Variant report

Variant	rs56366090
Chromosome Location	chr6:27836107-27836108
allele	C/G
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:15)
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	TAF7	chr6:27832651-27836396	H1-hESC	embryonic stem cell:	n/a	n/a
2	MXI1	chr6:27831650-27836500	SK-N-SH	brain:	n/a	n/a
3	POLR2A	chr6:27832456-27836599	H1-hESC	embryonic stem cell:	n/a	n/a

No data

(count:15 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr1:116915588..116917427-chr6:27834235..27836471,2	MCF-7	breast:
2	chr6:27098237..27102845-chr6:27835694..27840254,5	MCF-7	breast:
3	chr6:26154866..26157028-chr6:27832028..27836151,3	MCF-7	breast:
4	chr6:26249129..26252003-chr6:27832611..27836378,6	MCF-7	breast:
5	chr6:27836090..27837594-chr6:28374724..28377447,2	K562	blood:
6	chr6:26156108..26158898-chr6:27832756..27836611,3	MCF-7	breast:
7	chr6:26033297..26035200-chr6:27833856..27836117,3	MCF-7	breast:
8	chr6:27105570..27109142-chr6:27832678..27836176,3	K562	blood:
9	chr6:27834624..27836124-chr7:99722099..99724739,2	MCF-7	breast:
10	chr6:26044265..26046503-chr6:27834017..27836277,2	MCF-7	breast:
11	chr6:26019660..26022685-chr6:27833901..27836758,3	MCF-7	breast:
12	chr6:26123459..26125455-chr6:27834569..27837416,2	MCF-7	breast:
13	chr16:4663445..4665916-chr6:27834145..27836986,3	MCF-7	breast:
14	chr1:16840036..16842043-chr6:27834742..27837032,2	MCF-7	breast:
15	chr6:27113113..27117592-chr6:27831181..27837403,7	MCF-7	breast:

No data

Variant related genes	Relation type
HIST1H1B	TF binding region
HIST1H2BPS2	TF binding region
ENSG00000153443	Chromatin interaction
ENSG00000196532	Chromatin interaction
ENSG00000265565	Chromatin interaction
ENSG00000180573	Chromatin interaction
ENSG00000168298	Chromatin interaction
ENSG00000196787	Chromatin interaction
ENSG00000197459	Chromatin interaction
ENSG00000256316	Chromatin interaction
ENSG00000124635	Chromatin interaction
ENSG00000184825	Chromatin interaction
ENSG00000163399	Chromatin interaction
ENSG00000196176	Chromatin interaction
ENSG00000198366	Chromatin interaction
ENSG00000180596	Chromatin interaction
ENSG00000197903	Chromatin interaction
ENSG00000158373	Chromatin interaction
ENSG00000137259	Chromatin interaction
ENSG00000261135	Chromatin interaction
ENSG00000198339	Chromatin interaction
ENSG00000206652	Chromatin interaction
ENSG00000214309	Chromatin interaction

Extended variants
information (count: 47 )
Associated
traits (count: 0)

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

rs_ID	r²[population]
rs12111051	1.00[EUR][1000 genomes]
rs149854	1.00[EUR][1000 genomes]
rs149879	1.00[EUR][1000 genomes]
rs149898	1.00[EUR][1000 genomes]
rs156741	1.00[EUR][1000 genomes]
rs156742	1.00[EUR][1000 genomes]
rs16867899	1.00[EUR][1000 genomes]
rs16867901	1.00[EUR][1000 genomes]
rs169263	0.83[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs175953	1.00[EUR][1000 genomes]
rs175955	1.00[EUR][1000 genomes]
rs183926	1.00[EUR][1000 genomes]
rs187995	0.83[AMR][1000 genomes]
rs200959	0.83[AMR][1000 genomes]
rs200962	1.00[EUR][1000 genomes]
rs200970	0.82[AFR][1000 genomes];0.83[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs203867	1.00[EUR][1000 genomes]
rs203874	1.00[EUR][1000 genomes]
rs2200870	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs276366	1.00[EUR][1000 genomes]
rs276367	1.00[EUR][1000 genomes]
rs276368	0.82[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs276372	1.00[EUR][1000 genomes]
rs425159	1.00[EUR][1000 genomes]
rs55965630	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs56221999	0.83[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs56262840	0.83[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs58700542	0.83[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs60554811	1.00[EUR][1000 genomes]
rs61275289	1.00[AMR][1000 genomes]
rs73739606	0.83[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73739685	0.83[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73739773	1.00[AMR][1000 genomes]
rs73740805	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73740842	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73742455	0.83[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs839777	1.00[EUR][1000 genomes]
rs9295739	1.00[EUR][1000 genomes]
rs9461396	1.00[EUR][1000 genomes]
rs9468189	1.00[EUR][1000 genomes]
rs9468190	1.00[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1022797	chr6:27396961-27864277	Enhancers Weak transcription Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Flanking Active TSS Active TSS ZNF genes & repeats Strong transcription Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	390 gene(s)	inside rSNPs	diseases
2	nsv432858	chr6:27719375-28011652	Flanking Active TSS Weak transcription Enhancers Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Strong transcription Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	387 gene(s)	inside rSNPs	diseases
3	nsv1017440	chr6:27734824-27864277	Enhancers Weak transcription Flanking Active TSS Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats Genic enhancers Strong transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	370 gene(s)	inside rSNPs	diseases
4	nsv1022173	chr6:27734824-27959408	Enhancers Flanking Active TSS Active TSS Weak transcription Strong transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	379 gene(s)	inside rSNPs	diseases
5	nsv883512	chr6:27748631-27969004	Enhancers Weak transcription Flanking Bivalent TSS/Enh Active TSS Flanking Active TSS Bivalent/Poised TSS Bivalent Enhancer Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	379 gene(s)	inside rSNPs	diseases
6	nsv601208	chr6:27810626-27969004	Active TSS Bivalent/Poised TSS Flanking Active TSS Enhancers Flanking Bivalent TSS/Enh Genic enhancers Weak transcription Bivalent Enhancer Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	237 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:91 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:27833200-27836200	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
2	chr6:27835200-27838200	Weak transcription	Lung	lung
3	chr6:27835400-27838200	Weak transcription	Sigmoid Colon	Sigmoid Colon
4	chr6:27835400-27838800	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
5	chr6:27835400-27839000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
6	chr6:27835400-27839000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
7	chr6:27835400-27839400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
8	chr6:27835400-27839600	Weak transcription	Colonic Mucosa	Colon
9	chr6:27835400-27839600	Weak transcription	Esophagus	oesophagus
10	chr6:27835400-27839600	Weak transcription	Pancreas	Pancrea
11	chr6:27835600-27836200	Flanking Active TSS	HUES6 Cell Line	embryonic stem cell
12	chr6:27835600-27836200	Flanking Active TSS	Primary hematopoietic stem cells short term culture	blood
13	chr6:27835600-27836200	Flanking Active TSS	Brain Germinal Matrix	brain
14	chr6:27835600-27836400	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
15	chr6:27835600-27836400	Enhancers	Fetal Intestine Small	intestine
16	chr6:27835600-27836400	Flanking Active TSS	Dnd41	blood
17	chr6:27835600-27836600	Enhancers	Primary T helper cells fromperipheralblood	blood
18	chr6:27835600-27839000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
19	chr6:27835600-27839400	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
20	chr6:27835600-27839400	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
21	chr6:27835600-27839600	Weak transcription	Placenta	Placenta
22	chr6:27835600-27839600	Weak transcription	Right Ventricle	heart
23	chr6:27835600-27839600	Weak transcription	Spleen	Spleen
24	chr6:27835600-27839600	Weak transcription	HSMMtube	muscle
25	chr6:27835800-27836200	Flanking Active TSS	ES-I3 Cell Line	embryonic stem cell
26	chr6:27835800-27836200	Enhancers	Primary B cells from cord blood	blood
27	chr6:27835800-27836400	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
28	chr6:27835800-27836400	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
29	chr6:27835800-27836600	Enhancers	Cortex derived primary cultured neurospheres	brain
30	chr6:27835800-27838600	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
31	chr6:27835800-27838800	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
32	chr6:27835800-27838800	Weak transcription	Rectal Mucosa Donor 29	rectum
33	chr6:27835800-27839000	Weak transcription	Fetal Muscle Trunk	muscle
34	chr6:27835800-27839000	Weak transcription	Right Atrium	heart
35	chr6:27835800-27839200	Weak transcription	Fetal Stomach	stomach
36	chr6:27835800-27839200	Weak transcription	HMEC	breast
37	chr6:27835800-27839400	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
38	chr6:27835800-27839400	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
39	chr6:27835800-27839400	Weak transcription	Liver	Liver
40	chr6:27835800-27839400	Weak transcription	Fetal Heart	heart
41	chr6:27835800-27839400	Weak transcription	Rectal Mucosa Donor 31	rectum
42	chr6:27835800-27839600	Weak transcription	Placenta Amnion	Placenta Amnion
43	chr6:27836000-27836200	Enhancers	HUES64 Cell Line	embryonic stem cell
44	chr6:27836000-27836200	Enhancers	iPS-15b Cell Line	embryonic stem cell
45	chr6:27836000-27836200	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
46	chr6:27836000-27836200	Enhancers	Thymus	Thymus
47	chr6:27836000-27836200	Enhancers	NH-A	brain
48	chr6:27836000-27836400	Enhancers	H1 Cell Line	embryonic stem cell
49	chr6:27836000-27836400	Enhancers	H9 Cell Line	embryonic stem cell
50	chr6:27836000-27836400	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived

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