Variant report

Variant	rs3993757
Chromosome Location	chr6:31590746-31590747
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:21)
CpG islands
(count:0)
Chromatin interactive
region (count:14)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:21 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr6:31587351-31591130	GM12878	blood:	n/a	n/a
2	POLR2A	chr6:31587203-31590940	SK-N-MC	brain:	n/a	n/a
3	HEY1	chr6:31587125-31591017	K562	blood:	n/a	chr6:31588313-31588328 chr6:31588969-31588984
4	POLR2A	chr6:31590097-31590788	GM12892	blood:	n/a	n/a
5	POLR2A	chr6:31587597-31590981	PANC-1	pancreas:	n/a	n/a
6	POLR2A	chr6:31587263-31591139	H1-hESC	embryonic stem cell:	n/a	n/a
7	POLR2A	chr6:31590204-31591034	K562	blood:	n/a	n/a
8	MAX	chr6:31590602-31590881	NB4	blood:	n/a	n/a
9	POLR2A	chr6:31590248-31591026	PFSK-1	brain:	n/a	n/a
10	MYC	chr6:31590508-31590841	NB4	blood:	n/a	n/a
11	POLR2A	chr6:31590285-31590988	K562	blood:	n/a	n/a
12	POLR2A	chr6:31590734-31590764	HepG2	liver:	n/a	n/a
13	SPI1	chr6:31590550-31590959	HL-60	blood:	n/a	chr6:31590750-31590763
14	WRNIP1	chr6:31590353-31590870	GM12878	blood:	n/a	n/a
15	POLR2A	chr6:31587447-31591084	GM12878	blood:	n/a	n/a
16	POLR2A	chr6:31590322-31590862	MCF-7	breast:	n/a	n/a
17	SPI1	chr6:31590388-31591050	HL-60	blood:	n/a	chr6:31590750-31590763
18	MAX	chr6:31590288-31590838	MCF-7	breast:	n/a	n/a
19	POLR2A	chr6:31590522-31590937	HepG2	liver:	n/a	n/a
20	POLR2A	chr6:31590250-31590981	GM12891	blood:	n/a	n/a
21	POLR2A	chr6:31590466-31590976	K562	blood:	n/a	n/a

No data

(count:14 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr6:31463965..31465758-chr6:31589334..31591777,2	K562	blood:
2	chr6:31586339..31592286-chr6:31830032..31833457,6	K562	blood:
3	chr6:31513053..31519210-chr6:31585987..31595406,29	K562	blood:
4	chr6:31506740..31512488-chr6:31586502..31592966,30	K562	blood:
5	chr6:31590578..31592519-chr6:31620452..31622488,2	MCF-7	breast:
6	chr6:31463303..31465758-chr6:31589334..31591958,3	K562	blood:
7	chr6:31507082..31511713-chr6:31583957..31591905,17	MCF-7	breast:
8	chr6:31586074..31595285-chr6:31626460..31635395,11	MCF-7	breast:
9	chr6:31542086..31543755-chr6:31589416..31592351,2	K562	blood:
10	chr6:31506595..31512441-chr6:31585525..31590767,30	K562	blood:
11	chr6:31513697..31516891-chr6:31590663..31594798,6	K562	blood:
12	chr6:31546034..31550400-chr6:31586618..31591027,9	K562	blood:
13	chr6:31587220..31590773-chr6:31700977..31706290,6	MCF-7	breast:
14	chr6:31590485..31592545-chr6:31618288..31620102,2	MCF-7	breast:

No data

Variant related genes	Relation type
PRRC2A	TF binding region
SNORA38	TF binding region
ENSG00000201207	Chromatin interaction
ENSG00000204463	Chromatin interaction
ENSG00000263020	Chromatin interaction
ENSG00000204386	Chromatin interaction
ENSG00000213760	Chromatin interaction
ENSG00000234006	Chromatin interaction
ENSG00000204385	Chromatin interaction
ENSG00000204435	Chromatin interaction
ENSG00000213719	Chromatin interaction
ENSG00000198563	Chromatin interaction
ENSG00000204498	Chromatin interaction
ENSG00000254870	Chromatin interaction
ENSG00000201680	Chromatin interaction
ENSG00000232810	Chromatin interaction
ENSG00000204438	Chromatin interaction
ENSG00000204439	Chromatin interaction
ENSG00000227507	Chromatin interaction
ENSG00000265236	Chromatin interaction

Extended variants
information (count: 29 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:11)

rs_ID	r²[population]
rs2280801	0.95[ASN][1000 genomes]
rs2295663	0.88[ASN][1000 genomes]
rs28732150	0.93[ASN][1000 genomes]
rs28732154	0.95[ASN][1000 genomes]
rs28732157	0.93[ASN][1000 genomes]
rs28732158	0.93[ASN][1000 genomes]
rs9348877	1.00[AMR][1000 genomes]
rs9378164	0.91[ASN][1000 genomes]
rs9380266	0.93[ASN][1000 genomes]
rs9391731	0.93[ASN][1000 genomes]
rs9404941	0.93[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:18 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv601609	chr6:31280101-31799786	Active TSS Flanking Active TSS Bivalent/Poised TSS Strong transcription Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Enhancers Genic enhancers Weak transcription Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	332 gene(s)	inside rSNPs	diseases
2	nsv601610	chr6:31280101-31960770	Enhancers Flanking Active TSS Weak transcription Genic enhancers Strong transcription Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	370 gene(s)	inside rSNPs	diseases
3	nsv601628	chr6:31280327-31990098	Weak transcription Transcr. at gene 5' and 3' Active TSS Enhancers Flanking Active TSS Strong transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh Genic enhancers ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	376 gene(s)	inside rSNPs	diseases
4	nsv601629	chr6:31280327-31996185	Strong transcription Enhancers Weak transcription Flanking Active TSS Transcr. at gene 5' and 3' Genic enhancers Bivalent Enhancer Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	376 gene(s)	inside rSNPs	diseases
5	nsv601630	chr6:31280327-32011317	Genic enhancers Active TSS Weak transcription Enhancers Strong transcription Flanking Active TSS Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	378 gene(s)	inside rSNPs	diseases
6	nsv601631	chr6:31280327-32017540	Genic enhancers Enhancers Weak transcription Active TSS Strong transcription Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	378 gene(s)	inside rSNPs	diseases
7	nsv1023939	chr6:31325961-32026747	Active TSS Transcr. at gene 5' and 3' Flanking Active TSS Genic enhancers Enhancers Weak transcription ZNF genes & repeats Strong transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	372 gene(s)	inside rSNPs	diseases
8	nsv538188	chr6:31325961-32026747	Active TSS Weak transcription Flanking Active TSS Enhancers Strong transcription Bivalent/Poised TSS Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	372 gene(s)	inside rSNPs	diseases
9	nsv432868	chr6:31338844-31721033	Bivalent/Poised TSS Weak transcription Active TSS Enhancers Flanking Active TSS Strong transcription Bivalent Enhancer Transcr. at gene 5' and 3' Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	250 gene(s)	inside rSNPs	diseases
10	nsv1021747	chr6:31386219-31907266	Flanking Active TSS Active TSS Bivalent Enhancer Weak transcription Strong transcription Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Enhancers Genic enhancers Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	330 gene(s)	inside rSNPs	diseases
11	nsv830627	chr6:31496214-31659950	Transcr. at gene 5' and 3' Flanking Active TSS Weak transcription Genic enhancers Enhancers Strong transcription Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	182 gene(s)	inside rSNPs	diseases
12	nsv884418	chr6:31525448-31741078	Active TSS Genic enhancers Enhancers Flanking Active TSS Weak transcription Strong transcription Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	206 gene(s)	inside rSNPs	diseases
13	nsv1033154	chr6:31550614-32009410	Strong transcription Weak transcription Bivalent Enhancer Active TSS Flanking Active TSS Enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	326 gene(s)	inside rSNPs	diseases
14	nsv462871	chr6:31575276-31632134	Strong transcription Genic enhancers Active TSS Flanking Active TSS Enhancers Transcr. at gene 5' and 3' Weak transcription Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA	133 gene(s)	inside rSNPs	diseases
15	nsv601942	chr6:31575276-31632134	Flanking Active TSS Active TSS Genic enhancers Weak transcription Enhancers Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA	133 gene(s)	inside rSNPs	diseases
16	nsv884419	chr6:31585000-31632651	Weak transcription Transcr. at gene 5' and 3' Genic enhancers Active TSS Enhancers Flanking Active TSS Strong transcription ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA	138 gene(s)	inside rSNPs	diseases
17	nsv884420	chr6:31586827-31632651	Genic enhancers Weak transcription Enhancers Flanking Active TSS Transcr. at gene 5' and 3' Strong transcription Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA	138 gene(s)	inside rSNPs	diseases
18	nsv884421	chr6:31588151-31631907	Active TSS Flanking Active TSS Strong transcription Weak transcription Transcr. at gene 5' and 3' Genic enhancers Enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA	129 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	chr6:31588800-31591000	Transcr. at gene 5' and 3'	HUES6 Cell Line	embryonic stem cell
2	chr6:31589000-31591000	Transcr. at gene 5' and 3'	Dnd41	blood
3	chr6:31589200-31590800	Flanking Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
4	chr6:31589200-31591600	Weak transcription	Small Intestine	intestine
5	chr6:31589400-31590800	Transcr. at gene 5' and 3'	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
6	chr6:31589400-31590800	Transcr. at gene 5' and 3'	HUES64 Cell Line	embryonic stem cell
7	chr6:31589400-31590800	Transcr. at gene 5' and 3'	iPS-20b Cell Line	embryonic stem cell
8	chr6:31589400-31590800	Transcr. at gene 5' and 3'	K562	blood
9	chr6:31589400-31591000	Transcr. at gene 5' and 3'	NHEK	skin
10	chr6:31589600-31590800	Transcr. at gene 5' and 3'	H9 Derived Neuron Cultured Cells	ES cell derived
11	chr6:31589600-31590800	Transcr. at gene 5' and 3'	HUES48 Cell Line	embryonic stem cell
12	chr6:31589600-31590800	Flanking Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
13	chr6:31589600-31590800	Transcr. at gene 5' and 3'	Foreskin Melanocyte Primary Cells skin03	Skin
14	chr6:31589600-31591200	Enhancers	Primary monocytes fromperipheralblood	blood
15	chr6:31589600-31591600	Weak transcription	Ovary	ovary
16	chr6:31589800-31590800	Genic enhancers	Right Atrium	heart
17	chr6:31589800-31590800	Transcr. at gene 5' and 3'	Hela-S3	cervix
18	chr6:31589800-31591000	Transcr. at gene 5' and 3'	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
19	chr6:31589800-31591000	Enhancers	Primary B cells from cord blood	blood
20	chr6:31589800-31591000	Genic enhancers	Primary T cells from cord blood	blood
21	chr6:31589800-31591000	Transcr. at gene 5' and 3'	Foreskin Keratinocyte Primary Cells skin03	Skin
22	chr6:31589800-31591000	Enhancers	Esophagus	oesophagus
23	chr6:31589800-31591000	Enhancers	Placenta Amnion	Placenta Amnion
24	chr6:31589800-31591000	Transcr. at gene 5' and 3'	GM12878-XiMat	blood
25	chr6:31589800-31591400	Weak transcription	Aorta	Aorta
26	chr6:31589800-31591400	Weak transcription	Pancreas	Pancrea
27	chr6:31589800-31591600	Genic enhancers	Placenta	Placenta
28	chr6:31589800-31619400	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
29	chr6:31590000-31590800	Enhancers	Brain Angular Gyrus	brain
30	chr6:31590000-31591000	Genic enhancers	Fetal Intestine Large	intestine
31	chr6:31590000-31591000	Transcr. at gene 5' and 3'	NHLF	lung
32	chr6:31590000-31591000	Transcr. at gene 5' and 3'	Osteobl	bone
33	chr6:31590000-31591200	Weak transcription	Spleen	Spleen
34	chr6:31590000-31591400	Weak transcription	Brain Substantia Nigra	brain
35	chr6:31590000-31591400	Weak transcription	Gastric	stomach
36	chr6:31590000-31591800	Weak transcription	Primary T helper naive cells from peripheral blood	blood
37	chr6:31590200-31590800	Enhancers	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
38	chr6:31590200-31590800	Transcr. at gene 5' and 3'	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
39	chr6:31590200-31590800	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
40	chr6:31590200-31590800	Weak transcription	Primary T killer memory cells from peripheral blood	blood
41	chr6:31590200-31590800	Transcr. at gene 5' and 3'	Primary hematopoietic stem cells G-CSF-mobilized Male	--
42	chr6:31590200-31590800	Transcr. at gene 5' and 3'	Ganglion Eminence derived primary cultured neurospheres	brain
43	chr6:31590200-31590800	Genic enhancers	Fetal Muscle Leg	muscle
44	chr6:31590200-31590800	Transcr. at gene 5' and 3'	HSMM	muscle
45	chr6:31590200-31591000	Transcr. at gene 5' and 3'	Brain Germinal Matrix	brain
46	chr6:31590200-31591000	Transcr. at gene 5' and 3'	Fetal Brain Female	brain
47	chr6:31590200-31607000	Strong transcription	Primary T helper 17 cells PMA-I stimulated	--
48	chr6:31590200-31617600	Strong transcription	iPS DF 6.9 Cell Line	embryonic stem cell
49	chr6:31590200-31618800	Strong transcription	Primary B cells from peripheral blood	blood
50	chr6:31590400-31590800	Genic enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--

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