Variant report

Variant	rs10239592
Chromosome Location	chr7:27279633-27279634
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:3)
CpG islands
(count:0)
Chromatin interactive
region (count:8)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

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

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr7:27278584-27280266	H1-neurons	neurons:	n/a	n/a
2	POLR2A	chr7:27278696-27280095	H1-neurons	neurons:	n/a	n/a
3	SUZ12	chr7:27279396-27280282	H1-hESC	embryonic stem cell:	n/a	n/a

No data

(count:8 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type	Cell Stage
1	7:27143270-27156413..7:27264409-27279924	H1-hESC	embryonic stem cell:	embryo
2	7:27210222-27216016..7:27264409-27279924	H1-hESC	embryonic stem cell:	embryo
3	7:27216170-27221403..7:27264409-27279924	H1-hESC	embryonic stem cell:	embryo
4	7:27176959-27181770..7:27264409-27279924	H1-hESC	embryonic stem cell:	embryo
5	7:27165488-27167947..7:27264409-27279924	H1-hESC	embryonic stem cell:	embryo
6	7:27130634-27137201..7:27264409-27279924	H1-hESC	embryonic stem cell:	embryo
7	7:27203007-27207968..7:27264409-27279924	H1-hESC	embryonic stem cell:	embryo
8	7:27181770-27195105..7:27264409-27279924	H1-hESC	embryonic stem cell:	embryo

No data

Variant related genes	Relation type
EVX1	TF binding region
ENSG00000105997	Chromatin interaction
ENSG00000105991	Chromatin interaction
ENSG00000233429	Chromatin interaction
ENSG00000106006	Chromatin interaction
ENSG00000273433	Chromatin interaction
ENSG00000106004	Chromatin interaction
ENSG00000257184	Chromatin interaction
ENSG00000254369	Chromatin interaction
ENSG00000253293	Chromatin interaction
ENSG00000253552	Chromatin interaction
ENSG00000078399	Chromatin interaction
ENSG00000272801	Chromatin interaction

Extended variants
information (count: 38 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:13)

rs_ID	r²[population]
rs10215423	1.00[YRI][hapmap];0.96[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs10215610	1.00[YRI][hapmap];0.92[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs10233548	1.00[YRI][hapmap];0.92[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs10235918	1.00[YRI][hapmap];0.92[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs11564052	0.81[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs17472609	1.00[AMR][1000 genomes]
rs17472927	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs17501482	1.00[AMR][1000 genomes]
rs28483477	1.00[AMR][1000 genomes]
rs60364622	1.00[AMR][1000 genomes]
rs6461998	1.00[YRI][hapmap];0.80[AFR][1000 genomes]
rs73290370	1.00[AMR][1000 genomes]
rs73291911	1.00[AMR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:25 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1025538	chr7:26482342-27376045	Enhancers Bivalent/Poised TSS Weak transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Flanking Active TSS Transcr. at gene 5' and 3' Active TSS Genic enhancers Strong transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	213 gene(s)	inside rSNPs	diseases
2	nsv538805	chr7:26482342-27376045	Bivalent/Poised TSS Flanking Bivalent TSS/Enh Enhancers Bivalent Enhancer Active TSS Strong transcription Flanking Active TSS Genic enhancers Weak transcription Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	213 gene(s)	inside rSNPs	diseases
3	nsv887856	chr7:27073731-27297791	Flanking Bivalent TSS/Enh Active TSS Bivalent/Poised TSS Flanking Active TSS Bivalent Enhancer Enhancers Weak transcription Transcr. at gene 5' and 3' ZNF genes & repeats Genic enhancers Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	183 gene(s)	inside rSNPs	diseases
4	nsv824038	chr7:27119294-27284522	Flanking Bivalent TSS/Enh Bivalent Enhancer Flanking Active TSS Bivalent/Poised TSS Enhancers Weak transcription Active TSS Transcr. at gene 5' and 3' Genic enhancers Strong transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	183 gene(s)	inside rSNPs	diseases
5	nsv824039	chr7:27121825-27294951	Bivalent Enhancer Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh Enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Weak transcription Genic enhancers Strong transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	183 gene(s)	inside rSNPs	diseases
6	nsv824040	chr7:27121870-27295010	Flanking Active TSS Enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Weak transcription Transcr. at gene 5' and 3' Active TSS Genic enhancers Strong transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	183 gene(s)	inside rSNPs	diseases
7	nsv824041	chr7:27128039-27294951	Flanking Bivalent TSS/Enh Active TSS Weak transcription Bivalent/Poised TSS Bivalent Enhancer Enhancers Flanking Active TSS Strong transcription Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	183 gene(s)	inside rSNPs	diseases
8	nsv887869	chr7:27135314-27297791	Bivalent Enhancer Flanking Bivalent TSS/Enh Flanking Active TSS Active TSS Enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Weak transcription Strong transcription Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	181 gene(s)	inside rSNPs	diseases
9	nsv1020608	chr7:27139892-27324004	Bivalent Enhancer Active TSS Enhancers Transcr. at gene 5' and 3' Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Weak transcription Genic enhancers Strong transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	182 gene(s)	inside rSNPs	diseases
10	nsv538807	chr7:27139892-27324004	Flanking Bivalent TSS/Enh Bivalent Enhancer Weak transcription Active TSS Bivalent/Poised TSS Flanking Active TSS Enhancers Transcr. at gene 5' and 3' Strong transcription Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	182 gene(s)	inside rSNPs	diseases
11	nsv532118	chr7:27146920-27354205	Flanking Active TSS Bivalent Enhancer Enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh Active TSS Weak transcription Genic enhancers Strong transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	182 gene(s)	inside rSNPs	diseases
12	nsv887879	chr7:27175295-27297791	Flanking Active TSS Bivalent/Poised TSS Bivalent Enhancer Weak transcription Active TSS Flanking Bivalent TSS/Enh Genic enhancers Enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	151 gene(s)	inside rSNPs	diseases
13	esv1798853	chr7:27181568-27309266	Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Flanking Active TSS Enhancers Active TSS Weak transcription Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	150 gene(s)	inside rSNPs	diseases
14	nsv531024	chr7:27194426-27461954	Enhancers Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Flanking Active TSS Active TSS Weak transcription Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	148 gene(s)	inside rSNPs	diseases
15	nsv606468	chr7:27202289-27281304	Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Enhancers Bivalent/Poised TSS Weak transcription Active TSS Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	135 gene(s)	inside rSNPs	diseases
16	nsv887880	chr7:27205282-27294701	Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Flanking Active TSS Enhancers Active TSS Transcr. at gene 5' and 3' Weak transcription Genic enhancers ZNF genes & repeats Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	132 gene(s)	inside rSNPs	diseases
17	nsv887881	chr7:27205282-27297791	Bivalent/Poised TSS Flanking Bivalent TSS/Enh Active TSS Weak transcription Bivalent Enhancer Transcr. at gene 5' and 3' Enhancers Flanking Active TSS ZNF genes & repeats Genic enhancers Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	132 gene(s)	inside rSNPs	diseases
18	nsv887884	chr7:27206688-27297791	Flanking Active TSS Bivalent/Poised TSS Bivalent Enhancer Enhancers Flanking Bivalent TSS/Enh Active TSS Weak 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	130 gene(s)	inside rSNPs	diseases
19	nsv1026327	chr7:27207777-27288521	Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer Flanking Active TSS Enhancers Active TSS Weak transcription Transcr. at gene 5' and 3' ZNF genes & repeats Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	130 gene(s)	inside rSNPs	diseases
20	nsv538808	chr7:27207777-27288521	Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer Active TSS Flanking Active TSS Weak transcription Transcr. at gene 5' and 3' Enhancers Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	130 gene(s)	inside rSNPs	diseases
21	nsv887886	chr7:27215041-27297791	Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer Active TSS Flanking Active TSS Enhancers Genic enhancers Weak transcription Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	69 gene(s)	inside rSNPs	diseases
22	nsv887888	chr7:27217746-27281157	Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Active TSS Weak transcription Enhancers Flanking Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	66 gene(s)	inside rSNPs	diseases
23	nsv887889	chr7:27220831-27297791	Bivalent Enhancer Enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Flanking Active TSS Weak transcription Active TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	61 gene(s)	inside rSNPs	diseases
24	nsv887892	chr7:27223563-27297791	Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent/Poised TSS Bivalent Enhancer Active TSS Enhancers Weak transcription Transcr. at gene 5' and 3' ZNF genes & repeats Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	61 gene(s)	inside rSNPs	diseases
25	nsv519583	chr7:27243962-27298264	Bivalent Enhancer Bivalent/Poised TSS Active TSS Flanking Bivalent TSS/Enh Enhancers Weak transcription Flanking Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	23 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:58 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:27274800-27280200	Bivalent/Poised TSS	iPS-15b Cell Line	embryonic stem cell
2	chr7:27276000-27282000	Weak transcription	Pancreas	Pancrea
3	chr7:27278200-27281400	Bivalent Enhancer	iPS DF 19.11 Cell Line	embryonic stem cell
4	chr7:27278400-27280400	Bivalent Enhancer	Primary T helper cells PMA-I stimulated	--
5	chr7:27278400-27282800	Bivalent Enhancer	ES-UCSF4 Cell Line	embryonic stem cell
6	chr7:27278600-27280200	Bivalent Enhancer	Placenta	Placenta
7	chr7:27278600-27282600	Bivalent Enhancer	H1 Cell Line	embryonic stem cell
8	chr7:27278800-27279800	Bivalent Enhancer	Liver	Liver
9	chr7:27278800-27279800	Bivalent Enhancer	Fetal Intestine Large	intestine
10	chr7:27278800-27279800	Active TSS	Right Atrium	heart
11	chr7:27278800-27280000	Bivalent Enhancer	Primary Natural Killer cells fromperipheralblood	blood
12	chr7:27278800-27280000	Bivalent Enhancer	Fetal Stomach	stomach
13	chr7:27278800-27280200	Bivalent Enhancer	Primary B cells from peripheral blood	blood
14	chr7:27278800-27280200	Bivalent Enhancer	Primary T helper cells fromperipheralblood	blood
15	chr7:27278800-27280200	Bivalent Enhancer	Primary T cells effector/memory enriched fromperipheralblood	blood
16	chr7:27278800-27280400	Bivalent Enhancer	Primary T cells fromperipheralblood	blood
17	chr7:27278800-27285000	Active TSS	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
18	chr7:27279000-27280000	Bivalent Enhancer	H9 Derived Neuron Cultured Cells	ES cell derived
19	chr7:27279000-27280000	Bivalent/Poised TSS	Foreskin Fibroblast Primary Cells skin02	Skin
20	chr7:27279000-27280000	Bivalent Enhancer	Fetal Brain Male	brain
21	chr7:27279000-27280200	Bivalent Enhancer	Stomach Mucosa	stomach
22	chr7:27279200-27279800	Bivalent Enhancer	ES-WA7 Cell Line	embryonic stem cell
23	chr7:27279200-27279800	Bivalent Enhancer	Primary hematopoietic stem cells G-CSF-mobilized Female	--
24	chr7:27279200-27279800	Bivalent Enhancer	Brain Hippocampus Middle	brain
25	chr7:27279200-27279800	Bivalent Enhancer	Fetal Adrenal Gland	Adrenal Gland
26	chr7:27279200-27280000	Bivalent Enhancer	Brain Germinal Matrix	brain
27	chr7:27279200-27280200	Bivalent Enhancer	Fetal Muscle Trunk	muscle
28	chr7:27279400-27279800	Flanking Bivalent TSS/Enh	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
29	chr7:27279400-27279800	Flanking Bivalent TSS/Enh	iPS-18 Cell Line	embryonic stem cell
30	chr7:27279400-27279800	Bivalent Enhancer	iPS-20b Cell Line	embryonic stem cell
31	chr7:27279400-27279800	Bivalent Enhancer	Primary T regulatory cells fromperipheralblood	blood
32	chr7:27279400-27279800	Bivalent Enhancer	Brain Substantia Nigra	brain
33	chr7:27279400-27280000	Bivalent Enhancer	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
34	chr7:27279400-27280000	Bivalent Enhancer	HUES48 Cell Line	embryonic stem cell
35	chr7:27279400-27280000	Bivalent Enhancer	Colonic Mucosa	Colon
36	chr7:27279400-27280000	Bivalent Enhancer	Colon Smooth Muscle	Colon
37	chr7:27279400-27280400	Bivalent Enhancer	Skeletal Muscle Female	skeletal muscle
38	chr7:27279400-27280600	Bivalent Enhancer	iPS DF 6.9 Cell Line	embryonic stem cell
39	chr7:27279400-27280600	Bivalent Enhancer	Primary T killer naive cells fromperipheralblood	blood
40	chr7:27279600-27279800	Bivalent Enhancer	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
41	chr7:27279600-27279800	Flanking Bivalent TSS/Enh	HUES6 Cell Line	embryonic stem cell
42	chr7:27279600-27279800	Flanking Bivalent TSS/Enh	HUES64 Cell Line	embryonic stem cell
43	chr7:27279600-27279800	Bivalent Enhancer	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
44	chr7:27279600-27279800	Bivalent Enhancer	Primary T helper naive cells fromperipheralblood	blood
45	chr7:27279600-27279800	Bivalent Enhancer	Cortex derived primary cultured neurospheres	brain
46	chr7:27279600-27279800	Bivalent Enhancer	Ganglion Eminence derived primary cultured neurospheres	brain
47	chr7:27279600-27279800	Bivalent Enhancer	Fetal Brain Female	brain
48	chr7:27279600-27279800	Bivalent Enhancer	Fetal Lung	lung
49	chr7:27279600-27279800	Bivalent/Poised TSS	Right Ventricle	heart
50	chr7:27279600-27279800	Bivalent Enhancer	Stomach Smooth Muscle	stomach

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