Variant report

Variant	rs16871306
Chromosome Location	chr6:11386499-11386500
allele	A/C
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	NFIC	chr6:11386463-11387245	GM12878	blood:	n/a	n/a
2	ATF2	chr6:11386445-11387032	GM12878	blood:	n/a	n/a
3	RUNX3	chr6:11386481-11386929	GM12878	blood:	n/a	n/a
4	IRF4	chr6:11386453-11387024	GM12878	blood:	n/a	chr6:11386718-11386732
5	EBF1	chr6:11386484-11386886	GM12878	blood:	n/a	n/a
6	EP300	chr6:11386488-11386913	GM12878	blood:	n/a	chr6:11386546-11386560
7	POU2F2	chr6:11386488-11386885	GM12891	blood:	n/a	n/a
8	PAX5	chr6:11386458-11387046	GM12878	blood:	n/a	n/a
9	BCL11A	chr6:11386493-11386987	GM12878	blood:	n/a	n/a
10	POU2F2	chr6:11386454-11387025	GM12878	blood:	n/a	n/a
11	PML	chr6:11386364-11387087	GM12878	blood:	n/a	n/a
12	IRF4	chr6:11386456-11387000	GM12878	blood:	n/a	chr6:11386718-11386732
13	MEF2A	chr6:11386470-11387036	GM12878	blood:	n/a	n/a
14	NFIC	chr6:11386365-11387082	GM12878	blood:	n/a	n/a
15	BCLAF1	chr6:11386429-11386969	GM12878	blood:	n/a	n/a
16	ATF2	chr6:11386449-11387082	GM12878	blood:	n/a	n/a
17	CEBPB	chr6:11386471-11387071	GM12878	blood:	n/a	n/a
18	MTA3	chr6:11386460-11386977	GM12878	blood:	n/a	n/a
19	STAT5A	chr6:11386451-11386972	GM12878	blood:	n/a	n/a
20	TCF3	chr6:11386497-11386958	GM12878	blood:	n/a	n/a
21	BHLHE40	chr6:11386484-11387114	GM12878	blood:	n/a	n/a
22	SP1	chr6:11386471-11386882	GM12878	blood:	n/a	n/a
23	FOXM1	chr6:11386412-11387022	GM12878	blood:	n/a	n/a
24	MTA3	chr6:11386411-11387063	GM12878	blood:	n/a	n/a
25	RUNX3	chr6:11386415-11387013	GM12878	blood:	n/a	n/a
26	BCLAF1	chr6:11386442-11387085	GM12878	blood:	n/a	n/a
27	FOXM1	chr6:11386483-11387018	GM12878	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr6:11385040..11387245-chr6:11401910..11404147,2	K562	blood:
2	chr6:11229965..11235177-chr6:11385041..11393111,14	MCF-7	breast:
3	chr6:11342539..11346028-chr6:11385686..11392115,8	MCF-7	breast:
4	chr6:11384266..11387041-chr6:11387793..11390164,2	MCF-7	breast:

Variant related genes	Relation type
NEDD9	TF binding region
ENSG00000111859	Chromatin interaction

Extended variants
information (count: 23 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:20)

rs_ID	r²[population]
rs10484453	1.00[ASW][hapmap];1.00[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];0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10484454	1.00[ASW][hapmap];1.00[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];0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12524463	0.92[ASN][1000 genomes]
rs12525329	0.91[AFR][1000 genomes];0.89[AMR][1000 genomes];0.86[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12525704	0.91[AFR][1000 genomes];0.89[AMR][1000 genomes];0.86[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12525719	0.82[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12525737	0.82[AFR][1000 genomes]
rs12526759	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12527813	0.89[AMR][1000 genomes];0.86[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs16871291	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.86[AFR][1000 genomes];0.83[AMR][1000 genomes];0.86[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs16871294	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4607428	1.00[CEU][hapmap];1.00[JPT][hapmap];0.88[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6903648	0.85[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[ASN][1000 genomes]
rs6935901	0.83[YRI][hapmap]
rs73366863	0.92[ASN][1000 genomes]
rs73722961	0.85[ASN][1000 genomes]
rs7742703	0.92[ASN][1000 genomes]
rs7752886	0.92[ASN][1000 genomes]
rs7760294	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.86[AFR][1000 genomes];0.83[AMR][1000 genomes];0.88[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs926314	1.00[CEU][hapmap];1.00[JPT][hapmap];0.83[AMR][1000 genomes];0.86[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	nsv1021078	chr6:10819083-11558560	Enhancers Strong transcription Active TSS Flanking Active TSS Weak transcription Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	47 gene(s)	inside rSNPs	diseases
2	nsv538135	chr6:10819083-11558560	Weak transcription Enhancers Strong transcription Flanking Active TSS Bivalent Enhancer Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	47 gene(s)	inside rSNPs	diseases
3	nsv432848	chr6:11371614-11560114	Enhancers Active TSS Weak transcription ZNF genes & repeats Flanking Active TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:31 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:11377800-11386600	Weak transcription	HepG2	liver
2	chr6:11382600-11386800	Weak transcription	Colonic Mucosa	Colon
3	chr6:11382600-11389400	Weak transcription	Lung	lung
4	chr6:11382600-11392400	Weak transcription	Right Atrium	heart
5	chr6:11383000-11386800	Weak transcription	Rectal Mucosa Donor 29	rectum
6	chr6:11383200-11388600	Weak transcription	Primary hematopoietic stem cells	blood
7	chr6:11383200-11390200	Weak transcription	Spleen	Spleen
8	chr6:11383400-11386600	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
9	chr6:11383400-11388000	Weak transcription	Sigmoid Colon	Sigmoid Colon
10	chr6:11383400-11392600	Weak transcription	Duodenum Mucosa	Duodenum
11	chr6:11383600-11386600	Weak transcription	Primary monocytes fromperipheralblood	blood
12	chr6:11383600-11386800	Weak transcription	Primary T helper naive cells from peripheral blood	blood
13	chr6:11383600-11387000	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
14	chr6:11383600-11393000	Weak transcription	Small Intestine	intestine
15	chr6:11383800-11386600	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
16	chr6:11383800-11386600	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
17	chr6:11383800-11386600	Weak transcription	Monocytes-CD14+_RO01746	blood
18	chr6:11383800-11386800	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
19	chr6:11383800-11392600	Weak transcription	Primary T helper cells PMA-I stimulated	--
20	chr6:11384000-11388000	Weak transcription	Primary neutrophils fromperipheralblood	blood
21	chr6:11384200-11386800	Enhancers	Placenta Amnion	Placenta Amnion
22	chr6:11385200-11389200	Enhancers	Primary B cells from cord blood	blood
23	chr6:11385200-11389800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
24	chr6:11385600-11390400	Enhancers	Primary B cells from peripheral blood	blood
25	chr6:11385800-11386800	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
26	chr6:11385800-11388800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
27	chr6:11385800-11393400	Weak transcription	Aorta	Aorta
28	chr6:11386000-11388400	Weak transcription	Breast Myoepithelial Primary Cells	Breast
29	chr6:11386000-11393600	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
30	chr6:11386200-11386600	Weak transcription	Primary T helper cells fromperipheralblood	blood
31	chr6:11386200-11387400	Flanking Active TSS	GM12878-XiMat	blood

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