Variant report

Variant	rs16960862
Chromosome Location	chr19:36390123-36390124
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	MYC	chr19:36390074-36390270	MCF10A-Er-Src	breast:	n/a	n/a
2	POLR2A	chr19:36390067-36391782	GM12892	blood:	n/a	n/a
3	MXI1	chr19:36389396-36392037	SK-N-SH	brain:	n/a	n/a
4	ZBTB7A	chr19:36389711-36390345	ECC-1	luminal epithelium:	n/a	n/a
5	TCF12	chr19:36389907-36391960	A549	lung:	n/a	chr19:36390770-36390777 chr19:36391169-36391179
6	USF1	chr19:36390025-36390466	K562	blood:	n/a	chr19:36390267-36390278
7	MAX	chr19:36390093-36390954	GM12878	blood:	n/a	n/a
8	POLR2A	chr19:36389078-36391783	GM12878	blood:	n/a	n/a
9	USF1	chr19:36390037-36390459	H1-hESC	embryonic stem cell:	n/a	chr19:36390267-36390278
10	POLR2A	chr19:36389853-36390965	MCF10A-Er-Src	breast:	n/a	n/a
11	SIN3A	chr19:36390083-36390284	GM12878	blood:	n/a	n/a
12	STAT5A	chr19:36389733-36390226	GM12878	blood:	n/a	n/a
13	USF1	chr19:36390059-36390381	H1-hESC	embryonic stem cell:	n/a	chr19:36390267-36390278
14	POLR2A	chr19:36389500-36391774	GM15510	blood:	n/a	n/a
15	POLR2A	chr19:36383824-36391793	GM12878	blood:	n/a	n/a
16	NR2F2	chr19:36389961-36390437	MCF-7	breast:	n/a	n/a
17	NFIC	chr19:36389970-36391040	GM12878	blood:	n/a	n/a
18	POLR2A	chr19:36390068-36391929	K562	blood:	n/a	n/a
19	POLR2A	chr19:36390046-36390268	HCT-116	colon:	n/a	n/a
20	POLR2A	chr19:36388326-36390442	HL-60	blood:	n/a	n/a
21	POLR2A	chr19:36386218-36391884	GM12878	blood:	n/a	n/a
22	YY1	chr19:36390089-36390943	A549	lung:	n/a	chr19:36390660-36390669 chr19:36390654-36390668 chr19:36390788-36390802 chr19:36390658-36390669 chr19:36390789-36390803
23	ZNF384	chr19:36390024-36390833	GM12878	blood:	n/a	n/a
24	SPI1	chr19:36389862-36390131	GM12891	blood:	n/a	chr19:36389976-36389989
25	ELF1	chr19:36389880-36390223	K562	blood:	n/a	chr19:36390142-36390153 chr19:36390013-36390026 chr19:36390143-36390152 chr19:36389901-36389910
26	POLR2A	chr19:36389440-36391870	GM12892	blood:	n/a	n/a
27	MAX	chr19:36390104-36391896	A549	lung:	n/a	n/a
28	POLR2A	chr19:36389547-36391766	GM19193	blood:	n/a	n/a
29	SPI1	chr19:36389699-36390316	HL-60	blood:	n/a	chr19:36389976-36389989
30	NR2F2	chr19:36390045-36390806	K562	blood:	n/a	n/a
31	POLR2A	chr19:36389741-36390141	HUVEC	blood vessel:	n/a	n/a
32	POLR2A	chr19:36389614-36390186	HUVEC	blood vessel:	n/a	n/a
33	POLR2A	chr19:36390106-36390125	MCF-7	breast:	n/a	n/a
34	ELF1	chr19:36389639-36390468	GM12878	blood:	n/a	chr19:36390142-36390153 chr19:36390013-36390026 chr19:36390143-36390152 chr19:36389901-36389910
35	POLR2A	chr19:36389416-36391776	GM18505	blood:	n/a	n/a
36	POLR2A	chr19:36389637-36391900	Hela-S3	cervix:	n/a	n/a
37	STAT3	chr19:36390101-36390223	MCF10A-Er-Src	breast:	n/a	n/a
38	ZBTB7A	chr19:36389543-36390360	ECC-1	luminal epithelium:	n/a	n/a
39	MTA3	chr19:36389683-36391755	GM12878	blood:	n/a	n/a
40	JUN	chr19:36390085-36390962	K562	blood:	n/a	chr19:36390656-36390665 chr19:36390531-36390540
41	POLR2A	chr19:36389792-36390961	MCF10A-Er-Src	breast:	n/a	n/a
42	MAZ	chr19:36389664-36390241	GM12878	blood:	n/a	chr19:36389974-36389984
43	MAX	chr19:36390121-36390973	Hela-S3	cervix:	n/a	n/a
44	USF1	chr19:36390107-36390405	SK-N-SH_RA	brain:	n/a	chr19:36390267-36390278
45	CTCF	chr19:36390067-36390130	GM13976	blood:	n/a	n/a
46	POLR2A	chr19:36389609-36391817	MCF-7	breast:	n/a	n/a
47	MAX	chr19:36390087-36390301	K562	blood:	n/a	n/a
48	RELA	chr19:36389800-36391782	GM12891	blood:	n/a	chr19:36390871-36390880 chr19:36390834-36390843 chr19:36390834-36390843 chr19:36390871-36390880
49	MAZ	chr19:36390010-36390906	Hela-S3	cervix:	n/a	n/a
50	ELF1	chr19:36389714-36390289	GM12878	blood:	n/a	chr19:36390142-36390153 chr19:36390013-36390026 chr19:36390143-36390152 chr19:36389901-36389910

No.	Distal block	Cell Line	Cell type
1	chr19:36388870..36390539-chr19:36431114..36433630,2	MCF-7	breast:
2	chr19:36134320..36136453-chr19:36390020..36392248,2	MCF-7	breast:
3	chr19:36389776..36392991-chr19:36393581..36401271,10	K562	blood:
4	chr19:36370768..36374759-chr19:36390074..36391659,3	MCF-7	breast:
5	chr19:36334818..36337477-chr19:36389378..36392350,2	MCF-7	breast:
6	chr19:36377925..36382197-chr19:36388677..36391097,3	MCF-7	breast:
7	chr19:36388094..36390635-chr19:36498099..36499853,2	K562	blood:
8	chr19:36379784..36382461-chr19:36387954..36392218,4	MCF-7	breast:
9	chr19:36247959..36249985-chr19:36390079..36391606,2	MCF-7	breast:
10	chr19:36387498..36389148-chr19:36389747..36391411,2	K562	blood:
11	chr19:36390062..36392033-chr19:36425677..36427196,2	MCF-7	breast:
12	chr19:36359272..36362126-chr19:36389056..36392231,3	MCF-7	breast:

Variant related genes	Relation type
NFKBID	TF binding region
HCST	TF binding region
ENSG00000105290	Chromatin interaction
ENSG00000167604	Chromatin interaction
ENSG00000243968	Chromatin interaction
ENSG00000161270	Chromatin interaction
ENSG00000004776	Chromatin interaction
ENSG00000011600	Chromatin interaction
ENSG00000167595	Chromatin interaction
ENSG00000105672	Chromatin interaction
ENSG00000126243	Chromatin interaction
ENSG00000181392	Chromatin interaction

Extended variants
information (count: 41 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:34)

rs_ID	r²[population]
rs11878547	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[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs230260	1.00[JPT][hapmap];0.83[ASN][1000 genomes]
rs33964243	0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3761086	1.00[CEU][hapmap]
rs376240	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	0.89[CHB][hapmap];1.00[JPT][hapmap];0.91[ASN][1000 genomes]
rs7252902	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7253040	1.00[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[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]
rs7256952	1.00[CEU][hapmap]
rs7258154	1.00[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	0.89[CHB][hapmap];1.00[JPT][hapmap];0.90[ASN][1000 genomes]
rs8101472	1.00[CEU][hapmap]
rs8103718	1.00[CEU][hapmap]
rs8105153	0.86[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];0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs8106495	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs8108360	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs8108459	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs8110231	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs8111740	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs8113524	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs8113704	1.00[JPT][hapmap];0.88[ASN][1000 genomes]
rs879407	0.89[CHB][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:127 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr19:36386800-36391600	Transcr. at gene 5' and 3'	Primary T helper 17 cells PMA-I stimulated	--
2	chr19:36388600-36392000	Active TSS	Rectal Smooth Muscle	rectum
3	chr19:36388800-36391600	Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
4	chr19:36389000-36390200	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
5	chr19:36389000-36390400	Flanking Active TSS	Adipose Nuclei	Adipose
6	chr19:36389000-36391600	Active TSS	Gastric	stomach
7	chr19:36389000-36391800	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
8	chr19:36389000-36391800	Active TSS	Pancreatic Islets	Pancreatic Islet
9	chr19:36389000-36391800	Active TSS	NHDF-Ad	bronchial
10	chr19:36389000-36392000	Active TSS	Brain Angular Gyrus	brain
11	chr19:36389000-36392000	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
12	chr19:36389000-36392000	Active TSS	NHLF	lung
13	chr19:36389200-36390200	Flanking Active TSS	Brain Hippocampus Middle	brain
14	chr19:36389200-36390400	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
15	chr19:36389200-36390400	Flanking Active TSS	Cortex derived primary cultured neurospheres	brain
16	chr19:36389200-36390400	Enhancers	Fetal Brain Male	brain
17	chr19:36389200-36391400	Active TSS	Fetal Brain Female	brain
18	chr19:36389200-36391800	Active TSS	ES-I3 Cell Line	embryonic stem cell
19	chr19:36389200-36391800	Active TSS	Osteobl	bone
20	chr19:36389200-36392000	Active TSS	H1 Cell Line	embryonic stem cell
21	chr19:36389200-36392000	Active TSS	HUES64 Cell Line	embryonic stem cell
22	chr19:36389200-36392000	Flanking Active TSS	Placenta	Placenta
23	chr19:36389200-36392200	Active TSS	Right Atrium	heart
24	chr19:36389400-36390200	Flanking Active TSS	Fetal Adrenal Gland	Adrenal Gland
25	chr19:36389400-36390200	Enhancers	Fetal Heart	heart
26	chr19:36389400-36390200	Flanking Active TSS	Fetal Stomach	stomach
27	chr19:36389400-36390400	Flanking Active TSS	Primary mononuclear cells fromperipheralblood	Blood
28	chr19:36389400-36390400	Flanking Bivalent TSS/Enh	Fetal Muscle Leg	muscle
29	chr19:36389400-36390400	Flanking Active TSS	HUVEC	blood vessel
30	chr19:36389400-36390600	Flanking Active TSS	Primary B cells from cord blood	blood
31	chr19:36389400-36390600	Flanking Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
32	chr19:36389400-36391600	Active TSS	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
33	chr19:36389400-36391600	Active TSS	Esophagus	oesophagus
34	chr19:36389400-36391600	Active TSS	Sigmoid Colon	Sigmoid Colon
35	chr19:36389400-36391800	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
36	chr19:36389400-36391800	Active TSS	iPS-20b Cell Line	embryonic stem cell
37	chr19:36389400-36391800	Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
38	chr19:36389400-36391800	Active TSS	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
39	chr19:36389400-36391800	Active TSS	Primary T helper naive cells from peripheral blood	blood
40	chr19:36389400-36391800	Active TSS	Aorta	Aorta
41	chr19:36389400-36391800	Active TSS	Ovary	ovary
42	chr19:36389400-36391800	Active TSS	Psoas Muscle	Psoas
43	chr19:36389400-36391800	Active TSS	Rectal Mucosa Donor 29	rectum
44	chr19:36389400-36392000	Active TSS	H9 Cell Line	embryonic stem cell
45	chr19:36389400-36392000	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
46	chr19:36389400-36392000	Active TSS	HUES48 Cell Line	embryonic stem cell
47	chr19:36389400-36392000	Active TSS	iPS-15b Cell Line	embryonic stem cell
48	chr19:36389400-36392000	Active TSS	Primary T cells from cord blood	blood
49	chr19:36389400-36392000	Active TSS	HSMMtube	muscle
50	chr19:36389600-36390200	Bivalent/Poised TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived

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