Variant report

Variant	rs3093727
Chromosome Location	chr6:31547115-31547116
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:0)
CpG islands
(count:0)
Chromatin interactive
region (count:13)
LncRNA
region (count:1)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:13 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr6:31546034..31550400-chr6:31586618..31591027,9	K562	blood:
2	chr6:31546432..31549319-chr6:31626826..31629905,3	K562	blood:
3	chr6:31525235..31529478-chr6:31547066..31550176,3	K562	blood:
4	chr6:31511781..31517209-chr6:31545410..31553496,14	K562	blood:
5	chr6:31546371..31548675-chr6:31564943..31568111,3	MCF-7	breast:
6	chr6:31546482..31549319-chr6:31626826..31629309,2	K562	blood:
7	chr6:31545201..31547160-chr6:31587288..31589333,2	MCF-7	breast:
8	chr6:31545892..31550426-chr6:31586652..31590237,7	MCF-7	breast:
9	chr6:31544984..31547805-chr6:31562709..31565695,2	MCF-7	breast:
10	chr6:31546285..31547870-chr8:144951411..144953855,2	MCF-7	breast:
11	chr6:31545261..31548055-chr6:31619357..31622211,2	K562	blood:
12	chr6:31513283..31516765-chr6:31544904..31548194,5	MCF-7	breast:
13	chr6:31529623..31531832-chr6:31546596..31549041,2	K562	blood:

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

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-TNF-1	chr6:31546991-31548157	ucscGeneNc_uc003ntm_1

No data

Variant related genes	Relation type
ENSG00000204444	Chromatin interaction
ENSG00000204463	Chromatin interaction
ENSG00000204439	Chromatin interaction
ENSG00000200816	Chromatin interaction
ENSG00000213760	Chromatin interaction
ENSG00000227184	Chromatin interaction
ENSG00000204498	Chromatin interaction
ENSG00000204469	Chromatin interaction
ENSG00000254870	Chromatin interaction

Extended variants
information (count: 55 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:41)

rs_ID	r²[population]
rs17207190	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2516474	1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28381344	0.83[AMR][1000 genomes]
rs28732141	0.81[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28732142	0.81[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28732143	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28732144	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28732145	0.83[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs28732153	0.83[AMR][1000 genomes]
rs28732155	0.83[AMR][1000 genomes]
rs28732156	0.83[AMR][1000 genomes]
rs28732159	0.83[AMR][1000 genomes]
rs28732160	0.83[AMR][1000 genomes]
rs28895015	1.00[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2905741	0.83[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs3021366	1.00[ASN][1000 genomes]
rs3093661	0.98[EUR][1000 genomes]
rs3093668	1.00[EUR][1000 genomes]
rs3093726	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs361525	0.81[EUR][1000 genomes]
rs3828917	0.83[EUR][1000 genomes]
rs41293856	0.83[EUR][1000 genomes]
rs41293860	0.83[EUR][1000 genomes]
rs41293879	0.83[EUR][1000 genomes]
rs41293887	0.88[EUR][1000 genomes]
rs41293891	0.84[EUR][1000 genomes]
rs41293895	0.93[EUR][1000 genomes]
rs41293899	0.93[EUR][1000 genomes]
rs41293907	0.93[EUR][1000 genomes]
rs41293911	1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs41293915	1.00[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs41293919	1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs41293923	1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs41315808	0.83[AMR][1000 genomes]
rs4947326	0.85[EUR][1000 genomes]
rs4947327	0.85[EUR][1000 genomes]
rs4959077	0.88[EUR][1000 genomes]
rs4959078	0.93[EUR][1000 genomes]
rs7757162	0.83[AMR][1000 genomes];0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7757383	1.00[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs9267497	0.85[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:14 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1015372	chr6:30704734-31582152	Active TSS Flanking Active TSS Enhancers Weak transcription Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Strong transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	334 gene(s)	inside rSNPs	diseases
2	nsv538173	chr6:30704734-31582152	Flanking Active TSS Enhancers Weak transcription Active TSS Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Strong transcription Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	334 gene(s)	inside rSNPs	diseases
3	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
4	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
5	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
6	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
7	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
8	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
9	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
10	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
11	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
12	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
13	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
14	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

No data

Chromatin state (count:70 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:31536000-31548400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
2	chr6:31540200-31548000	Weak transcription	Small Intestine	intestine
3	chr6:31543800-31547400	Weak transcription	Primary hematopoietic stem cells short term culture	blood
4	chr6:31543800-31548200	Weak transcription	Brain Anterior Caudate	brain
5	chr6:31543800-31548400	Weak transcription	Left Ventricle	heart
6	chr6:31543800-31548400	Weak transcription	Lung	lung
7	chr6:31543800-31548400	Weak transcription	Psoas Muscle	Psoas
8	chr6:31544000-31548000	Weak transcription	Skeletal Muscle Female	skeletal muscle
9	chr6:31544000-31548200	Weak transcription	Brain Hippocampus Middle	brain
10	chr6:31544200-31548400	Weak transcription	Right Atrium	heart
11	chr6:31544400-31548200	Weak transcription	Liver	Liver
12	chr6:31544400-31548400	Weak transcription	HSMMtube	muscle
13	chr6:31544800-31548200	Weak transcription	Rectal Mucosa Donor 31	rectum
14	chr6:31544800-31548200	Weak transcription	K562	blood
15	chr6:31545000-31547200	Genic enhancers	Fetal Thymus	thymus
16	chr6:31545000-31547800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
17	chr6:31545000-31548000	Weak transcription	Dnd41	blood
18	chr6:31545000-31548200	Weak transcription	Adipose Nuclei	Adipose
19	chr6:31545000-31548400	Weak transcription	Esophagus	oesophagus
20	chr6:31545000-31548400	Weak transcription	Gastric	stomach
21	chr6:31545000-31548400	Weak transcription	Right Ventricle	heart
22	chr6:31545200-31547400	Weak transcription	Thymus	Thymus
23	chr6:31545200-31547600	Genic enhancers	Primary B cells from peripheral blood	blood
24	chr6:31545200-31547600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
25	chr6:31545200-31548000	Weak transcription	Rectal Smooth Muscle	rectum
26	chr6:31545200-31548400	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
27	chr6:31545200-31548600	Weak transcription	Placenta Amnion	Placenta Amnion
28	chr6:31545400-31547600	Weak transcription	Primary hematopoietic stem cells	blood
29	chr6:31545400-31547800	Enhancers	Primary T killer naive cells fromperipheralblood	blood
30	chr6:31545400-31547800	Weak transcription	Duodenum Mucosa	Duodenum
31	chr6:31545400-31548200	Weak transcription	Colonic Mucosa	Colon
32	chr6:31545600-31547400	Weak transcription	Primary neutrophils fromperipheralblood	blood
33	chr6:31545600-31547400	Enhancers	Primary T killer memory cells from peripheral blood	blood
34	chr6:31545800-31547400	Genic enhancers	Primary mononuclear cells fromperipheralblood	Blood
35	chr6:31546000-31547800	Flanking Active TSS	Primary T helper memory cells from peripheral blood 2	blood
36	chr6:31546200-31547600	Flanking Active TSS	Breast Myoepithelial Primary Cells	Breast
37	chr6:31546200-31548600	Flanking Active TSS	GM12878-XiMat	blood
38	chr6:31546400-31547200	Enhancers	Pancreas	Pancrea
39	chr6:31546400-31547400	Weak transcription	HUES64 Cell Line	embryonic stem cell
40	chr6:31546400-31547400	Genic enhancers	Primary B cells from cord blood	blood
41	chr6:31546400-31547600	Enhancers	Primary T helper naive cells fromperipheralblood	blood
42	chr6:31546600-31547400	Weak transcription	Primary monocytes fromperipheralblood	blood
43	chr6:31546600-31548200	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
44	chr6:31546800-31547200	Enhancers	Primary T cells from cord blood	blood
45	chr6:31546800-31547400	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
46	chr6:31546800-31547600	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
47	chr6:31546800-31547600	Weak transcription	Spleen	Spleen
48	chr6:31546800-31547800	Flanking Active TSS	Primary T helper cells PMA-I stimulated	--
49	chr6:31546800-31548000	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
50	chr6:31546800-31548000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell

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