Variant report

Variant	rs9992927
Chromosome Location	chr4:8393907-8393908
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	BATF	chr4:8393671-8394070	GM12878	blood:	n/a	chr4:8393850-8393861
2	ETS1	chr4:8393747-8394063	GM12878	blood:	n/a	n/a
3	BATF	chr4:8393629-8394080	GM12878	blood:	n/a	chr4:8393850-8393861
4	EGR1	chr4:8393763-8394006	GM12878	blood:	n/a	chr4:8393903-8393917
5	POLR2A	chr4:8393578-8394165	GM12878	blood:	n/a	n/a
6	MTA3	chr4:8393569-8394159	GM12878	blood:	n/a	n/a
7	CTCF	chr4:8393840-8393990	GM12871	blood:	n/a	n/a
8	MYC	chr4:8393690-8394063	NB4	blood:	n/a	chr4:8393822-8393832
9	PBX3	chr4:8393734-8394010	GM12878	blood:	n/a	n/a
10	USF1	chr4:8393726-8393914	SK-N-SH_RA	brain:	n/a	n/a
11	WRNIP1	chr4:8393796-8394086	GM12878	blood:	n/a	n/a
12	IRF4	chr4:8393661-8394149	GM12878	blood:	n/a	n/a
13	MYC	chr4:8393671-8394054	MCF10A-Er-Src	breast:	n/a	chr4:8393822-8393832
14	EP300	chr4:8393619-8394039	GM12878	blood:	n/a	n/a
15	BCL11A	chr4:8393722-8394039	GM12878	blood:	n/a	n/a
16	RUNX3	chr4:8393633-8394120	GM12878	blood:	n/a	n/a
17	ATF2	chr4:8393604-8394136	GM12878	blood:	n/a	n/a
18	EP300	chr4:8393661-8394106	GM12878	blood:	n/a	n/a
19	POLR2A	chr4:8393709-8394005	SK-N-SH	brain:	n/a	n/a
20	TCF3	chr4:8393684-8394084	GM12878	blood:	n/a	n/a
21	FOXP2	chr4:8393731-8394204	PFSK-1	brain:	n/a	n/a
22	HDAC2	chr4:8393612-8394151	MCF-7	breast:	n/a	n/a
23	MEF2C	chr4:8393647-8393988	GM12878	blood:	n/a	n/a
24	TCF12	chr4:8393571-8394208	SK-N-SH	brain:	n/a	n/a
25	TBL1XR1	chr4:8393440-8394208	GM12878	blood:	n/a	n/a
26	EP300	chr4:8393705-8394069	SK-N-SH_RA	brain:	n/a	n/a
27	HDAC2	chr4:8393652-8393976	MCF-7	breast:	n/a	n/a
28	PAX5	chr4:8393680-8393980	GM12878	blood:	n/a	n/a
29	EBF1	chr4:8393612-8394035	GM12878	blood:	n/a	n/a
30	ZNF217	chr4:8393688-8394039	MCF-7	breast:	n/a	n/a
31	MXI1	chr4:8393407-8394097	IMR90	lung:	n/a	n/a
32	SIN3AK20	chr4:8393432-8394226	MCF-7	breast:	n/a	n/a
33	MXI1	chr4:8393364-8394350	SK-N-SH	brain:	n/a	n/a
34	ELK1	chr4:8393721-8394037	GM12878	blood:	n/a	n/a
35	CTCF	chr4:8393760-8393910	HCM	heart:	n/a	n/a
36	SP1	chr4:8393627-8394087	GM12878	blood:	n/a	n/a
37	BCLAF1	chr4:8393699-8394095	GM12878	blood:	n/a	n/a
38	CTCF	chr4:8393880-8394030	HPF	lung:	n/a	n/a
39	IRF4	chr4:8393667-8394106	GM12878	blood:	n/a	n/a
40	SMC3	chr4:8393632-8394060	GM12878	blood:	n/a	n/a
41	PBX3	chr4:8393742-8393956	GM12878	blood:	n/a	n/a
42	POLR2A	chr4:8393684-8394040	GM12891	blood:	n/a	n/a
43	ZNF143	chr4:8393725-8394048	GM12878	blood:	n/a	n/a
44	STAT1	chr4:8393730-8393965	GM12878	blood:	n/a	n/a
45	BCL11A	chr4:8393709-8394001	GM12878	blood:	n/a	n/a
46	POLR2A	chr4:8393794-8394126	HUVEC	blood vessel:	n/a	n/a
47	CEBPB	chr4:8393636-8393996	MCF-7	breast:	n/a	n/a
48	FOS	chr4:8393702-8394029	MCF10A-Er-Src	breast:	n/a	chr4:8393848-8393859
49	EBF1	chr4:8393645-8394055	GM12878	blood:	n/a	n/a
50	MAX	chr4:8393678-8394214	GM12878	blood:	n/a	chr4:8393822-8393832

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr4:8389242..8391252-chr4:8392488..8394168,2	MCF-7	breast:

Variant related genes	Relation type
RNA5SP152	TF binding region

Extended variants
information (count: 35 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:23)

rs_ID	r²[population]
rs10009196	1.00[AMR][1000 genomes]
rs10011431	1.00[AMR][1000 genomes]
rs10019143	1.00[AMR][1000 genomes]
rs10022276	1.00[AMR][1000 genomes]
rs13434465	0.93[AFR][1000 genomes]
rs13434523	1.00[AMR][1000 genomes]
rs28416714	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs28527486	1.00[AMR][1000 genomes]
rs28591490	1.00[AMR][1000 genomes]
rs28609497	1.00[AMR][1000 genomes]
rs28621881	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs28647609	1.00[AMR][1000 genomes]
rs28707116	1.00[AMR][1000 genomes]
rs28839770	1.00[AMR][1000 genomes]
rs28860567	1.00[AMR][1000 genomes]
rs28877981	1.00[AMR][1000 genomes]
rs7695149	1.00[AMR][1000 genomes]
rs9884532	1.00[AMR][1000 genomes]
rs9985915	1.00[AMR][1000 genomes]
rs9985917	1.00[AMR][1000 genomes]
rs9986108	1.00[AMR][1000 genomes]
rs9997393	1.00[AMR][1000 genomes]
rs9997800	1.00[AMR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:12 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1002794	chr4:8110083-8490934	Weak transcription Bivalent Enhancer Enhancers Flanking Active TSS Strong transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS Genic enhancers Active TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	30 gene(s)	inside rSNPs	diseases
2	nsv878601	chr4:8214767-8440951	Flanking Active TSS Enhancers Strong transcription Weak transcription Bivalent Enhancer Active TSS Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	19 gene(s)	inside rSNPs	diseases
3	nsv878602	chr4:8214767-8448992	Weak transcription Enhancers Flanking Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Active TSS Genic enhancers ZNF genes & repeats Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	19 gene(s)	inside rSNPs	diseases
4	nsv1009011	chr4:8225669-8424831	Weak transcription Enhancers Genic enhancers Strong transcription Bivalent Enhancer Bivalent/Poised TSS Flanking Active TSS Flanking Bivalent TSS/Enh Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	15 gene(s)	inside rSNPs	diseases
5	nsv878604	chr4:8315938-8618916	Enhancers Flanking Active TSS Strong transcription Weak transcription Active TSS Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	19 gene(s)	inside rSNPs	diseases
6	nsv1002680	chr4:8357163-8721214	Active TSS Flanking Active TSS Strong transcription Weak transcription Enhancers Bivalent Enhancer Bivalent/Poised TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	18 gene(s)	inside rSNPs	diseases
7	nsv461220	chr4:8372944-8458394	Enhancers Active TSS Flanking Active TSS Strong transcription Weak transcription Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
8	nsv593638	chr4:8372944-8458394	Flanking Active TSS Active TSS Genic enhancers Enhancers Strong transcription Weak transcription Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
9	nsv878609	chr4:8373832-8407406	Weak transcription Strong transcription Enhancers Genic enhancers Flanking Active TSS ZNF genes & repeats Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
10	nsv878610	chr4:8377058-8416976	ZNF genes & repeats Weak transcription Genic enhancers Transcr. at gene 5' and 3' Strong transcription Enhancers Flanking Active TSS Active TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region	6 gene(s)	inside rSNPs	diseases
11	esv1005399	chr4:8387281-8397983	Weak transcription Genic enhancers Enhancers Strong transcription Transcr. at gene 5' and 3' Flanking Active TSS ZNF genes & repeats Active TSS	TF binding region CpG island Chromatin interactive region	3 gene(s)	inside rSNPs	diseases
12	nsv470014	chr4:8390646-8429817	Strong transcription Weak transcription Flanking Active TSS Enhancers Genic enhancers Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region	6 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:119 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:8360400-8394000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
2	chr4:8360400-8395600	Weak transcription	NHEK	skin
3	chr4:8362000-8395400	Weak transcription	Fetal Brain Male	brain
4	chr4:8366400-8411600	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
5	chr4:8373400-8401600	Strong transcription	Fetal Intestine Small	intestine
6	chr4:8375000-8401600	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
7	chr4:8378600-8398600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
8	chr4:8378600-8398800	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
9	chr4:8378800-8397800	Weak transcription	HUES48 Cell Line	embryonic stem cell
10	chr4:8379000-8395400	Weak transcription	HUES6 Cell Line	embryonic stem cell
11	chr4:8381800-8394400	Strong transcription	Brain Germinal Matrix	brain
12	chr4:8381800-8398600	Weak transcription	H9 Cell Line	embryonic stem cell
13	chr4:8382400-8401600	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
14	chr4:8383800-8419000	Weak transcription	Pancreatic Islets	Pancreatic Islet
15	chr4:8384000-8394600	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
16	chr4:8384000-8395600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
17	chr4:8384000-8399600	Strong transcription	Spleen	Spleen
18	chr4:8384800-8401600	Strong transcription	Thymus	Thymus
19	chr4:8384800-8418600	Strong transcription	Primary T cells from cord blood	blood
20	chr4:8385200-8395200	Weak transcription	Fetal Kidney	kidney
21	chr4:8385200-8411600	Weak transcription	Primary T killer memory cells from peripheral blood	blood
22	chr4:8385400-8395600	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
23	chr4:8385600-8407000	Weak transcription	Stomach Mucosa	stomach
24	chr4:8386400-8398200	Strong transcription	Primary T helper cells fromperipheralblood	blood
25	chr4:8386400-8408400	Strong transcription	Fetal Intestine Large	intestine
26	chr4:8386600-8398600	Strong transcription	Monocytes-CD14+_RO01746	blood
27	chr4:8386600-8399400	Strong transcription	Primary monocytes fromperipheralblood	blood
28	chr4:8386600-8400600	Strong transcription	Primary hematopoietic stem cells short term culture	blood
29	chr4:8386800-8396600	Strong transcription	Lung	lung
30	chr4:8387200-8394600	Strong transcription	Rectal Mucosa Donor 29	rectum
31	chr4:8387200-8395000	Strong transcription	Breast Myoepithelial Primary Cells	Breast
32	chr4:8387200-8395600	Weak transcription	Primary hematopoietic stem cells	blood
33	chr4:8387400-8399600	Weak transcription	Primary T helper naive cells from peripheral blood	blood
34	chr4:8387400-8412000	Weak transcription	iPS-15b Cell Line	embryonic stem cell
35	chr4:8387600-8394600	Strong transcription	Fetal Lung	lung
36	chr4:8388000-8395000	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
37	chr4:8388400-8394000	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
38	chr4:8388400-8394400	Strong transcription	Left Ventricle	heart
39	chr4:8388400-8396200	Strong transcription	Duodenum Mucosa	Duodenum
40	chr4:8388400-8399200	Strong transcription	Liver	Liver
41	chr4:8388800-8394200	Strong transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
42	chr4:8388800-8394800	Strong transcription	Primary T cells fromperipheralblood	blood
43	chr4:8389000-8399600	Strong transcription	Pancreas	Pancrea
44	chr4:8389400-8399200	Genic enhancers	Fetal Muscle Trunk	muscle
45	chr4:8389400-8399200	Genic enhancers	Fetal Muscle Leg	muscle
46	chr4:8389800-8411400	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
47	chr4:8390200-8395600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
48	chr4:8390200-8396000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
49	chr4:8390400-8394800	Strong transcription	Esophagus	oesophagus
50	chr4:8391000-8395600	Weak transcription	Dnd41	blood

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