Variant report

Variant	rs72855817
Chromosome Location	chr6:49430012-49430013
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:14)
CpG islands
(count:0)
Chromatin interactive
region (count:8)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

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

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	NFYB	chr6:49429699-49430125	GM12878	blood:	n/a	n/a
2	HCFC1	chr6:49429845-49431540	Hela-S3	cervix:	n/a	n/a
3	RFX5	chr6:49429907-49430158	GM12878	blood:	n/a	n/a
4	RFX5	chr6:49430011-49431401	Hela-S3	cervix:	n/a	n/a
5	MXI1	chr6:49429642-49431594	GM12878	blood:	n/a	n/a
6	POLR2A	chr6:49429912-49431522	IMR90	lung:	n/a	n/a
7	STAT3	chr6:49429751-49430245	GM12878	blood:	n/a	chr6:49429770-49429777
8	POLR2A	chr6:49429792-49431845	MCF10A-Er-Src	breast:	n/a	n/a
9	POLR2A	chr6:49429891-49432113	Hela-S3	cervix:	n/a	n/a
10	TBP	chr6:49429863-49430454	GM12878	blood:	n/a	n/a
11	POLR2A	chr6:49429981-49431412	MCF10A-Er-Src	breast:	n/a	n/a
12	MAX	chr6:49429667-49430033	NB4	blood:	n/a	chr6:49429780-49429790
13	POLR2A	chr6:49429738-49431811	GM12891	blood:	n/a	n/a
14	MXI1	chr6:49429538-49431842	SK-N-SH	brain:	n/a	n/a

No data

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

No.	Distal block	Cell Line	Cell type
1	chr6:49429949..49432434-chr6:49603239..49605832,3	K562	blood:
2	chr6:49428636..49430625-chr6:49435581..49438306,2	MCF-7	breast:
3	chr6:49352086..49353625-chr6:49427377..49430292,2	K562	blood:
4	chr6:49419838..49421598-chr6:49428414..49430900,2	K562	blood:
5	chr6:49428075..49430840-chr6:49629508..49632761,3	K562	blood:
6	chr6:49429390..49432411-chr6:49516710..49519961,3	MCF-7	breast:
7	chr6:49428409..49430841-chr6:49452599..49454961,2	K562	blood:
8	chr6:49427543..49430477-chr6:49436132..49438156,2	K562	blood:

No data

Variant related genes	Relation type
CENPQ	TF binding region
ENSG00000197261	Chromatin interaction
ENSG00000112077	Chromatin interaction

Extended variants
information (count: 10 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:2)

rs_ID	r²[population]
rs72855821	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs72869250	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]

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	nsv1024959	chr6:49290141-49652124	Enhancers Weak transcription Flanking Active TSS Strong transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Active TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	19 gene(s)	inside rSNPs	diseases
2	nsv1021136	chr6:49295037-49631278	Weak transcription Enhancers Strong transcription Active TSS Bivalent Enhancer Flanking Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	19 gene(s)	inside rSNPs	diseases
3	nsv915806	chr6:49313295-49430422	Enhancers Flanking Active TSS Weak transcription Active TSS Strong transcription Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region miRNA target site	7 gene(s)	inside rSNPs	diseases
4	nsv603081	chr6:49421241-49446233	Weak transcription Active TSS Enhancers Flanking Active TSS Strong transcription Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region	10 gene(s)	inside rSNPs	diseases
5	nsv603082	chr6:49421241-49446509	ZNF genes & repeats Weak transcription Strong transcription Flanking Active TSS Enhancers Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region	10 gene(s)	inside rSNPs	diseases
6	nsv603083	chr6:49429706-49446233	Strong transcription Weak transcription Flanking Active TSS Active TSS Enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Genic enhancers Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region	10 gene(s)	inside rSNPs	diseases
7	nsv603084	chr6:49429706-49446509	Enhancers Flanking Active TSS Weak transcription Strong transcription Transcr. at gene 5' and 3' Active TSS Genic enhancers Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region	10 gene(s)	inside rSNPs	diseases
8	nsv603085	chr6:49429706-49450341	Active TSS Weak transcription Enhancers Strong transcription Flanking Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Genic enhancers	TF binding region CpG island Chromatin interactive region	10 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:124 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:49406800-49430400	Weak transcription	Esophagus	oesophagus
2	chr6:49407800-49430400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
3	chr6:49407800-49430400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
4	chr6:49407800-49430400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
5	chr6:49407800-49430400	Weak transcription	Lung	lung
6	chr6:49408000-49430400	Weak transcription	Gastric	stomach
7	chr6:49409200-49430400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
8	chr6:49410400-49430400	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
9	chr6:49427400-49430200	Weak transcription	Placenta	Placenta
10	chr6:49428000-49430400	Flanking Active TSS	Liver	Liver
11	chr6:49428800-49430200	Enhancers	Primary B cells from peripheral blood	blood
12	chr6:49429000-49434200	Active TSS	GM12878-XiMat	blood
13	chr6:49429200-49430200	Enhancers	Small Intestine	intestine
14	chr6:49429200-49430400	Enhancers	Sigmoid Colon	Sigmoid Colon
15	chr6:49429200-49430800	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
16	chr6:49429200-49432000	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
17	chr6:49429400-49430200	Flanking Active TSS	H9 Derived Neuron Cultured Cells	ES cell derived
18	chr6:49429400-49430200	Enhancers	Primary monocytes fromperipheralblood	blood
19	chr6:49429400-49430200	Flanking Active TSS	Brain Germinal Matrix	brain
20	chr6:49429400-49430400	Flanking Active TSS	Dnd41	blood
21	chr6:49429400-49430600	Flanking Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
22	chr6:49429400-49430800	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
23	chr6:49429400-49432000	Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
24	chr6:49429400-49432000	Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
25	chr6:49429400-49432200	Active TSS	Ovary	ovary
26	chr6:49429400-49432200	Active TSS	Right Atrium	heart
27	chr6:49429600-49430200	Flanking Active TSS	iPS-20b Cell Line	embryonic stem cell
28	chr6:49429600-49430200	Enhancers	Primary neutrophils fromperipheralblood	blood
29	chr6:49429600-49430200	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
30	chr6:49429600-49430200	Flanking Active TSS	Foreskin Melanocyte Primary Cells skin03	Skin
31	chr6:49429600-49430200	Flanking Active TSS	Fetal Brain Female	brain
32	chr6:49429600-49430200	Flanking Active TSS	NHEK	skin
33	chr6:49429600-49430400	Flanking Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
34	chr6:49429600-49430400	Enhancers	Primary mononuclear cells fromperipheralblood	Blood
35	chr6:49429600-49430400	Flanking Active TSS	Brain Anterior Caudate	brain
36	chr6:49429600-49430400	Flanking Active TSS	Colon Smooth Muscle	Colon
37	chr6:49429600-49430400	Weak transcription	Pancreas	Pancrea
38	chr6:49429600-49430600	Flanking Active TSS	Primary T helper naive cells fromperipheralblood	blood
39	chr6:49429600-49430600	Flanking Active TSS	Primary T regulatory cells fromperipheralblood	blood
40	chr6:49429600-49430600	Flanking Active TSS	Cortex derived primary cultured neurospheres	brain
41	chr6:49429600-49430600	Flanking Active TSS	Adipose Nuclei	Adipose
42	chr6:49429600-49430600	Flanking Active TSS	Duodenum Mucosa	Duodenum
43	chr6:49429600-49430600	Flanking Active TSS	Rectal Mucosa Donor 31	rectum
44	chr6:49429600-49430600	Flanking Active TSS	HUVEC	blood vessel
45	chr6:49429600-49430800	Flanking Active TSS	Primary hematopoietic stem cells	blood
46	chr6:49429600-49430800	Flanking Active TSS	Primary T helper naive cells from peripheral blood	blood
47	chr6:49429600-49430800	Flanking Active TSS	Primary T helper cells fromperipheralblood	blood
48	chr6:49429600-49431600	Active TSS	Brain Cingulate Gyrus	brain
49	chr6:49429600-49431600	Active TSS	Brain Substantia Nigra	brain
50	chr6:49429600-49431600	Active TSS	Stomach Smooth Muscle	stomach

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