Variant report

Variant	rs3856156
Chromosome Location	chr1:225655667-225655668
allele	A/G
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	GABPA	chr1:225654595-225655775	HL-60	blood:	n/a	n/a
2	SPI1	chr1:225655254-225655733	HL-60	blood:	n/a	chr1:225655683-225655696
3	TCF3	chr1:225655308-225655722	GM12878	blood:	n/a	n/a
4	FOXM1	chr1:225654717-225655883	GM12878	blood:	n/a	n/a
5	POLR2A	chr1:225654628-225656401	GM18951	blood:	n/a	n/a
6	POLR2A	chr1:225654309-225656619	GM12892	blood:	n/a	n/a
7	POLR2A	chr1:225654808-225655879	HUVEC	blood vessel:	n/a	n/a
8	POLR2A	chr1:225654635-225656409	GM15510	blood:	n/a	n/a
9	STAT1	chr1:225655404-225655850	GM12878	blood:	n/a	n/a
10	YY1	chr1:225655270-225655731	GM12878	blood:	n/a	n/a
11	POLR2A	chr1:225654622-225655850	HUVEC	blood vessel:	n/a	n/a
12	SPI1	chr1:225655009-225655908	GM12878	blood:	n/a	chr1:225655683-225655696 chr1:225655116-225655129
13	MAX	chr1:225654617-225655733	GM12878	blood:	n/a	chr1:225655478-225655488
14	POLR2A	chr1:225654390-225656619	GM12892	blood:	n/a	n/a
15	ATF2	chr1:225654627-225655750	GM12878	blood:	n/a	n/a
16	POLR2A	chr1:225654400-225656275	GM12892	blood:	n/a	n/a
17	GABPA	chr1:225655319-225655743	K562	blood:	n/a	n/a
18	EBF1	chr1:225654777-225655765	GM12878	blood:	n/a	chr1:225655015-225655024 chr1:225655013-225655026
19	POLR2A	chr1:225654288-225656480	GM12891	blood:	n/a	n/a
20	POLR2A	chr1:225654584-225655936	HL-60	blood:	n/a	n/a
21	SPI1	chr1:225655313-225655668	GM12878	blood:	n/a	n/a
22	POLR2A	chr1:225654584-225656659	GM18505	blood:	n/a	n/a
23	BRCA1	chr1:225655508-225655704	GM12878	blood:	n/a	n/a
24	TAF1	chr1:225655205-225655739	GM12891	blood:	n/a	n/a
25	RUNX3	chr1:225654721-225655838	GM12878	blood:	n/a	n/a
26	TAF1	chr1:225655246-225655754	GM12878	blood:	n/a	n/a
27	BCLAF1	chr1:225654674-225655751	GM12878	blood:	n/a	chr1:225655522-225655531 chr1:225655480-225655493
28	POLR2A	chr1:225654441-225655901	GM12892	blood:	n/a	n/a
29	MYC	chr1:225654683-225655770	NB4	blood:	n/a	chr1:225655478-225655488
30	POU2F2	chr1:225655321-225655743	GM12878	blood:	n/a	chr1:225655707-225655719
31	REST	chr1:225654670-225655816	HL-60	blood:	n/a	chr1:225655746-225655754
32	POLR2A	chr1:225654420-225656160	GM12878	blood:	n/a	n/a
33	FOS	chr1:225654768-225655716	HUVEC	blood vessel:	n/a	n/a
34	POLR2A	chr1:225654636-225655922	HL-60	blood:	n/a	n/a
35	POLR2A	chr1:225654575-225655874	GM12878	blood:	n/a	n/a
36	RELA	chr1:225654783-225655870	GM19099	blood:	n/a	n/a
37	RUNX3	chr1:225654682-225656375	GM12878	blood:	n/a	n/a
38	GATA1	chr1:225654747-225655671	PBDE	blood:	n/a	chr1:225655521-225655531 chr1:225655331-225655343
39	MAZ	chr1:225654728-225656053	GM12878	blood:	n/a	chr1:225655478-225655488
40	EGR1	chr1:225655439-225655708	GM12878	blood:	n/a	chr1:225655522-225655531
41	ETS1	chr1:225655244-225655785	GM12878	blood:	n/a	chr1:225655519-225655532 chr1:225655522-225655531 chr1:225655259-225655272 chr1:225655519-225655534
42	RELA	chr1:225654760-225656233	GM10847	blood:	n/a	n/a
43	MTA3	chr1:225654516-225655889	GM12878	blood:	n/a	n/a
44	POLR2A	chr1:225655273-225655781	PFSK-1	brain:	n/a	n/a
45	STAT5A	chr1:225654519-225655904	GM12878	blood:	n/a	chr1:225654744-225654756
46	POLR2A	chr1:225654522-225656622	Raji	blood:	n/a	n/a
47	RELA	chr1:225654751-225656350	GM15510	blood:	n/a	n/a
48	POU2F2	chr1:225655401-225655710	GM12878	blood:	n/a	n/a
49	ELF1	chr1:225655251-225655791	GM12878	blood:	n/a	n/a
50	ZNF263	chr1:225655447-225655687	HEK293-T-REx	kidney:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr1:225653928..225656403-chr1:225964311..225965919,2	MCF-7	breast:
2	chr1:225654995..225657413-chr1:226069983..226072182,2	MCF-7	breast:
3	chr1:225655109..225657230-chr1:226022691..226024869,2	K562	blood:

Variant related genes	Relation type
ENSG00000234476	TF binding region
ENSG00000143742	Chromatin interaction
ENSG00000196187	Chromatin interaction

Extended variants
information (count: 52 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:49)

rs_ID	r²[population]
rs10753406	1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs10799311	0.93[AFR][1000 genomes];0.99[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs10799314	0.87[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs10799315	0.80[AMR][1000 genomes]
rs10799317	0.95[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs10799318	0.86[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs10799319	0.84[AFR][1000 genomes];0.83[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs10915830	0.89[AFR][1000 genomes];0.97[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs10915833	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs10915834	0.90[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs10915839	0.91[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs10915847	0.95[EUR][1000 genomes]
rs11584675	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs12028305	0.84[AFR][1000 genomes];0.82[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs12729655	0.80[AMR][1000 genomes]
rs2639703	0.83[EUR][1000 genomes]
rs2639716	0.81[EUR][1000 genomes]
rs2657564	0.83[EUR][1000 genomes]
rs2657569	0.81[EUR][1000 genomes]
rs2840958	0.83[EUR][1000 genomes]
rs2840967	0.81[EUR][1000 genomes]
rs2840968	0.81[EUR][1000 genomes]
rs3820226	0.82[AFR][1000 genomes];0.87[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs4653639	0.80[AMR][1000 genomes]
rs4653643	0.86[AFR][1000 genomes];0.87[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs476540	0.84[EUR][1000 genomes]
rs487591	0.90[EUR][1000 genomes]
rs498350	0.88[EUR][1000 genomes]
rs510293	0.81[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs511649	0.90[EUR][1000 genomes]
rs516249	0.91[EUR][1000 genomes]
rs551996	0.81[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs554744	0.81[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs554992	0.87[EUR][1000 genomes]
rs561656	0.88[EUR][1000 genomes]
rs576861	0.81[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs6426076	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs6668770	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs6702555	0.89[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs6751	0.86[AFR][1000 genomes];0.84[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs712062	0.89[EUR][1000 genomes]
rs7515907	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7524766	0.97[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7540181	0.81[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs7541598	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7555139	0.95[EUR][1000 genomes]
rs7555553	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs947034	0.86[AFR][1000 genomes];0.97[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs9804142	0.82[AMR][1000 genomes];0.97[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv832714	chr1:225592333-225805396	Enhancers Flanking Active TSS Weak transcription ZNF genes & repeats Strong transcription Genic enhancers Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	20 gene(s)	inside rSNPs	diseases
2	nsv1004851	chr1:225614140-225684184	Enhancers Weak transcription Bivalent Enhancer Flanking Active TSS Active TSS Strong transcription ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	19 gene(s)	inside rSNPs	diseases
3	esv34905	chr1:225631404-225676582	Flanking Active TSS Enhancers Weak transcription Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats Strong transcription Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	17 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs3856156	RP11-496N12.9	cis	Thyroid	GTEx

Chromatin state (count:77 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:225649800-225662600	Weak transcription	Pancreas	Pancrea
2	chr1:225651400-225662400	Weak transcription	Fetal Brain Male	brain
3	chr1:225653600-225662400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
4	chr1:225653600-225662400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
5	chr1:225653800-225659600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
6	chr1:225654000-225656000	Enhancers	Hela-S3	cervix
7	chr1:225654400-225656400	Flanking Active TSS	Dnd41	blood
8	chr1:225654600-225655800	Enhancers	Spleen	Spleen
9	chr1:225654600-225656000	Flanking Active TSS	Primary B cells from cord blood	blood
10	chr1:225654600-225656200	Flanking Active TSS	Rectal Mucosa Donor 29	rectum
11	chr1:225654600-225656400	Flanking Active TSS	Primary T helper 17 cells PMA-I stimulated	--
12	chr1:225654600-225656400	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
13	chr1:225654600-225656400	Flanking Active TSS	Fetal Thymus	thymus
14	chr1:225654600-225656400	Flanking Active TSS	GM12878-XiMat	blood
15	chr1:225654600-225656600	Enhancers	Lung	lung
16	chr1:225654800-225656000	Flanking Active TSS	Primary monocytes fromperipheralblood	blood
17	chr1:225654800-225656000	Flanking Active TSS	Primary hematopoietic stem cells	blood
18	chr1:225654800-225656000	Flanking Active TSS	Primary hematopoietic stem cells short term culture	blood
19	chr1:225654800-225656200	Flanking Active TSS	Primary neutrophils fromperipheralblood	blood
20	chr1:225654800-225656200	Flanking Active TSS	Primary T helper memory cells from peripheral blood 1	blood
21	chr1:225654800-225656200	Flanking Active TSS	Primary Natural Killer cells fromperipheralblood	blood
22	chr1:225654800-225656200	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
23	chr1:225654800-225656200	Flanking Active TSS	Stomach Smooth Muscle	stomach
24	chr1:225654800-225656400	Flanking Active TSS	Primary T cells fromperipheralblood	blood
25	chr1:225654800-225656400	Flanking Active TSS	Primary T helper cells fromperipheralblood	blood
26	chr1:225654800-225656400	Flanking Active TSS	Primary T regulatory cells fromperipheralblood	blood
27	chr1:225654800-225656400	Flanking Active TSS	Primary T cells effector/memory enriched fromperipheralblood	blood
28	chr1:225654800-225656400	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
29	chr1:225655000-225655800	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
30	chr1:225655000-225655800	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
31	chr1:225655000-225655800	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
32	chr1:225655000-225655800	Active TSS	Liver	Liver
33	chr1:225655000-225655800	Active TSS	Brain Hippocampus Middle	brain
34	chr1:225655000-225655800	Flanking Active TSS	Colonic Mucosa	Colon
35	chr1:225655000-225655800	Flanking Active TSS	Fetal Adrenal Gland	Adrenal Gland
36	chr1:225655000-225655800	Flanking Active TSS	Placenta	Placenta
37	chr1:225655000-225655800	Active TSS	Sigmoid Colon	Sigmoid Colon
38	chr1:225655000-225655800	Flanking Active TSS	Skeletal Muscle Male	skeletal muscle
39	chr1:225655000-225655800	Active TSS	Thymus	Thymus
40	chr1:225655000-225655800	Flanking Active TSS	HUVEC	blood vessel
41	chr1:225655000-225656000	Active TSS	Primary T helper memory cells from peripheral blood 2	blood
42	chr1:225655000-225656000	Flanking Active TSS	Adipose Nuclei	Adipose
43	chr1:225655000-225656000	Flanking Active TSS	Fetal Muscle Leg	muscle
44	chr1:225655000-225656200	Flanking Active TSS	Primary mononuclear cells fromperipheralblood	Blood
45	chr1:225655000-225656400	Flanking Active TSS	Rectal Smooth Muscle	rectum
46	chr1:225655200-225655800	Active TSS	Primary T helper naive cells from peripheral blood	blood
47	chr1:225655200-225655800	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
48	chr1:225655200-225655800	Active TSS	Brain Anterior Caudate	brain
49	chr1:225655200-225655800	Active TSS	Brain Cingulate Gyrus	brain
50	chr1:225655200-225655800	Active TSS	Esophagus	oesophagus

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