Variant report

Variant	rs4849402
Chromosome Location	chr2:111873932-111873933
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	ATF2	chr2:111873498-111874121	GM12878	blood:	n/a	n/a
2	CTCF	chr2:111873049-111875558	A549	lung:	n/a	chr2:111875132-111875153 chr2:111874765-111874786 chr2:111875130-111875148 chr2:111873712-111873728 chr2:111875135-111875143
3	RUNX3	chr2:111873408-111874352	GM12878	blood:	n/a	n/a
4	BCLAF1	chr2:111873517-111873948	GM12878	blood:	n/a	n/a
5	BCL3	chr2:111873469-111874018	GM12878	blood:	n/a	n/a
6	MEF2C	chr2:111873494-111874093	GM12878	blood:	n/a	chr2:111873821-111873836
7	MAZ	chr2:111873371-111874331	GM12878	blood:	n/a	n/a
8	ZNF384	chr2:111873510-111874302	GM12878	blood:	n/a	n/a
9	IRF4	chr2:111873463-111874259	GM12878	blood:	n/a	n/a
10	SP1	chr2:111873527-111874204	GM12878	blood:	n/a	n/a
11	STAT5A	chr2:111873440-111874110	GM12878	blood:	n/a	n/a
12	BCL11A	chr2:111873498-111874315	GM12878	blood:	n/a	n/a
13	RELA	chr2:111873521-111874192	GM19099	blood:	n/a	n/a
14	BCLAF1	chr2:111873461-111874247	GM12878	blood:	n/a	n/a
15	TBL1XR1	chr2:111873466-111875169	GM12878	blood:	n/a	n/a
16	ZEB1	chr2:111873882-111874214	GM12878	blood:	n/a	n/a
17	MXI1	chr2:111873483-111874911	GM12878	blood:	n/a	n/a
18	SMC3	chr2:111873459-111875292	GM12878	blood:	n/a	chr2:111874765-111874779
19	POU2F2	chr2:111873567-111873974	GM12878	blood:	n/a	chr2:111873678-111873691 chr2:111873668-111873681 chr2:111873666-111873680 chr2:111873668-111873681 chr2:111873668-111873681
20	MEF2A	chr2:111873394-111874096	GM12878	blood:	n/a	chr2:111873821-111873836
21	SP1	chr2:111873589-111873940	GM12878	blood:	n/a	n/a
22	STAT1	chr2:111873580-111874175	GM12878	blood:	n/a	n/a
23	IKZF1	chr2:111873367-111874812	GM12878	blood:	n/a	n/a
24	EP300	chr2:111873495-111873989	GM12878	blood:	n/a	n/a
25	CTCF	chr2:111873338-111875311	GM12878	blood:	n/a	chr2:111875132-111875153 chr2:111874765-111874786 chr2:111875130-111875148 chr2:111873712-111873728 chr2:111875135-111875143
26	BATF	chr2:111873546-111874273	GM12878	blood:	n/a	n/a
27	RAD21	chr2:111873500-111875165	GM12878	blood:	n/a	chr2:111874765-111874779 chr2:111875131-111875150 chr2:111874764-111874783 chr2:111874715-111874722
28	FOXM1	chr2:111873441-111874300	GM12878	blood:	n/a	n/a
29	POU2F2	chr2:111873468-111874274	GM12878	blood:	n/a	chr2:111873678-111873691 chr2:111873668-111873681 chr2:111873666-111873680 chr2:111873668-111873681 chr2:111873668-111873681
30	MTA3	chr2:111873491-111874075	GM12878	blood:	n/a	n/a
31	RUNX3	chr2:111873372-111874425	GM12878	blood:	n/a	n/a
32	RELA	chr2:111873407-111874460	GM12878	blood:	n/a	n/a
33	PAX5	chr2:111873472-111874294	GM12878	blood:	n/a	n/a
34	TBP	chr2:111873617-111874018	GM12878	blood:	n/a	n/a
35	CUX1	chr2:111873535-111874354	GM12878	blood:	n/a	n/a
36	PML	chr2:111873403-111874220	GM12878	blood:	n/a	n/a
37	EP300	chr2:111873445-111874964	GM12878	blood:	n/a	n/a
38	ZNF143	chr2:111873526-111874074	GM12878	blood:	n/a	n/a
39	ELK1	chr2:111873599-111874103	GM12878	blood:	n/a	n/a
40	POU2F2	chr2:111873612-111873941	GM12878	blood:	n/a	chr2:111873678-111873691 chr2:111873668-111873681 chr2:111873666-111873680 chr2:111873668-111873681 chr2:111873668-111873681
41	NFIC	chr2:111873365-111874305	GM12878	blood:	n/a	n/a
42	FOXM1	chr2:111873345-111874080	GM12878	blood:	n/a	n/a
43	STAT3	chr2:111873501-111874367	GM12878	blood:	n/a	n/a
44	CREB1	chr2:111873469-111874201	GM12878	blood:	n/a	n/a
45	CEBPB	chr2:111873413-111874171	GM12878	blood:	n/a	chr2:111873688-111873700
46	MAX	chr2:111873553-111874209	GM12878	blood:	n/a	n/a
47	EP300	chr2:111873500-111874750	GM12878	blood:	n/a	n/a
48	BATF	chr2:111873502-111874332	GM12878	blood:	n/a	n/a
49	NFIC	chr2:111873299-111874416	GM12878	blood:	n/a	n/a
50	NFATC1	chr2:111873440-111874182	GM12878	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr2:111807803..111810295-chr2:111873286..111875323,2	MCF-7	breast:
2	chr2:111786376..111787035-chr2:111873340..111875017,8	MCF-7	breast:

Variant related genes	Relation type
BCL2L11	TF binding region
ENSG00000204581	TF binding region

Extended variants
information (count: 35 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:32)

rs_ID	r²[population]
rs10166773	0.86[JPT][hapmap]
rs10189015	1.00[CEU][hapmap];0.91[CHB][hapmap];1.00[JPT][hapmap];0.82[AMR][1000 genomes];0.93[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs10211562	0.82[ASN][1000 genomes]
rs1054873	0.88[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.89[LWK][hapmap];1.00[MEX][hapmap];0.94[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.91[AFR][1000 genomes];0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11674517	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[AMR][1000 genomes];0.93[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs13398360	0.86[JPT][hapmap]
rs1439287	0.96[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];0.96[GIH][hapmap];1.00[JPT][hapmap];0.86[LWK][hapmap];1.00[MEX][hapmap];0.85[MKK][hapmap];1.00[TSI][hapmap];0.85[YRI][hapmap];0.82[AFR][1000 genomes];0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1821968	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.85[MKK][hapmap];0.98[TSI][hapmap];0.87[AMR][1000 genomes];0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1837366	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1837367	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[YRI][hapmap];0.84[AFR][1000 genomes];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1837368	1.00[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1837369	1.00[CEU][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.85[MKK][hapmap];1.00[TSI][hapmap];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2241841	0.88[AFR][1000 genomes];0.87[AMR][1000 genomes];0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2241842	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[YRI][hapmap];0.82[AFR][1000 genomes];0.85[AMR][1000 genomes];0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2241844	0.87[AMR][1000 genomes];0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs3789061	1.00[CEU][hapmap];0.91[CHB][hapmap];1.00[JPT][hapmap];0.82[AMR][1000 genomes];0.93[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs3789064	0.82[AMR][1000 genomes];0.93[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs3789065	1.00[CEU][hapmap];0.91[CHB][hapmap];0.98[CHD][hapmap];0.81[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.95[TSI][hapmap];0.82[AMR][1000 genomes];0.93[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs3789068	1.00[CEU][hapmap];0.91[CHB][hapmap];0.98[CHD][hapmap];0.83[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.95[TSI][hapmap];0.82[AMR][1000 genomes];0.93[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs4302219	0.90[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs4627572	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[YRI][hapmap];0.90[AFR][1000 genomes];0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4849403	1.00[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs56952027	0.86[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs60286362	0.87[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6708784	0.89[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs6726007	0.86[CEU][hapmap];0.89[JPT][hapmap]
rs6732491	0.86[JPT][hapmap]
rs6734942	0.87[ASN][1000 genomes]
rs6760053	0.90[JPT][hapmap]
rs7577824	0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7593638	0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7602904	0.80[AFR][1000 genomes];0.85[AMR][1000 genomes];0.94[EUR][1000 genomes];0.90[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	nsv874838	chr2:111376870-112046226	Weak transcription Strong transcription ZNF genes & repeats Active TSS Enhancers Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Flanking Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	33 gene(s)	inside rSNPs	diseases
2	nsv834331	chr2:111812139-112004678	Enhancers ZNF genes & repeats Flanking Active TSS Weak transcription Genic enhancers Flanking Bivalent TSS/Enh Active TSS Strong transcription Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	22 gene(s)	inside rSNPs	diseases
3	nsv874842	chr2:111870220-111892984	Bivalent/Poised TSS Flanking Active TSS Weak transcription Flanking Bivalent TSS/Enh Active TSS Strong transcription Enhancers Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	17 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs4849402	BCL2L11	cis	cerebellum	SCAN
rs4849402	SULT1C2	cis	cerebellum	SCAN
rs4849402	DPP10	cis	parietal	SCAN

Chromatin state (count:6 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:111860200-111875000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
2	chr2:111867000-111874400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
3	chr2:111869000-111874600	Weak transcription	Breast Myoepithelial Primary Cells	Breast
4	chr2:111873000-111874000	Enhancers	Fetal Intestine Small	intestine
5	chr2:111873400-111874400	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
6	chr2:111873400-111874400	Bivalent Enhancer	GM12878-XiMat	blood

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