Variant report

Variant	rs852394
Chromosome Location	chr7:5721448-5721449
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	REST	chr7:5720983-5721503	ECC-1	luminal epithelium:	n/a	chr7:5721177-5721186 chr7:5721171-5721191 chr7:5721171-5721185 chr7:5721171-5721191 chr7:5721171-5721191
2	POLR2A	chr7:5721266-5721630	K562	blood:	n/a	n/a
3	MTA3	chr7:5720309-5721448	GM12878	blood:	n/a	n/a
4	REST	chr7:5720806-5721540	PFSK-1	brain:	n/a	chr7:5721177-5721186 chr7:5721171-5721191 chr7:5721171-5721185 chr7:5721171-5721191 chr7:5721171-5721191
5	REST	chr7:5720934-5721468	ECC-1	luminal epithelium:	n/a	chr7:5721177-5721186 chr7:5721171-5721191 chr7:5721171-5721185 chr7:5721171-5721191 chr7:5721171-5721191
6	REST	chr7:5720858-5721618	HL-60	blood:	n/a	chr7:5721177-5721186 chr7:5721171-5721191 chr7:5721171-5721185 chr7:5721171-5721191 chr7:5721171-5721191

No.	Distal block	Cell Line	Cell type
1	chr7:5720320..5722351-chr7:5726225..5727971,2	K562	blood:
2	chr7:5595299..5597821-chr7:5720043..5723343,4	MCF-7	breast:
3	chr7:5629871..5633923-chr7:5720945..5722828,3	K562	blood:
4	chr7:5707494..5709701-chr7:5721366..5724112,2	MCF-7	breast:
5	chr7:5631239..5634081-chr7:5720945..5723370,2	K562	blood:
6	chr7:5652719..5654979-chr7:5720841..5722728,2	MCF-7	breast:
7	chr7:5568217..5571108-chr7:5721320..5723273,2	MCF-7	breast:

Variant related genes	Relation type
RNF216-IT1	TF binding region
ENSG00000075624	Chromatin interaction
ENSG00000075618	Chromatin interaction
ENSG00000272719	Chromatin interaction

Extended variants
information (count: 23 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:7)

rs_ID	r²[population]
rs12539336	0.83[LWK][hapmap];1.00[YRI][hapmap];0.82[AFR][1000 genomes]
rs4720638	0.81[ASN][1000 genomes]
rs61405954	0.87[AFR][1000 genomes]
rs852374	0.95[LWK][hapmap];0.93[YRI][hapmap];0.81[AFR][1000 genomes]
rs852400	1.00[YRI][hapmap];0.81[AFR][1000 genomes]
rs852417	0.91[LWK][hapmap];0.93[YRI][hapmap];0.81[AFR][1000 genomes]
rs860424	0.81[AFR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:16 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv869165	chr7:4889618-5799719	Weak transcription Genic enhancers Transcr. at gene 5' and 3' Enhancers ZNF genes & repeats Strong transcription Flanking Active TSS Bivalent/Poised TSS Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	352 gene(s)	inside rSNPs	diseases
2	nsv530979	chr7:5101631-5864814	Active TSS Enhancers ZNF genes & repeats Flanking Active TSS Weak transcription Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	350 gene(s)	inside rSNPs	diseases
3	nsv530981	chr7:5157150-5920006	Weak transcription Genic enhancers Flanking Active TSS Bivalent/Poised TSS Enhancers Flanking Bivalent TSS/Enh Active TSS Strong transcription Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	348 gene(s)	inside rSNPs	diseases
4	nsv530983	chr7:5370746-6070852	Active TSS Strong transcription Flanking Bivalent TSS/Enh Weak transcription Flanking Active TSS Enhancers ZNF genes & repeats Bivalent Enhancer Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	368 gene(s)	inside rSNPs	diseases
5	nsv916391	chr7:5417945-5889565	Flanking Active TSS Enhancers ZNF genes & repeats Weak transcription Genic enhancers Active TSS Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	336 gene(s)	inside rSNPs	diseases
6	nsv533108	chr7:5488018-6316581	Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Active TSS Weak transcription Enhancers Genic enhancers Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	390 gene(s)	inside rSNPs	diseases
7	nsv482449	chr7:5557585-5743673	Genic enhancers Weak transcription Flanking Bivalent TSS/Enh Strong transcription Flanking Active TSS Enhancers Transcr. at gene 5' and 3' Active TSS Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	294 gene(s)	inside rSNPs	diseases
8	nsv1033556	chr7:5565080-6186815	Weak transcription Active TSS Flanking Active TSS Bivalent Enhancer Strong transcription Enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats Genic enhancers Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	357 gene(s)	inside rSNPs	diseases
9	nsv538710	chr7:5565080-6186815	Bivalent Enhancer Flanking Active TSS Enhancers Active TSS Weak transcription Strong transcription Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	357 gene(s)	inside rSNPs	diseases
10	nsv530467	chr7:5617816-5815082	Strong transcription Weak transcription Enhancers Flanking Active TSS Genic enhancers ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	44 gene(s)	inside rSNPs	diseases
11	nsv1017612	chr7:5629728-5819144	Genic enhancers Weak transcription Flanking Active TSS Enhancers Active TSS Transcr. at gene 5' and 3' Strong transcription Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	44 gene(s)	inside rSNPs	diseases
12	nsv1021989	chr7:5629728-6186815	Strong transcription Flanking Active TSS Weak transcription Enhancers Genic enhancers Active TSS ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	126 gene(s)	inside rSNPs	diseases
13	nsv887417	chr7:5667645-5760860	Weak transcription Enhancers Genic enhancers Strong transcription Flanking Active TSS Transcr. at gene 5' and 3' Active TSS ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA	10 gene(s)	inside rSNPs	diseases
14	nsv887418	chr7:5675305-5772551	Enhancers Weak transcription Strong transcription Genic enhancers Flanking Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Active TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA	10 gene(s)	inside rSNPs	diseases
15	nsv887419	chr7:5703669-5820383	Weak transcription Strong transcription Flanking Active TSS Enhancers Genic enhancers Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA	10 gene(s)	inside rSNPs	diseases
16	nsv1028652	chr7:5706207-5769489	Weak transcription Strong transcription Flanking Active TSS Enhancers Genic enhancers Active TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	9 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	chr7:5674800-5728200	Weak transcription	Small Intestine	intestine
2	chr7:5699200-5723000	Weak transcription	H9 Cell Line	embryonic stem cell
3	chr7:5702000-5730600	Weak transcription	Placenta Amnion	Placenta Amnion
4	chr7:5702800-5727200	Weak transcription	Psoas Muscle	Psoas
5	chr7:5713000-5730200	Weak transcription	Gastric	stomach
6	chr7:5713200-5724000	Weak transcription	Brain Germinal Matrix	brain
7	chr7:5715400-5723200	Enhancers	Adipose Nuclei	Adipose
8	chr7:5716200-5721800	Enhancers	Right Atrium	heart
9	chr7:5716400-5722000	Enhancers	Fetal Heart	heart
10	chr7:5716600-5722400	Weak transcription	iPS-18 Cell Line	embryonic stem cell
11	chr7:5716800-5724000	Enhancers	Primary monocytes fromperipheralblood	blood
12	chr7:5717000-5723200	Enhancers	Placenta	Placenta
13	chr7:5717200-5723400	Enhancers	Skeletal Muscle Female	skeletal muscle
14	chr7:5717200-5726600	Genic enhancers	Fetal Muscle Leg	muscle
15	chr7:5717400-5723000	Weak transcription	Aorta	Aorta
16	chr7:5717400-5723800	Enhancers	Primary B cells from peripheral blood	blood
17	chr7:5717600-5722600	Weak transcription	HUES64 Cell Line	embryonic stem cell
18	chr7:5717600-5722600	Weak transcription	Fetal Kidney	kidney
19	chr7:5717600-5723800	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
20	chr7:5717600-5726600	Genic enhancers	Primary T cells fromperipheralblood	blood
21	chr7:5717600-5727600	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
22	chr7:5717800-5722400	Weak transcription	HUES48 Cell Line	embryonic stem cell
23	chr7:5717800-5722600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
24	chr7:5717800-5723000	Weak transcription	NHLF	lung
25	chr7:5717800-5723800	Weak transcription	Hela-S3	cervix
26	chr7:5717800-5724000	Weak transcription	Muscle Satellite Cultured Cells	--
27	chr7:5718000-5728200	Weak transcription	HMEC	breast
28	chr7:5718200-5721600	Weak transcription	Brain Anterior Caudate	brain
29	chr7:5718200-5722000	Strong transcription	Dnd41	blood
30	chr7:5718200-5722600	Weak transcription	HUES6 Cell Line	embryonic stem cell
31	chr7:5718200-5723200	Weak transcription	NH-A	brain
32	chr7:5718200-5724000	Weak transcription	Fetal Brain Female	brain
33	chr7:5718400-5722800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
34	chr7:5718400-5723000	Weak transcription	Brain Angular Gyrus	brain
35	chr7:5718400-5731200	Weak transcription	HUVEC	blood vessel
36	chr7:5718400-5735600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
37	chr7:5718800-5722000	Genic enhancers	Fetal Adrenal Gland	Adrenal Gland
38	chr7:5719000-5721800	Enhancers	Right Ventricle	heart
39	chr7:5719200-5721600	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
40	chr7:5719400-5721800	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
41	chr7:5719400-5722400	Weak transcription	A549	lung
42	chr7:5719400-5723400	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
43	chr7:5719400-5723800	Weak transcription	NHEK	skin
44	chr7:5719600-5723000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
45	chr7:5719800-5721600	Weak transcription	Primary hematopoietic stem cells	blood
46	chr7:5719800-5721600	Genic enhancers	GM12878-XiMat	blood
47	chr7:5719800-5722600	Weak transcription	iPS-20b Cell Line	embryonic stem cell
48	chr7:5719800-5723000	Weak transcription	K562	blood
49	chr7:5719800-5727200	Weak transcription	NHDF-Ad	bronchial
50	chr7:5720000-5721800	Enhancers	Foreskin Melanocyte Primary Cells skin01	Skin

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