Variant report

Variant	rs7543548
Chromosome Location	chr1:93441080-93441081
allele	C/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	SP1	chr1:93441032-93441548	GM12878	blood:	n/a	n/a
2	NFIC	chr1:93440942-93441886	GM12878	blood:	n/a	n/a
3	TCF3	chr1:93441041-93441539	GM12878	blood:	n/a	chr1:93441277-93441287 chr1:93441279-93441292
4	BATF	chr1:93440966-93441529	GM12878	blood:	n/a	chr1:93441246-93441257
5	STAT5A	chr1:93441005-93441601	GM12878	blood:	n/a	n/a
6	BATF	chr1:93441065-93441448	GM12878	blood:	n/a	chr1:93441246-93441257
7	MEF2A	chr1:93441028-93441557	GM12878	blood:	n/a	chr1:93441221-93441236
8	EBF1	chr1:93441071-93441521	GM12878	blood:	n/a	n/a
9	EBF1	chr1:93441034-93441598	GM12878	blood:	n/a	n/a
10	FOXM1	chr1:93441026-93441550	GM12878	blood:	n/a	n/a
11	NFATC1	chr1:93441020-93441673	GM12878	blood:	n/a	n/a
12	POU2F2	chr1:93440953-93441597	GM12878	blood:	n/a	n/a
13	BCL3	chr1:93441046-93441539	GM12878	blood:	n/a	n/a
14	NFATC1	chr1:93441059-93441590	GM12878	blood:	n/a	n/a
15	FOXM1	chr1:93440980-93441632	GM12878	blood:	n/a	n/a
16	BHLHE40	chr1:93440696-93441658	GM12878	blood:	n/a	n/a
17	MEF2C	chr1:93441017-93441543	GM12878	blood:	n/a	chr1:93441221-93441236
18	SPI1	chr1:93440832-93441847	GM12878	blood:	n/a	n/a
19	EP300	chr1:93441030-93441482	GM12878	blood:	n/a	n/a
20	POU2F2	chr1:93441027-93441510	GM12891	blood:	n/a	n/a
21	POLR2A	chr1:93440454-93441511	GM18505	blood:	n/a	n/a
22	MAX	chr1:93440732-93441606	GM12878	blood:	n/a	chr1:93441397-93441407
23	ATF2	chr1:93441044-93441545	GM12878	blood:	n/a	n/a
24	MTA3	chr1:93441032-93441575	GM12878	blood:	n/a	n/a
25	YY1	chr1:93440800-93441466	GM12878	blood:	n/a	n/a
26	PAX5	chr1:93441011-93441516	GM12878	blood:	n/a	n/a
27	RELA	chr1:93440451-93441566	GM10847	blood:	n/a	n/a
28	PML	chr1:93441008-93441666	GM12878	blood:	n/a	n/a
29	STAT5A	chr1:93441060-93441518	GM12878	blood:	n/a	n/a
30	YY1	chr1:93440971-93441541	GM12878	blood:	n/a	n/a
31	SPI1	chr1:93441060-93441548	GM12878	blood:	n/a	n/a
32	RUNX3	chr1:93440971-93441615	GM12878	blood:	n/a	n/a
33	RELA	chr1:93441025-93441578	GM18951	blood:	n/a	n/a
34	SPI1	chr1:93441036-93441621	GM12891	blood:	n/a	n/a
35	SP1	chr1:93441022-93441565	GM12878	blood:	n/a	n/a
36	CEBPB	chr1:93441028-93441654	GM12878	blood:	n/a	n/a
37	RELA	chr1:93440553-93441607	GM19099	blood:	n/a	n/a
38	YY1	chr1:93440970-93441501	GM12892	blood:	n/a	n/a
39	IRF4	chr1:93441006-93441598	GM12878	blood:	n/a	n/a
40	RELA	chr1:93441037-93441569	GM12878	blood:	n/a	n/a
41	EP300	chr1:93441063-93441795	GM12878	blood:	n/a	n/a
42	POLR2A	chr1:93440437-93441560	Raji	blood:	n/a	n/a
43	PAX5	chr1:93441076-93441495	GM12878	blood:	n/a	n/a
44	MTA3	chr1:93440935-93441669	GM12878	blood:	n/a	n/a
45	POLR2A	chr1:93440405-93441618	GM12878	blood:	n/a	n/a
46	SPI1	chr1:93441014-93441668	GM12891	blood:	n/a	n/a
47	PAX5	chr1:93441026-93441504	GM12878	blood:	n/a	n/a
48	BCLAF1	chr1:93441023-93441633	GM12878	blood:	n/a	n/a
49	BCL11A	chr1:93441037-93441495	GM12878	blood:	n/a	n/a
50	IRF4	chr1:93440986-93441533	GM12878	blood:	n/a	n/a

Variant related genes	Relation type
RN7SL692P	TF binding region

Extended variants
information (count: 62 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:61)

rs_ID	r²[population]
rs10493863	0.85[EUR][1000 genomes]
rs10874751	0.82[EUR][1000 genomes]
rs10874753	0.80[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs11164835	0.84[EUR][1000 genomes]
rs11164836	0.84[EUR][1000 genomes]
rs11164840	0.83[EUR][1000 genomes]
rs11164842	0.85[EUR][1000 genomes]
rs11164843	0.85[EUR][1000 genomes]
rs11164844	0.85[EUR][1000 genomes]
rs11164845	0.85[EUR][1000 genomes]
rs11577636	0.85[EUR][1000 genomes]
rs11578986	0.85[EUR][1000 genomes]
rs11583491	0.88[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11587920	0.85[EUR][1000 genomes]
rs12059883	0.84[EUR][1000 genomes]
rs12060952	0.84[EUR][1000 genomes]
rs12065253	0.85[EUR][1000 genomes]
rs12066638	0.83[EUR][1000 genomes]
rs12069727	0.85[EUR][1000 genomes]
rs12074608	0.85[EUR][1000 genomes]
rs12081675	0.86[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12745968	0.85[EUR][1000 genomes]
rs17380908	0.85[EUR][1000 genomes]
rs2255717	0.83[EUR][1000 genomes]
rs2255723	0.84[EUR][1000 genomes]
rs2263247	0.83[EUR][1000 genomes]
rs2774954	0.82[EUR][1000 genomes]
rs2774956	0.83[EUR][1000 genomes]
rs2811589	0.83[EUR][1000 genomes]
rs2811590	0.83[EUR][1000 genomes]
rs2811591	0.81[EUR][1000 genomes]
rs34041593	0.86[ASN][1000 genomes]
rs34084844	0.84[EUR][1000 genomes]
rs34098754	0.86[ASN][1000 genomes]
rs34389767	0.81[EUR][1000 genomes]
rs34398175	0.84[EUR][1000 genomes]
rs35367625	0.85[EUR][1000 genomes]
rs35807969	0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4351651	0.83[EUR][1000 genomes]
rs4420089	0.84[EUR][1000 genomes]
rs4450029	0.85[EUR][1000 genomes]
rs4561051	0.84[EUR][1000 genomes]
rs4592265	0.85[EUR][1000 genomes]
rs56193705	0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6604028	0.83[EUR][1000 genomes]
rs6604029	0.85[EUR][1000 genomes]
rs6604030	0.85[EUR][1000 genomes]
rs6666223	0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs6694051	0.85[EUR][1000 genomes]
rs6698082	0.84[EUR][1000 genomes]
rs6698179	0.85[EUR][1000 genomes]
rs6698233	0.85[EUR][1000 genomes]
rs7417198	0.85[EUR][1000 genomes]
rs7515257	0.85[EUR][1000 genomes]
rs7517935	0.85[EUR][1000 genomes]
rs7542608	0.85[EUR][1000 genomes]
rs7550347	0.85[EUR][1000 genomes]
rs9439948	0.83[EUR][1000 genomes]
rs9440134	0.83[EUR][1000 genomes]
rs949915	0.83[EUR][1000 genomes]
rs9651257	0.84[EUR][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	nsv1008602	chr1:93176811-93640808	Enhancers Weak transcription Strong transcription Active TSS Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	51 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs7543548	FAM69A,RPL5	cis	cerebellar cortex	BrainEAC
rs7543548	FAM69A,RPL5	cis	brain	BrainEAC
rs7543548	FAM69A,RPL5	cis	hippocampus	BrainEAC
rs7543548	FAM69A,RPL5	cis	temporal cortex	BrainEAC

Chromatin state (count:30 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:93428400-93445800	Weak transcription	Rectal Mucosa Donor 31	rectum
2	chr1:93433200-93445000	Enhancers	Primary B cells from cord blood	blood
3	chr1:93434200-93445600	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
4	chr1:93436200-93441800	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
5	chr1:93437000-93441800	Enhancers	Primary monocytes fromperipheralblood	blood
6	chr1:93437600-93441400	Enhancers	Primary T cells fromperipheralblood	blood
7	chr1:93438000-93441800	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
8	chr1:93438000-93443600	Enhancers	Primary T helper cells fromperipheralblood	blood
9	chr1:93438200-93443400	Enhancers	Primary T regulatory cells fromperipheralblood	blood
10	chr1:93438800-93446000	Weak transcription	Sigmoid Colon	Sigmoid Colon
11	chr1:93439000-93444400	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
12	chr1:93439400-93441600	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
13	chr1:93439400-93446400	Weak transcription	Thymus	Thymus
14	chr1:93439600-93441200	Weak transcription	Primary T helper naive cells from peripheral blood	blood
15	chr1:93439600-93441200	Weak transcription	Primary T killer memory cells from peripheral blood	blood
16	chr1:93439600-93441200	Weak transcription	K562	blood
17	chr1:93439600-93443000	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
18	chr1:93439600-93445600	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
19	chr1:93439600-93446000	Weak transcription	Fetal Thymus	thymus
20	chr1:93439600-93446400	Weak transcription	Duodenum Mucosa	Duodenum
21	chr1:93439800-93441200	Weak transcription	Primary T cells from cord blood	blood
22	chr1:93440200-93441800	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
23	chr1:93440400-93441600	Flanking Active TSS	GM12878-XiMat	blood
24	chr1:93440400-93441600	Enhancers	Monocytes-CD14+_RO01746	blood
25	chr1:93440600-93441400	Enhancers	Primary hematopoietic stem cells short term culture	blood
26	chr1:93440600-93441400	Enhancers	Skeletal Muscle Female	skeletal muscle
27	chr1:93440600-93441600	Enhancers	Dnd41	blood
28	chr1:93440600-93443000	Enhancers	Primary T helper cells PMA-I stimulated	--
29	chr1:93440800-93441400	Weak transcription	Rectal Mucosa Donor 29	rectum
30	chr1:93441000-93447800	Enhancers	Primary B cells from peripheral blood	blood

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