Variant report

Variant	rs10915833
Chromosome Location	chr1:225655806-225655807
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	FOXM1	chr1:225654717-225655883	GM12878	blood:	n/a	n/a
2	POLR2A	chr1:225654628-225656401	GM18951	blood:	n/a	n/a
3	POLR2A	chr1:225654309-225656619	GM12892	blood:	n/a	n/a
4	POLR2A	chr1:225654808-225655879	HUVEC	blood vessel:	n/a	n/a
5	POLR2A	chr1:225654635-225656409	GM15510	blood:	n/a	n/a
6	STAT1	chr1:225655404-225655850	GM12878	blood:	n/a	n/a
7	POLR2A	chr1:225654622-225655850	HUVEC	blood vessel:	n/a	n/a
8	SPI1	chr1:225655009-225655908	GM12878	blood:	n/a	chr1:225655683-225655696 chr1:225655116-225655129
9	POLR2A	chr1:225654390-225656619	GM12892	blood:	n/a	n/a
10	POLR2A	chr1:225654400-225656275	GM12892	blood:	n/a	n/a
11	POLR2A	chr1:225654288-225656480	GM12891	blood:	n/a	n/a
12	POLR2A	chr1:225654584-225655936	HL-60	blood:	n/a	n/a
13	POLR2A	chr1:225654584-225656659	GM18505	blood:	n/a	n/a
14	RUNX3	chr1:225654721-225655838	GM12878	blood:	n/a	n/a
15	POLR2A	chr1:225654441-225655901	GM12892	blood:	n/a	n/a
16	REST	chr1:225654670-225655816	HL-60	blood:	n/a	chr1:225655746-225655754
17	POLR2A	chr1:225654420-225656160	GM12878	blood:	n/a	n/a
18	POLR2A	chr1:225654636-225655922	HL-60	blood:	n/a	n/a
19	POLR2A	chr1:225654575-225655874	GM12878	blood:	n/a	n/a
20	RELA	chr1:225654783-225655870	GM19099	blood:	n/a	n/a
21	RUNX3	chr1:225654682-225656375	GM12878	blood:	n/a	n/a
22	MAZ	chr1:225654728-225656053	GM12878	blood:	n/a	chr1:225655478-225655488
23	RELA	chr1:225654760-225656233	GM10847	blood:	n/a	n/a
24	MTA3	chr1:225654516-225655889	GM12878	blood:	n/a	n/a
25	STAT5A	chr1:225654519-225655904	GM12878	blood:	n/a	chr1:225654744-225654756
26	POLR2A	chr1:225654522-225656622	Raji	blood:	n/a	n/a
27	RELA	chr1:225654751-225656350	GM15510	blood:	n/a	n/a
28	POLR2A	chr1:225654715-225656273	GM12878	blood:	n/a	n/a
29	POLR2A	chr1:225654548-225656523	GM19193	blood:	n/a	n/a
30	POLR2A	chr1:225654683-225656362	GM12891	blood:	n/a	n/a
31	CREB1	chr1:225655286-225655807	GM12878	blood:	n/a	n/a
32	POU2F2	chr1:225654564-225655854	GM12891	blood:	n/a	chr1:225655707-225655719 chr1:225655820-225655832
33	BHLHE40	chr1:225654779-225655825	GM12878	blood:	n/a	chr1:225655162-225655178 chr1:225655462-225655478
34	POLR2A	chr1:225654234-225655897	GM12878	blood:	n/a	n/a
35	POLR2A	chr1:225654561-225655817	GM12891	blood:	n/a	n/a
36	POLR2A	chr1:225654627-225655957	NB4	blood:	n/a	n/a
37	POLR2A	chr1:225654543-225656638	GM12878	blood:	n/a	n/a
38	POLR2A	chr1:225654604-225656042	GM18526	blood:	n/a	n/a
39	POLR2A	chr1:225655222-225655848	HUVEC	blood vessel:	n/a	n/a
40	MTA3	chr1:225654500-225656210	GM12878	blood:	n/a	n/a
41	POLR2A	chr1:225654595-225655870	GM12878	blood:	n/a	n/a
42	POLR2A	chr1:225654788-225655822	GM10847	blood:	n/a	n/a
43	FOXM1	chr1:225655201-225655856	GM12878	blood:	n/a	n/a
44	POLR2A	chr1:225654539-225656584	GM12891	blood:	n/a	n/a
45	POLR2A	chr1:225654364-225657030	GM12891	blood:	n/a	n/a
46	ZNF143	chr1:225654791-225655873	GM12878	blood:	n/a	n/a
47	STAT5A	chr1:225655746-225656061	GM12878	blood:	n/a	n/a
48	POLR2A	chr1:225654658-225656535	GM12892	blood:	n/a	n/a
49	NFIC	chr1:225654509-225656190	GM12878	blood:	n/a	n/a
50	PML	chr1:225654495-225656296	GM12878	blood:	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
ENSG00000196187	Chromatin interaction
ENSG00000143742	Chromatin interaction

Extended variants
information (count: 68 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:65)

rs_ID	r²[population]
rs10753406	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs10799311	0.96[AMR][1000 genomes];0.93[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs10799313	0.83[AFR][1000 genomes];0.82[AMR][1000 genomes];0.84[ASN][1000 genomes]
rs10799314	0.92[AMR][1000 genomes];0.86[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs10799316	0.82[ASN][1000 genomes]
rs10799317	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs10799318	0.85[AFR][1000 genomes];0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs10799319	0.81[AMR][1000 genomes];0.97[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs10915828	0.89[ASN][1000 genomes]
rs10915830	0.95[AMR][1000 genomes];0.92[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs10915834	0.90[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs10915835	0.90[AFR][1000 genomes];0.82[AMR][1000 genomes];0.84[ASN][1000 genomes]
rs10915837	0.89[AFR][1000 genomes];0.82[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs10915838	0.82[AFR][1000 genomes];0.81[AMR][1000 genomes]
rs10915839	0.81[AFR][1000 genomes];0.91[AMR][1000 genomes];0.99[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs10915847	0.95[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs11584675	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12028305	0.80[AMR][1000 genomes];0.96[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs1222440	0.81[AMR][1000 genomes];0.84[ASN][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	0.85[AMR][1000 genomes];0.95[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs3856156	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs4653637	0.85[ASN][1000 genomes]
rs4653639	0.80[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs4653643	0.85[AMR][1000 genomes];0.98[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs476540	0.84[EUR][1000 genomes]
rs487591	0.90[EUR][1000 genomes]
rs498350	0.88[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs510293	0.94[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs511649	0.90[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs516249	0.91[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs551996	0.94[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs554744	0.94[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs554992	0.87[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs561656	0.88[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs576861	0.94[EUR][1000 genomes]
rs6426076	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6426077	0.95[AFR][1000 genomes];0.82[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs6426078	0.94[AFR][1000 genomes];0.81[AMR][1000 genomes];0.84[ASN][1000 genomes]
rs6668770	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs6676201	0.88[AFR][1000 genomes];0.82[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs6678806	0.83[AFR][1000 genomes];0.82[AMR][1000 genomes];0.81[ASN][1000 genomes]
rs6697783	0.86[ASN][1000 genomes]
rs6702452	0.84[ASN][1000 genomes]
rs6702538	0.86[ASN][1000 genomes]
rs6702555	0.85[AFR][1000 genomes];0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs6751	0.82[AMR][1000 genomes];0.98[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs712062	0.89[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs7515907	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7515939	0.86[ASN][1000 genomes]
rs7515963	0.88[AFR][1000 genomes];0.82[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs7524766	0.80[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs7540181	0.95[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs7541598	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7549456	0.84[ASN][1000 genomes]
rs7555139	0.95[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs7555553	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs947034	0.95[AMR][1000 genomes];0.91[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs9804142	0.85[AFR][1000 genomes];0.87[AMR][1000 genomes];0.97[EUR][1000 genomes];0.83[ASN][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:2)

SNP	Gene	Cis/trans	Tissue	Source
rs10915833	RP11-496N12.9	cis	Thyroid	GTEx
rs10915833	LBR	cis	Artery Tibial	GTEx

Chromatin state (count:63 , 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	chr1:225654600-225656000	Flanking Active TSS	Primary B cells from cord blood	blood
9	chr1:225654600-225656200	Flanking Active TSS	Rectal Mucosa Donor 29	rectum
10	chr1:225654600-225656400	Flanking Active TSS	Primary T helper 17 cells PMA-I stimulated	--
11	chr1:225654600-225656400	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
12	chr1:225654600-225656400	Flanking Active TSS	Fetal Thymus	thymus
13	chr1:225654600-225656400	Flanking Active TSS	GM12878-XiMat	blood
14	chr1:225654600-225656600	Enhancers	Lung	lung
15	chr1:225654800-225656000	Flanking Active TSS	Primary monocytes fromperipheralblood	blood
16	chr1:225654800-225656000	Flanking Active TSS	Primary hematopoietic stem cells	blood
17	chr1:225654800-225656000	Flanking Active TSS	Primary hematopoietic stem cells short term culture	blood
18	chr1:225654800-225656200	Flanking Active TSS	Primary neutrophils fromperipheralblood	blood
19	chr1:225654800-225656200	Flanking Active TSS	Primary T helper memory cells from peripheral blood 1	blood
20	chr1:225654800-225656200	Flanking Active TSS	Primary Natural Killer cells fromperipheralblood	blood
21	chr1:225654800-225656200	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
22	chr1:225654800-225656200	Flanking Active TSS	Stomach Smooth Muscle	stomach
23	chr1:225654800-225656400	Flanking Active TSS	Primary T cells fromperipheralblood	blood
24	chr1:225654800-225656400	Flanking Active TSS	Primary T helper cells fromperipheralblood	blood
25	chr1:225654800-225656400	Flanking Active TSS	Primary T regulatory cells fromperipheralblood	blood
26	chr1:225654800-225656400	Flanking Active TSS	Primary T cells effector/memory enriched fromperipheralblood	blood
27	chr1:225654800-225656400	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
28	chr1:225655000-225656000	Active TSS	Primary T helper memory cells from peripheral blood 2	blood
29	chr1:225655000-225656000	Flanking Active TSS	Adipose Nuclei	Adipose
30	chr1:225655000-225656000	Flanking Active TSS	Fetal Muscle Leg	muscle
31	chr1:225655000-225656200	Flanking Active TSS	Primary mononuclear cells fromperipheralblood	Blood
32	chr1:225655000-225656400	Flanking Active TSS	Rectal Smooth Muscle	rectum
33	chr1:225655200-225656000	Active TSS	Primary T killer naive cells fromperipheralblood	blood
34	chr1:225655200-225656000	Active TSS	Primary T killer memory cells from peripheral blood	blood
35	chr1:225655200-225656000	Active TSS	Fetal Intestine Small	intestine
36	chr1:225655200-225656000	Enhancers	NH-A	brain
37	chr1:225655400-225656000	Active TSS	Duodenum Mucosa	Duodenum
38	chr1:225655400-225656200	Enhancers	Stomach Mucosa	stomach
39	chr1:225655400-225656400	Flanking Active TSS	Primary T helper cells PMA-I stimulated	--
40	chr1:225655400-225656400	Enhancers	Fetal Stomach	stomach
41	chr1:225655400-225662400	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
42	chr1:225655600-225656200	Flanking Active TSS	Primary B cells from peripheral blood	blood
43	chr1:225655600-225656400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
44	chr1:225655600-225658800	Weak transcription	HUES6 Cell Line	embryonic stem cell
45	chr1:225655600-225677000	Weak transcription	Right Atrium	heart
46	chr1:225655800-225656000	Enhancers	Colonic Mucosa	Colon
47	chr1:225655800-225656000	Flanking Active TSS	Duodenum Smooth Muscle	Duodenum
48	chr1:225655800-225656200	Weak transcription	Liver	Liver
49	chr1:225655800-225656200	Enhancers	Placenta	Placenta
50	chr1:225655800-225656200	Flanking Active TSS	Thymus	Thymus

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