Variant report

Variant	rs9295750
Chromosome Location	chr6:27784428-27784429
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:2)
CpG islands
(count:0)
Chromatin interactive
region (count:11)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:2 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr6:27784406-27784428	MCF-7	breast:	n/a	n/a
2	CUX1	chr6:27784424-27784565	GM12878	blood:	n/a	n/a

No data

(count:11 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr6:27100161..27102247-chr6:27781053..27784459,3	MCF-7	breast:
2	chr5:65439509..65441854-chr6:27782836..27785587,2	MCF-7	breast:
3	chr6:26216490..26219190-chr6:27783241..27786059,2	MCF-7	breast:
4	chr6:26155301..26160613-chr6:27781458..27785146,6	MCF-7	breast:
5	chr20:45986636..45989209-chr6:27782881..27785567,2	MCF-7	breast:
6	chr6:27093465..27120217-chr6:27768366..27817187,256	K562	blood:
7	chr6:26233018..26235518-chr6:27781228..27784528,3	MCF-7	breast:
8	chr6:27111360..27127716-chr6:27768319..27787545,69	MCF-7	breast:
9	chr6:26020260..26024010-chr6:27780504..27784636,5	MCF-7	breast:
10	chr6:27154833..27157823-chr6:27782934..27785900,2	K562	blood:
11	chr6:27105231..27107098-chr6:27782990..27785264,2	K562	blood:

No data

Variant related genes	Relation type
HIST1H2AJ	TF binding region
ENSG00000187990	Chromatin interaction
ENSG00000153914	Chromatin interaction
ENSG00000124575	Chromatin interaction
ENSG00000197903	Chromatin interaction
ENSG00000265565	Chromatin interaction
ENSG00000198339	Chromatin interaction
ENSG00000253744	Chromatin interaction
ENSG00000158373	Chromatin interaction
ENSG00000168274	Chromatin interaction
ENSG00000196787	Chromatin interaction
ENSG00000184825	Chromatin interaction
ENSG00000168298	Chromatin interaction
ENSG00000196176	Chromatin interaction
ENSG00000124635	Chromatin interaction
ENSG00000198366	Chromatin interaction
ENSG00000218281	Chromatin interaction

Extended variants
information (count: 31 )
Associated
traits (count: 0)

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

rs_ID	r²[population]
rs10484401	0.85[YRI][hapmap]
rs12332927	1.00[CHB][hapmap];0.87[CHD][hapmap]
rs1497525	0.82[CHB][hapmap]
rs1497526	0.82[CHB][hapmap]
rs16893533	0.82[CHB][hapmap]
rs16893540	0.82[CHB][hapmap]
rs17763319	0.82[CHB][hapmap];0.85[CHD][hapmap];1.00[JPT][hapmap];0.85[ASN][1000 genomes]
rs1873213	0.82[CHB][hapmap]
rs41269271	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6456803	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.94[LWK][hapmap];0.88[MEX][hapmap];0.89[YRI][hapmap];0.91[ASN][1000 genomes]
rs6900413	1.00[CHB][hapmap];0.82[JPT][hapmap];0.89[YRI][hapmap];0.88[ASN][1000 genomes]
rs73386612	0.84[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs73386649	0.88[ASN][1000 genomes]
rs7760871	0.82[CHB][hapmap]
rs9461416	0.94[ASN][1000 genomes]
rs9461419	0.82[ASN][1000 genomes]
rs9461424	0.82[CHB][hapmap]
rs9461425	0.82[CHB][hapmap]
rs9468249	0.91[ASN][1000 genomes]
rs9468250	0.88[ASN][1000 genomes]
rs9468252	1.00[CHB][hapmap];0.87[CHD][hapmap];0.83[LWK][hapmap]
rs9468264	0.82[CHB][hapmap]
rs9885649	1.00[CHB][hapmap];0.87[CHD][hapmap];0.84[LWK][hapmap]

Variant overlapped rSNPs/rCNVs (count:8 , 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	nsv830618	chr6:27593274-27789605	Active TSS Enhancers Weak transcription Flanking Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Strong transcription Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	143 gene(s)	inside rSNPs	diseases
3	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
4	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
5	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
6	nsv1017057	chr6:27745777-27789683	Enhancers Weak transcription Flanking Active TSS Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Strong transcription	TF binding region CpG island Chromatin interactive region	125 gene(s)	inside rSNPs	diseases
7	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
8	nsv970094	chr6:27782238-27786201	Active TSS Genic enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Enhancers Weak transcription Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	41 gene(s)	inside rSNPs	n/a

No data

Chromatin state (count:29 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:27783200-27787600	Weak transcription	Hela-S3	cervix
2	chr6:27783400-27784800	Weak transcription	HepG2	liver
3	chr6:27783400-27791200	Weak transcription	Liver	Liver
4	chr6:27783400-27791800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
5	chr6:27783600-27784800	Weak transcription	Fetal Intestine Small	intestine
6	chr6:27783600-27785200	Weak transcription	Primary T helper cells PMA-I stimulated	--
7	chr6:27783600-27787000	Weak transcription	Right Atrium	heart
8	chr6:27783600-27787600	Weak transcription	Primary T killer memory cells from peripheral blood	blood
9	chr6:27783600-27789400	Weak transcription	Rectal Mucosa Donor 31	rectum
10	chr6:27783600-27791000	Weak transcription	Primary hematopoietic stem cells	blood
11	chr6:27783800-27784800	Enhancers	iPS-20b Cell Line	embryonic stem cell
12	chr6:27783800-27787400	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
13	chr6:27783800-27787800	Weak transcription	Duodenum Mucosa	Duodenum
14	chr6:27784000-27784600	Enhancers	Primary hematopoietic stem cells short term culture	blood
15	chr6:27784000-27784600	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
16	chr6:27784000-27784800	Weak transcription	H9 Cell Line	embryonic stem cell
17	chr6:27784000-27785200	Enhancers	iPS-18 Cell Line	embryonic stem cell
18	chr6:27784000-27785600	Enhancers	Fetal Thymus	thymus
19	chr6:27784000-27787400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
20	chr6:27784000-27787400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
21	chr6:27784000-27787600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
22	chr6:27784000-27791000	Weak transcription	HUES48 Cell Line	embryonic stem cell
23	chr6:27784000-27791200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
24	chr6:27784200-27784600	Active TSS	GM12878-XiMat	blood
25	chr6:27784200-27791000	Weak transcription	HUES6 Cell Line	embryonic stem cell
26	chr6:27784400-27785000	Enhancers	iPS-15b Cell Line	embryonic stem cell
27	chr6:27784400-27785200	Enhancers	HUES64 Cell Line	embryonic stem cell
28	chr6:27784400-27787400	Weak transcription	A549	lung
29	chr6:27784400-27791000	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin

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