Variant report

Variant	rs2486411
Chromosome Location	chr6:149387231-149387232
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	RXRA	chr6:149387178-149387441	GM12878	blood:	n/a	n/a
2	BATF	chr6:149387143-149387632	GM12878	blood:	n/a	n/a
3	FOXM1	chr6:149386910-149387787	GM12878	blood:	n/a	n/a
4	BCL11A	chr6:149387229-149387469	GM12878	blood:	n/a	n/a
5	TBP	chr6:149387084-149387856	GM12878	blood:	n/a	n/a
6	POU2F2	chr6:149387201-149387470	GM12878	blood:	n/a	n/a
7	POLR2A	chr6:149386790-149387780	GM12878	blood:	n/a	n/a
8	MEF2A	chr6:149387119-149387731	GM12878	blood:	n/a	n/a
9	RCOR1	chr6:149387105-149387796	GM12878	blood:	n/a	n/a
10	RFX5	chr6:149387091-149387634	GM12878	blood:	n/a	n/a
11	BCL11A	chr6:149387177-149387603	GM12878	blood:	n/a	n/a
12	WRNIP1	chr6:149386917-149387691	GM12878	blood:	n/a	n/a
13	PAX5	chr6:149387213-149387518	GM12878	blood:	n/a	n/a
14	SPI1	chr6:149387085-149387692	GM12891	blood:	n/a	chr6:149387124-149387137
15	POLR2A	chr6:149386906-149387715	GM12892	blood:	n/a	n/a
16	EBF1	chr6:149387112-149387533	GM12878	blood:	n/a	n/a
17	CHD2	chr6:149387018-149387851	GM12878	blood:	n/a	n/a
18	POLR2A	chr6:149387076-149387704	GM12891	blood:	n/a	n/a
19	TBL1XR1	chr6:149387159-149387898	GM12878	blood:	n/a	n/a
20	YY1	chr6:149387002-149387557	GM12878	blood:	n/a	chr6:149387268-149387284
21	EP300	chr6:149386978-149387688	GM12878	blood:	n/a	n/a
22	MTA3	chr6:149386651-149387884	GM12878	blood:	n/a	n/a
23	SMC3	chr6:149387103-149387753	GM12878	blood:	n/a	n/a
24	RELA	chr6:149387077-149387859	GM18505	blood:	n/a	n/a
25	IRF4	chr6:149387043-149387648	GM12878	blood:	n/a	n/a
26	SP1	chr6:149387136-149387613	GM12878	blood:	n/a	n/a
27	CTCF	chr6:149387015-149387521	GM12878	blood:	n/a	n/a
28	NFIC	chr6:149386765-149388020	GM12878	blood:	n/a	n/a
29	ELK1	chr6:149387226-149387693	GM12878	blood:	n/a	n/a
30	POLR2A	chr6:149386866-149387741	GM12878	blood:	n/a	n/a
31	POLR2A	chr6:149386760-149387778	GM12878	blood:	n/a	n/a
32	SPI1	chr6:149387107-149387653	GM12878	blood:	n/a	chr6:149387124-149387137
33	MAZ	chr6:149386963-149387769	GM12878	blood:	n/a	n/a
34	TAF1	chr6:149387082-149387465	GM12878	blood:	n/a	n/a
35	CHD1	chr6:149386880-149387717	GM12878	blood:	n/a	n/a
36	POLR2A	chr6:149387102-149387495	GM12891	blood:	n/a	n/a
37	STAT1	chr6:149387178-149387531	GM12878	blood:	n/a	n/a
38	POLR2A	chr6:149387067-149387493	GM12878	blood:	n/a	n/a
39	ZNF143	chr6:149387182-149387640	GM12878	blood:	n/a	n/a
40	CEBPB	chr6:149386923-149387923	GM12878	blood:	n/a	n/a
41	PML	chr6:149386894-149387777	GM12878	blood:	n/a	n/a
42	RELA	chr6:149387098-149387691	GM18951	blood:	n/a	n/a
43	POLR2A	chr6:149387142-149387511	GM12878	blood:	n/a	n/a
44	YY1	chr6:149387066-149387582	GM12892	blood:	n/a	chr6:149387268-149387284
45	CUX1	chr6:149387123-149387711	GM12878	blood:	n/a	n/a
46	POLR2A	chr6:149387128-149387524	GM12891	blood:	n/a	n/a
47	SP1	chr6:149387099-149387655	GM12878	blood:	n/a	chr6:149387614-149387628 chr6:149387619-149387628
48	USF2	chr6:149387112-149387601	GM12878	blood:	n/a	n/a
49	POLR2A	chr6:149386993-149387690	GM12891	blood:	n/a	n/a
50	ATF2	chr6:149387099-149387716	GM12878	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr6:149376456..149387248-chr6:149393069..149406749,44	MCF-7	breast:

Variant related genes	Relation type
UST	TF binding region

Extended variants
information (count: 13 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:9)

rs_ID	r²[population]
rs2340798	0.82[CEU][hapmap]
rs2486409	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.89[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2500549	0.88[CEU][hapmap]
rs6904550	0.83[CEU][hapmap]
rs6931675	0.81[CEU][hapmap]
rs7748978	0.89[CEU][hapmap]
rs7774457	0.85[CEU][hapmap]
rs9377188	0.89[CEU][hapmap]
rs9399678	0.82[CEU][hapmap]

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	nsv1032690	chr6:149206106-149398712	Enhancers Weak transcription Flanking Active TSS Active TSS Strong transcription ZNF genes & repeats Genic enhancers Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	11 gene(s)	inside rSNPs	diseases
2	nsv1032319	chr6:149271433-149550525	Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Strong transcription Active TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	15 gene(s)	inside rSNPs	diseases
3	nsv538470	chr6:149271433-149550525	Enhancers Weak transcription Active TSS Strong transcription Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	15 gene(s)	inside rSNPs	diseases
4	nsv830842	chr6:149272321-149427340	Enhancers Bivalent Enhancer ZNF genes & repeats Weak transcription Flanking Active TSS Strong transcription Genic enhancers Active TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	11 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:77 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:149354400-149400600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
2	chr6:149362800-149401400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
3	chr6:149363200-149394000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
4	chr6:149369000-149398800	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
5	chr6:149371400-149396400	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
6	chr6:149371800-149397000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
7	chr6:149379400-149388600	Enhancers	Fetal Thymus	thymus
8	chr6:149380800-149387400	Weak transcription	Cortex derived primary cultured neurospheres	brain
9	chr6:149380800-149388400	Enhancers	Fetal Stomach	stomach
10	chr6:149380800-149396200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
11	chr6:149381000-149394800	Weak transcription	HUES64 Cell Line	embryonic stem cell
12	chr6:149381000-149395000	Weak transcription	HUES48 Cell Line	embryonic stem cell
13	chr6:149381800-149394600	Weak transcription	H1 Cell Line	embryonic stem cell
14	chr6:149382200-149400000	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
15	chr6:149382400-149396000	Weak transcription	Fetal Muscle Trunk	muscle
16	chr6:149382800-149401400	Weak transcription	Esophagus	oesophagus
17	chr6:149383000-149389200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
18	chr6:149383000-149394800	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
19	chr6:149383000-149397000	Weak transcription	Pancreas	Pancrea
20	chr6:149383400-149387600	Enhancers	HepG2	liver
21	chr6:149384200-149387800	Weak transcription	Placenta	Placenta
22	chr6:149385200-149387600	Enhancers	Stomach Smooth Muscle	stomach
23	chr6:149385200-149404000	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
24	chr6:149385400-149387400	Weak transcription	Right Ventricle	heart
25	chr6:149385600-149387800	Enhancers	Fetal Lung	lung
26	chr6:149385600-149396400	Weak transcription	Aorta	Aorta
27	chr6:149385800-149397000	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
28	chr6:149386000-149387600	Enhancers	Liver	Liver
29	chr6:149386200-149397000	Weak transcription	Rectal Smooth Muscle	rectum
30	chr6:149386400-149387400	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
31	chr6:149386400-149387600	Enhancers	Primary T killer memory cells from peripheral blood	blood
32	chr6:149386400-149387800	Enhancers	Brain Hippocampus Middle	brain
33	chr6:149386400-149388400	Enhancers	Primary T killer naive cells fromperipheralblood	blood
34	chr6:149386400-149388600	Flanking Active TSS	Dnd41	blood
35	chr6:149386400-149388800	Enhancers	Primary monocytes fromperipheralblood	blood
36	chr6:149386400-149397000	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
37	chr6:149386600-149388200	Flanking Active TSS	GM12878-XiMat	blood
38	chr6:149386600-149397200	Weak transcription	Colon Smooth Muscle	Colon
39	chr6:149386800-149387600	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
40	chr6:149386800-149388200	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
41	chr6:149386800-149388600	Enhancers	Primary B cells from peripheral blood	blood
42	chr6:149386800-149388600	Enhancers	Primary T cells fromperipheralblood	blood
43	chr6:149387000-149387400	Enhancers	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
44	chr6:149387000-149387400	Flanking Active TSS	Primary T cells from cord blood	blood
45	chr6:149387000-149387400	Flanking Active TSS	Primary T helper naive cells from peripheral blood	blood
46	chr6:149387000-149387400	Flanking Active TSS	Primary T helper cells fromperipheralblood	blood
47	chr6:149387000-149387400	Flanking Active TSS	Primary T regulatory cells fromperipheralblood	blood
48	chr6:149387000-149387400	Enhancers	Colonic Mucosa	Colon
49	chr6:149387000-149387400	Enhancers	Duodenum Mucosa	Duodenum
50	chr6:149387000-149387400	Enhancers	Fetal Adrenal Gland	Adrenal Gland

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