Variant report

Variant	rs13003982
Chromosome Location	chr2:100759078-100759079
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	BCL11A	chr2:100758830-100759309	GM12878	blood:	n/a	n/a
2	ETS1	chr2:100758826-100759331	GM12878	blood:	n/a	chr2:100759066-100759077
3	TCF12	chr2:100758851-100759297	GM12878	blood:	n/a	n/a
4	PAX5	chr2:100758696-100759269	GM12878	blood:	n/a	chr2:100759066-100759075
5	FOXM1	chr2:100758755-100759528	GM12878	blood:	n/a	n/a
6	POLR2A	chr2:100758215-100759360	GM12891	blood:	n/a	n/a
7	TCF3	chr2:100758828-100759319	GM12878	blood:	n/a	chr2:100759099-100759108
8	BCLAF1	chr2:100758783-100759361	GM12878	blood:	n/a	n/a
9	MTA3	chr2:100758908-100759382	GM12878	blood:	n/a	n/a
10	ELF1	chr2:100758903-100759406	GM12878	blood:	n/a	n/a
11	CEBPB	chr2:100758940-100759267	GM12878	blood:	n/a	n/a
12	CTCF	chr2:100759040-100759190	GM12873	blood:	n/a	n/a
13	POLR2A	chr2:100758240-100759315	GM12891	blood:	n/a	n/a
14	FOXM1	chr2:100758774-100759383	GM12878	blood:	n/a	n/a
15	ATF2	chr2:100758814-100759382	GM12878	blood:	n/a	n/a
16	STAT5A	chr2:100758906-100759371	GM12878	blood:	n/a	n/a
17	IRF4	chr2:100758773-100759471	GM12878	blood:	n/a	n/a
18	IKZF1	chr2:100758923-100759426	GM12878	blood:	n/a	n/a
19	RELA	chr2:100758758-100759286	GM19193	blood:	n/a	n/a
20	EP300	chr2:100758905-100759536	GM12878	blood:	n/a	chr2:100759110-100759124
21	BCL3	chr2:100758876-100759278	GM12878	blood:	n/a	n/a
22	ELF1	chr2:100758947-100759300	GM12878	blood:	n/a	n/a
23	NFIC	chr2:100758220-100759447	GM12878	blood:	n/a	n/a
24	WRNIP1	chr2:100758989-100759188	GM12878	blood:	n/a	n/a
25	SPI1	chr2:100758776-100759378	GM12891	blood:	n/a	n/a
26	RUNX3	chr2:100758361-100759428	GM12878	blood:	n/a	n/a
27	RELA	chr2:100758892-100759360	GM10847	blood:	n/a	n/a
28	SPI1	chr2:100758535-100759678	GM12878	blood:	n/a	chr2:100759648-100759661
29	TCF3	chr2:100758802-100759377	GM12878	blood:	n/a	chr2:100759099-100759108
30	PAX5	chr2:100758922-100759245	GM12891	blood:	n/a	chr2:100759066-100759075
31	MAZ	chr2:100758968-100759247	GM12878	blood:	n/a	n/a
32	YY1	chr2:100758932-100759346	GM12878	blood:	n/a	n/a
33	POLR2A	chr2:100758799-100759172	GM12878	blood:	n/a	n/a
34	MXI1	chr2:100758937-100759159	GM12878	blood:	n/a	n/a
35	RUNX3	chr2:100758248-100759419	GM12878	blood:	n/a	n/a
36	POLR2A	chr2:100758611-100759280	GM12878	blood:	n/a	n/a
37	RCOR1	chr2:100758931-100759438	GM12878	blood:	n/a	n/a
38	EGR1	chr2:100758946-100759254	GM12878	blood:	n/a	n/a
39	SRF	chr2:100758946-100759202	GM12878	blood:	n/a	n/a
40	POLR2A	chr2:100758566-100759332	GM12892	blood:	n/a	n/a
41	POLR2A	chr2:100758635-100759312	GM12892	blood:	n/a	n/a
42	RELA	chr2:100758424-100759389	GM15510	blood:	n/a	n/a
43	PAX5	chr2:100758571-100759349	GM12878	blood:	n/a	chr2:100759066-100759075
44	NFIC	chr2:100758721-100759401	GM12878	blood:	n/a	n/a
45	REST	chr2:100758957-100759193	GM12878	blood:	n/a	n/a
46	BATF	chr2:100758884-100759321	GM12878	blood:	n/a	n/a
47	POU2F2	chr2:100758943-100759165	GM12878	blood:	n/a	n/a
48	EBF1	chr2:100758849-100759316	GM12878	blood:	n/a	n/a
49	EP300	chr2:100759004-100759251	GM12878	blood:	n/a	chr2:100759110-100759124
50	RAD21	chr2:100758922-100759185	GM12878	blood:	n/a	n/a

Variant related genes	Relation type
AFF3	TF binding region

Extended variants
information (count: 54 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:50)

rs_ID	r²[population]
rs10185059	0.82[AFR][1000 genomes];0.89[AMR][1000 genomes];0.92[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10185510	0.82[AFR][1000 genomes];0.89[AMR][1000 genomes];0.92[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10197987	0.89[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10496344	0.96[CEU][hapmap];0.82[CHB][hapmap];0.88[CHD][hapmap];1.00[GIH][hapmap];0.95[JPT][hapmap];1.00[MEX][hapmap];0.98[TSI][hapmap];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11123809	0.87[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11123810	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11123811	1.00[CHB][hapmap];1.00[JPT][hapmap];0.99[ASN][1000 genomes]
rs11123812	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11123813	0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11679078	0.82[ASN][1000 genomes]
rs11681227	1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11681966	1.00[ASW][hapmap];0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11682173	0.81[ASN][1000 genomes]
rs11690905	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.95[TSI][hapmap];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11891046	0.89[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11899489	0.87[AFR][1000 genomes];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11900482	1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11902705	0.90[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12712064	1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12712065	1.00[CHB][hapmap];1.00[JPT][hapmap];0.99[ASN][1000 genomes]
rs12712067	0.89[ASW][hapmap];0.92[CEU][hapmap];1.00[CHB][hapmap];0.93[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.93[LWK][hapmap];0.95[MEX][hapmap];1.00[MKK][hapmap];0.98[TSI][hapmap];0.86[YRI][hapmap];0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12712068	1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12712071	0.82[AFR][1000 genomes];0.89[AMR][1000 genomes];0.91[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12987209	1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12987212	0.96[CEU][hapmap];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13005282	0.81[AMR][1000 genomes];0.89[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs13019618	0.82[ASN][1000 genomes]
rs13032454	1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs13415465	1.00[AMR][1000 genomes];0.93[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs13415583	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1370353	0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1821826	0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1821827	0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2009094	0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2009095	0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2118280	0.86[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs2164712	0.82[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs2309752	0.96[ASN][1000 genomes]
rs4490209	0.94[AFR][1000 genomes];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4850920	0.82[ASN][1000 genomes]
rs4850921	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[YRI][hapmap];0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4851252	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4851253	0.88[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4851254	0.81[ASN][1000 genomes]
rs4851256	0.91[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4851257	0.89[AFR][1000 genomes];0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs56054309	0.90[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7590378	0.89[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7593261	0.89[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7608424	0.92[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1003343	chr2:100241560-100848900	Weak transcription Enhancers Strong transcription Active TSS Bivalent Enhancer Flanking Active TSS ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
2	nsv535843	chr2:100241560-100848900	Genic enhancers Enhancers Weak transcription Bivalent Enhancer Active TSS Strong transcription Flanking Active TSS Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
3	nsv582530	chr2:100739970-100774287	Active TSS Bivalent Enhancer Weak transcription Flanking Active TSS Enhancers Strong transcription Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
4	nsv527481	chr2:100753490-100763006	Enhancers ZNF genes & repeats Weak transcription Flanking Active TSS Active TSS Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs13003982	MRPL30	cis	cerebellum	SCAN
rs13003982	MGAT4A	cis	parietal	SCAN
rs13003982	AFF3	cis	parietal	SCAN

Chromatin state (count:32 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:100746200-100764800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
2	chr2:100753800-100759800	Flanking Active TSS	Dnd41	blood
3	chr2:100756800-100759800	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
4	chr2:100757400-100759200	Active TSS	Primary B cells from peripheral blood	blood
5	chr2:100757400-100759600	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
6	chr2:100757800-100759400	Flanking Active TSS	Primary T helper cells fromperipheralblood	blood
7	chr2:100758200-100759200	Flanking Active TSS	Primary hematopoietic stem cells	blood
8	chr2:100758200-100759200	Active TSS	Primary T helper naive cells from peripheral blood	blood
9	chr2:100758200-100759200	Active TSS	Primary T regulatory cells fromperipheralblood	blood
10	chr2:100758200-100759400	Flanking Active TSS	Primary hematopoietic stem cells short term culture	blood
11	chr2:100758200-100759400	Flanking Active TSS	Primary T helper naive cells fromperipheralblood	blood
12	chr2:100758200-100761600	Enhancers	Primary monocytes fromperipheralblood	blood
13	chr2:100758400-100759200	Flanking Active TSS	Primary T helper 17 cells PMA-I stimulated	--
14	chr2:100758400-100759200	Flanking Active TSS	Primary Natural Killer cells fromperipheralblood	blood
15	chr2:100758400-100759400	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
16	chr2:100758400-100759600	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
17	chr2:100758400-100759600	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
18	chr2:100758600-100759200	Enhancers	Primary neutrophils fromperipheralblood	blood
19	chr2:100758600-100759200	Flanking Active TSS	Primary T cells fromperipheralblood	blood
20	chr2:100758600-100759200	Active TSS	Primary T killer memory cells from peripheral blood	blood
21	chr2:100758800-100759200	Flanking Active TSS	Fetal Thymus	thymus
22	chr2:100758800-100759400	Weak transcription	Spleen	Spleen
23	chr2:100758800-100765600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
24	chr2:100759000-100759200	Active TSS	Primary B cells from cord blood	blood
25	chr2:100759000-100759200	Enhancers	Primary mononuclear cells fromperipheralblood	Blood
26	chr2:100759000-100759200	Weak transcription	GM12878-XiMat	blood
27	chr2:100759000-100759400	Flanking Active TSS	Primary T cells from cord blood	blood
28	chr2:100759000-100759400	Flanking Active TSS	Primary T helper cells PMA-I stimulated	--
29	chr2:100759000-100759400	Flanking Active TSS	Thymus	Thymus
30	chr2:100759000-100759600	Enhancers	Primary T cells effector/memory enriched fromperipheralblood	blood
31	chr2:100759000-100759800	Enhancers	Primary T killer naive cells fromperipheralblood	blood
32	chr2:100759000-100763000	Weak transcription	Adipose Nuclei	Adipose

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