873	0.98[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs9818590	0.89[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs9821311	0.89[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs9827021	0.89[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs9837027	0.82[AMR][1000 genomes]
rs9841110	0.92[AFR][1000 genomes];0.97[AMR][1000 genomes];0.88[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs9850072	0.91[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs9853683	0.91[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs9858280	0.82[AMR][1000 genomes]
rs9858418	0.86[AMR][1000 genomes]
rs9871380	0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9878943	0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[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	nsv834687	chr3:49448632-49631788	Flanking Active TSS Strong transcription Enhancers Weak transcription Active TSS Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	56 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs9859556	FAM212A	cis	Muscle Skeletal	GTEx
rs9859556	RBM6	Cis_1M	lymphoblastoid	RTeQTL
rs9859556	IHPK2	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:126 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:49450400-49459000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
2	chr3:49450400-49459400	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
3	chr3:49450600-49459000	Weak transcription	iPS-18 Cell Line	embryonic stem cell
4	chr3:49450800-49457800	Genic enhancers	Primary Natural Killer cells fromperipheralblood	blood
5	chr3:49450800-49459000	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
6	chr3:49450800-49459200	Weak transcription	Pancreatic Islets	Pancreatic Islet
7	chr3:49450800-49459200	Genic enhancers	Placenta	Placenta
8	chr3:49451000-49458000	Weak transcription	Small Intestine	intestine
9	chr3:49451200-49459000	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
10	chr3:49451200-49459400	Weak transcription	Fetal Brain Male	brain
11	chr3:49451200-49466200	Weak transcription	Psoas Muscle	Psoas
12	chr3:49451400-49459400	Weak transcription	Ovary	ovary
13	chr3:49451600-49458000	Strong transcription	NHLF	lung
14	chr3:49451600-49458200	Strong transcription	Fetal Intestine Small	intestine
15	chr3:49452000-49457400	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
16	chr3:49452000-49458200	Strong transcription	Brain Dorsolateral Prefrontal Cortex	brain
17	chr3:49452200-49457800	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
18	chr3:49452200-49458000	Strong transcription	Fetal Intestine Large	intestine
19	chr3:49452400-49457000	Genic enhancers	Skeletal Muscle Female	skeletal muscle
20	chr3:49452400-49458400	Strong transcription	Fetal Brain Female	brain
21	chr3:49453400-49457000	Genic enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
22	chr3:49453400-49458200	Weak transcription	NH-A	brain
23	chr3:49453400-49458400	Genic enhancers	Fetal Adrenal Gland	Adrenal Gland
24	chr3:49453600-49459000	Weak transcription	Rectal Smooth Muscle	rectum
25	chr3:49453800-49459000	Strong transcription	Breast Myoepithelial Primary Cells	Breast
26	chr3:49454000-49456400	Weak transcription	Duodenum Smooth Muscle	Duodenum
27	chr3:49454000-49458200	Strong transcription	Brain Cingulate Gyrus	brain
28	chr3:49454000-49459400	Weak transcription	Brain Angular Gyrus	brain
29	chr3:49454200-49457400	Enhancers	Primary T helper cells fromperipheralblood	blood
30	chr3:49454400-49456200	Weak transcription	HMEC	breast
31	chr3:49454400-49458600	Weak transcription	HUVEC	blood vessel
32	chr3:49454600-49456000	Enhancers	Primary T killer memory cells from peripheral blood	blood
33	chr3:49454600-49456400	Weak transcription	Colon Smooth Muscle	Colon
34	chr3:49454600-49456800	Enhancers	Fetal Heart	heart
35	chr3:49454600-49457800	Genic enhancers	Primary T cells fromperipheralblood	blood
36	chr3:49454600-49458200	Strong transcription	Fetal Lung	lung
37	chr3:49454600-49458800	Strong transcription	Fetal Stomach	stomach
38	chr3:49454800-49456200	Weak transcription	K562	blood
39	chr3:49454800-49456400	Weak transcription	Brain Hippocampus Middle	brain
40	chr3:49454800-49456600	Weak transcription	HUES48 Cell Line	embryonic stem cell
41	chr3:49454800-49456600	Genic enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
42	chr3:49454800-49457400	Enhancers	Primary T helper naive cells fromperipheralblood	blood
43	chr3:49454800-49457400	Enhancers	Primary T helper cells PMA-I stimulated	--
44	chr3:49454800-49457800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
45	chr3:49454800-49457800	Genic enhancers	Pancreas	Pancrea
46	chr3:49454800-49458000	Weak transcription	HSMM	muscle
47	chr3:49454800-49458200	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
48	chr3:49454800-49458200	Strong transcription	Stomach Smooth Muscle	stomach
49	chr3:49454800-49458200	Weak transcription	HSMMtube	muscle
50	chr3:49454800-49458800	Weak transcription	Stomach Mucosa	stomach

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