Variant report

Variant	rs11878547
Chromosome Location	chr19:36393186-36393187
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:50)
CpG islands
(count:0)
Chromatin interactive
region (count:3)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:50 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	NFIC	chr19:36392761-36393684	GM12878	blood:	n/a	n/a
2	RUNX3	chr19:36392704-36393592	GM12878	blood:	n/a	n/a
3	STAT3	chr19:36393019-36393207	MCF10A-Er-Src	breast:	n/a	n/a
4	POLR2A	chr19:36392901-36393716	GM12891	blood:	n/a	n/a
5	POLR2A	chr19:36393168-36393712	GM15510	blood:	n/a	n/a
6	POLR2A	chr19:36392650-36393769	GM12878	blood:	n/a	n/a
7	SPI1	chr19:36392716-36393794	HL-60	blood:	n/a	n/a
8	POLR2A	chr19:36392680-36393837	GM12892	blood:	n/a	n/a
9	ELF1	chr19:36393162-36393592	K562	blood:	n/a	n/a
10	MTA3	chr19:36392654-36393933	GM12878	blood:	n/a	n/a
11	MAFK	chr19:36393119-36393318	HepG2	liver:	n/a	chr19:36393188-36393203
12	POLR2A	chr19:36392730-36393882	GM18505	blood:	n/a	n/a
13	SP1	chr19:36393164-36393586	GM12878	blood:	n/a	n/a
14	RUNX3	chr19:36392748-36393889	GM12878	blood:	n/a	n/a
15	MAFK	chr19:36393177-36393220	HepG2	liver:	n/a	chr19:36393188-36393203
16	STAT3	chr19:36392933-36393239	MCF10A-Er-Src	breast:	n/a	n/a
17	POLR2A	chr19:36392694-36394049	HL-60	blood:	n/a	n/a
18	POU2F2	chr19:36392815-36393692	GM12878	blood:	n/a	n/a
19	POLR2A	chr19:36392781-36393837	Raji	blood:	n/a	n/a
20	IKZF1	chr19:36392799-36393797	GM12878	blood:	n/a	chr19:36393654-36393662
21	POLR2A	chr19:36393118-36393960	GM12892	blood:	n/a	n/a
22	WRNIP1	chr19:36392800-36393548	GM12878	blood:	n/a	n/a
23	POLR2A	chr19:36393071-36393653	GM19193	blood:	n/a	n/a
24	STAT5A	chr19:36392919-36393581	GM12878	blood:	n/a	n/a
25	EBF1	chr19:36392857-36393416	GM12878	blood:	n/a	n/a
26	POLR2A	chr19:36393006-36393651	GM12878	blood:	n/a	n/a
27	POLR2A	chr19:36392715-36393988	GM12878	blood:	n/a	n/a
28	TCF3	chr19:36393184-36393704	GM12878	blood:	n/a	n/a
29	PML	chr19:36393087-36393810	GM12878	blood:	n/a	n/a
30	POLR2A	chr19:36392876-36393780	HL-60	blood:	n/a	n/a
31	MAX	chr19:36392772-36393563	NB4	blood:	n/a	n/a
32	MYC	chr19:36392649-36393763	NB4	blood:	n/a	n/a
33	TCF7L2	chr19:36392959-36393227	Hela-S3	cervix:	n/a	n/a
34	RELA	chr19:36392927-36393814	GM18505	blood:	n/a	n/a
35	FOS	chr19:36392985-36393192	MCF10A-Er-Src	breast:	n/a	n/a
36	POLR2A	chr19:36393147-36393841	GM12891	blood:	n/a	n/a
37	POLR2A	chr19:36393136-36393622	GM18951	blood:	n/a	n/a
38	EBF1	chr19:36393185-36393649	GM12878	blood:	n/a	n/a
39	POLR2A	chr19:36392633-36395066	GM12891	blood:	n/a	n/a
40	MXI1	chr19:36392883-36393537	GM12878	blood:	n/a	n/a
41	POLR2A	chr19:36393138-36393753	GM12892	blood:	n/a	n/a
42	POLR2A	chr19:36392517-36395149	GM12878	blood:	n/a	n/a
43	TBP	chr19:36392880-36393529	GM12878	blood:	n/a	n/a
44	POLR2A	chr19:36392756-36393984	GM12892	blood:	n/a	n/a
45	POLR2A	chr19:36393169-36393814	GM12878	blood:	n/a	n/a
46	POLR2A	chr19:36393151-36393692	GM12892	blood:	n/a	n/a
47	POLR2A	chr19:36392749-36393627	GM12878	blood:	n/a	n/a
48	ELF1	chr19:36393137-36393838	GM12878	blood:	n/a	n/a
49	RELA	chr19:36392852-36393576	GM19099	blood:	n/a	n/a
50	MAZ	chr19:36392813-36393576	GM12878	blood:	n/a	n/a

No data

(count:3 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr19:36359598..36361922-chr19:36393124..36395167,2	K562	blood:
2	chr19:36393181..36395162-chr19:36544398..36547293,2	K562	blood:
3	chr19:36390133..36392611-chr19:36392789..36396319,5	MCF-7	breast:

No data

Variant related genes	Relation type
HCST	TF binding region
NFKBID	TF binding region
ENSG00000167604	Chromatin interaction
ENSG00000105290	Chromatin interaction
ENSG00000161277	Chromatin interaction
ENSG00000075702	Chromatin interaction
ENSG00000161270	Chromatin interaction

Extended variants
information (count: 44 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:37)

rs_ID	r²[population]
rs11880785	1.00[MEX][hapmap]
rs1268319	1.00[MEX][hapmap]
rs16960862	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17173033	0.83[ASN][1000 genomes]
rs17549166	0.83[EUR][1000 genomes]
rs1802029	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];0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs230260	0.87[CHD][hapmap];1.00[JPT][hapmap];0.83[ASN][1000 genomes]
rs230261	1.00[MEX][hapmap]
rs33964243	0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3761086	1.00[CEU][hapmap]
rs376240	0.87[CHD][hapmap];1.00[JPT][hapmap];0.83[ASN][1000 genomes]
rs56264349	0.83[ASN][1000 genomes]
rs58422001	0.91[ASN][1000 genomes]
rs7245383	1.00[CEU][hapmap]
rs7247769	1.00[CEU][hapmap]
rs7251744	0.90[ASN][1000 genomes]
rs7251879	0.90[CHB][hapmap];0.91[CHD][hapmap];0.84[GIH][hapmap];1.00[JPT][hapmap];0.91[ASN][1000 genomes]
rs7252902	0.85[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7253040	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7253826	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7254113	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];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7256952	1.00[CEU][hapmap]
rs7258154	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7258214	0.90[ASN][1000 genomes]
rs7258909	0.90[CHB][hapmap];0.91[CHD][hapmap];1.00[JPT][hapmap];0.90[ASN][1000 genomes]
rs8101472	1.00[CEU][hapmap]
rs8103718	1.00[CEU][hapmap]
rs8105153	0.91[CHD][hapmap];1.00[GIH][hapmap];1.00[LWK][hapmap];1.00[MKK][hapmap];0.91[YRI][hapmap];0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs8106480	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs8106495	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.90[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.98[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs8108360	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs8108459	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs8110231	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];0.93[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs8111740	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs8113524	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];0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs8113704	0.81[CHB][hapmap];0.87[CHD][hapmap];0.84[GIH][hapmap];1.00[JPT][hapmap];0.88[ASN][1000 genomes]
rs879407	0.90[CHB][hapmap];0.91[CHD][hapmap];1.00[JPT][hapmap];0.91[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:7 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv432045	chr19:35556260-36520760	Flanking Active TSS Enhancers Active TSS Weak transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer Strong transcription Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	191 gene(s)	inside rSNPs	diseases
2	nsv911638	chr19:36265508-36537959	Enhancers Flanking Active TSS Strong transcription Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Weak transcription Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	67 gene(s)	inside rSNPs	diseases
3	esv3526489	chr19:36306483-36741945	Enhancers Weak transcription Strong transcription Flanking Active TSS Bivalent/Poised TSS Active TSS Flanking Bivalent TSS/Enh Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	114 gene(s)	inside rSNPs	diseases
4	esv3526490	chr19:36306483-36741945	Genic enhancers Weak transcription Strong transcription Flanking Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer Enhancers Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	114 gene(s)	inside rSNPs	diseases
5	esv1831737	chr19:36324324-36690874	Weak transcription Strong transcription Active TSS Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Enhancers ZNF genes & repeats Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	103 gene(s)	inside rSNPs	diseases
6	nsv833812	chr19:36331913-36507594	Flanking Active TSS Active TSS Enhancers Bivalent Enhancer Weak transcription Transcr. at gene 5' and 3' Strong transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	54 gene(s)	inside rSNPs	diseases
7	nsv833813	chr19:36341181-36499431	Flanking Active TSS Weak transcription Strong transcription Enhancers Bivalent Enhancer Genic enhancers ZNF genes & repeats Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	47 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:103 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr19:36390800-36395400	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
2	chr19:36391000-36395000	Flanking Active TSS	Primary hematopoietic stem cells	blood
3	chr19:36391600-36393200	Weak transcription	Esophagus	oesophagus
4	chr19:36391600-36393200	Weak transcription	Lung	lung
5	chr19:36391600-36394400	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
6	chr19:36391600-36394400	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
7	chr19:36391600-36394400	Weak transcription	Gastric	stomach
8	chr19:36391600-36394400	Weak transcription	Sigmoid Colon	Sigmoid Colon
9	chr19:36391600-36394400	Enhancers	HMEC	breast
10	chr19:36391600-36394600	Flanking Active TSS	Primary B cells from cord blood	blood
11	chr19:36391600-36395000	Flanking Active TSS	Primary Natural Killer cells fromperipheralblood	blood
12	chr19:36391600-36395000	Flanking Active TSS	Fetal Thymus	thymus
13	chr19:36391600-36395000	Enhancers	Spleen	Spleen
14	chr19:36391600-36397400	Weak transcription	Stomach Mucosa	stomach
15	chr19:36391800-36393200	Flanking Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
16	chr19:36391800-36393200	Flanking Active TSS	Thymus	Thymus
17	chr19:36391800-36393400	Flanking Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
18	chr19:36391800-36393400	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
19	chr19:36391800-36393400	Flanking Active TSS	Primary T helper naive cells from peripheral blood	blood
20	chr19:36391800-36393400	Weak transcription	Pancreas	Pancrea
21	chr19:36391800-36393400	Weak transcription	Right Ventricle	heart
22	chr19:36391800-36393600	Flanking Active TSS	ES-I3 Cell Line	embryonic stem cell
23	chr19:36391800-36393600	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
24	chr19:36391800-36393800	Flanking Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
25	chr19:36391800-36394000	Flanking Active TSS	Primary T helper cells PMA-I stimulated	--
26	chr19:36391800-36394000	Flanking Active TSS	Primary T helper 17 cells PMA-I stimulated	--
27	chr19:36391800-36394200	Enhancers	Breast Myoepithelial Primary Cells	Breast
28	chr19:36391800-36394200	Enhancers	K562	blood
29	chr19:36391800-36394200	Enhancers	NHEK	skin
30	chr19:36391800-36394400	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
31	chr19:36391800-36395000	Flanking Active TSS	Primary T helper naive cells fromperipheralblood	blood
32	chr19:36391800-36395000	Flanking Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
33	chr19:36391800-36395200	Flanking Active TSS	Primary monocytes fromperipheralblood	blood
34	chr19:36391800-36395200	Flanking Active TSS	Primary T cells fromperipheralblood	blood
35	chr19:36391800-36395200	Flanking Active TSS	Primary T helper cells fromperipheralblood	blood
36	chr19:36391800-36395200	Flanking Active TSS	Primary T regulatory cells fromperipheralblood	blood
37	chr19:36391800-36395200	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
38	chr19:36391800-36396000	Flanking Active TSS	Primary neutrophils fromperipheralblood	blood
39	chr19:36391800-36396000	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
40	chr19:36391800-36396400	Flanking Active TSS	Primary hematopoietic stem cells short term culture	blood
41	chr19:36392000-36393200	Enhancers	HUES48 Cell Line	embryonic stem cell
42	chr19:36392000-36393200	Weak transcription	Rectal Mucosa Donor 31	rectum
43	chr19:36392000-36393400	Weak transcription	Brain Substantia Nigra	brain
44	chr19:36392000-36393400	Enhancers	Placenta	Placenta
45	chr19:36392000-36393400	Enhancers	Stomach Smooth Muscle	stomach
46	chr19:36392000-36393600	Enhancers	Fetal Adrenal Gland	Adrenal Gland
47	chr19:36392000-36393600	Enhancers	Placenta Amnion	Placenta Amnion
48	chr19:36392000-36394000	Flanking Active TSS	Primary T killer memory cells from peripheral blood	blood
49	chr19:36392000-36394000	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
50	chr19:36392000-36394200	Enhancers	H1 Cell Line	embryonic stem cell

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