Variant report

Variant	rs9998786
Chromosome Location	chr4:678788-678789
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr4:514891..517080-chr4:677730..679355,2	MCF-7	breast:
2	chr4:678244..681266-chr4:735203..738855,3	MCF-7	breast:

Variant related genes	Relation type
ENSG00000174227	Chromatin interaction
ENSG00000185619	Chromatin interaction

Extended variants
information (count: 29 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:5)

rs_ID	r²[population]
rs11248032	0.81[EUR][1000 genomes]
rs28655411	0.83[EUR][1000 genomes]
rs35466919	0.82[EUR][1000 genomes]
rs7690350	0.89[EUR][1000 genomes]
rs9991613	0.87[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:24 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1011715	chr4:43860-823487	Active TSS Weak transcription Bivalent Enhancer Bivalent/Poised TSS Strong transcription Enhancers Flanking Active TSS ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	76 gene(s)	inside rSNPs	diseases
2	esv2830422	chr4:72247-681939	Flanking Active TSS Enhancers Strong transcription Weak transcription ZNF genes & repeats Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	54 gene(s)	inside rSNPs	diseases
3	nsv931097	chr4:72447-683874	Strong transcription Active TSS Enhancers Genic enhancers Flanking Active TSS ZNF genes & repeats Weak transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	54 gene(s)	inside rSNPs	diseases
4	nsv532702	chr4:72447-755236	Active TSS ZNF genes & repeats Strong transcription Weak transcription Flanking Active TSS Enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	60 gene(s)	inside rSNPs	diseases
5	nsv1005224	chr4:507005-900281	Enhancers Flanking Active TSS ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer Strong transcription Weak transcription Active TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	41 gene(s)	inside rSNPs	diseases
6	nsv536976	chr4:507005-900281	Weak transcription Enhancers Active TSS ZNF genes & repeats Bivalent Enhancer Flanking Active TSS Strong transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	41 gene(s)	inside rSNPs	diseases
7	nsv878245	chr4:509178-694613	Active TSS Flanking Active TSS Enhancers Strong transcription Weak transcription Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	22 gene(s)	inside rSNPs	diseases
8	nsv822425	chr4:540105-1413799	Weak transcription Flanking Bivalent TSS/Enh Active TSS Flanking Active TSS Enhancers ZNF genes & repeats Strong transcription Bivalent Enhancer Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	108 gene(s)	inside rSNPs	diseases
9	nsv878246	chr4:592507-696848	Flanking Active TSS Weak transcription Active TSS Strong transcription Enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	20 gene(s)	inside rSNPs	diseases
10	esv2757916	chr4:603208-931354	Weak transcription Strong transcription Genic enhancers Enhancers Bivalent Enhancer Bivalent/Poised TSS Flanking Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	40 gene(s)	inside rSNPs	diseases
11	esv2759217	chr4:603208-931354	Weak transcription Enhancers Strong transcription Active TSS Genic enhancers ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Flanking Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	40 gene(s)	inside rSNPs	diseases
12	nsv878247	chr4:607202-925149	Bivalent Enhancer Flanking Active TSS Strong transcription Bivalent/Poised TSS Enhancers Active TSS Flanking Bivalent TSS/Enh Genic enhancers Weak transcription Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	38 gene(s)	inside rSNPs	diseases
13	nsv530490	chr4:614355-1399150	Bivalent Enhancer Enhancers Flanking Active TSS Weak transcription Genic enhancers ZNF genes & repeats Strong transcription Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	104 gene(s)	inside rSNPs	diseases
14	nsv593206	chr4:625962-735150	Weak transcription Flanking Active TSS Strong transcription Enhancers Genic enhancers Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	22 gene(s)	inside rSNPs	diseases
15	nsv878248	chr4:645300-685993	Weak transcription Transcr. at gene 5' and 3' Flanking Active TSS Enhancers Active TSS Genic enhancers Bivalent Enhancer Strong transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	18 gene(s)	inside rSNPs	diseases
16	nsv878249	chr4:649639-691026	Bivalent Enhancer Flanking Active TSS Weak transcription Active TSS Enhancers Strong transcription Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	18 gene(s)	inside rSNPs	diseases
17	esv1829397	chr4:655939-1041957	Enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Active TSS Weak transcription Flanking Active TSS Strong transcription Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	50 gene(s)	inside rSNPs	diseases
18	nsv829834	chr4:665477-775524	Active TSS Genic enhancers Weak transcription Strong transcription Flanking Active TSS Transcr. at gene 5' and 3' Enhancers Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	30 gene(s)	inside rSNPs	diseases
19	nsv10413	chr4:667204-684301	Weak transcription Active TSS Enhancers Flanking Active TSS Bivalent Enhancer Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases
20	nsv593208	chr4:668000-682233	Enhancers Active TSS Weak transcription Strong transcription Flanking Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases
21	nsv878250	chr4:668567-683842	Active TSS Enhancers Bivalent Enhancer Weak transcription Transcr. at gene 5' and 3' Flanking Active TSS Flanking Bivalent TSS/Enh Genic enhancers Strong transcription Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	15 gene(s)	inside rSNPs	diseases
22	nsv878251	chr4:669857-683842	Flanking Active TSS Enhancers Active TSS Weak transcription ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases
23	nsv878252	chr4:669857-685993	Enhancers Flanking Active TSS Weak transcription Genic enhancers Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh Strong transcription Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases
24	esv3358167	chr4:677602-680100	Enhancers Weak transcription Genic enhancers Transcr. at gene 5' and 3' Strong transcription Bivalent Enhancer Flanking Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Active TSS	TF binding region CpG island Chromatin interactive region	7 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs9998786	RP11-1191J2.2	cis	lung	GTEx
rs9998786	RP11-1191J2.2	cis	Nerve Tibial	GTEx
rs9998786	RP11-1191J2.2	cis	Thyroid	GTEx

Chromatin state (count:83 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:675000-680800	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
2	chr4:675200-678800	Enhancers	Placenta	Placenta
3	chr4:675200-680400	Weak transcription	NHDF-Ad	bronchial
4	chr4:675200-680600	Weak transcription	Placenta Amnion	Placenta Amnion
5	chr4:675200-680600	Weak transcription	NH-A	brain
6	chr4:675200-680800	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
7	chr4:675200-680800	Weak transcription	NHLF	lung
8	chr4:675200-682200	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
9	chr4:675200-682400	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
10	chr4:675200-682600	Weak transcription	GM12878-XiMat	blood
11	chr4:675400-680600	Weak transcription	Osteobl	bone
12	chr4:675400-680800	Weak transcription	Primary B cells from cord blood	blood
13	chr4:675400-681600	Weak transcription	iPS-20b Cell Line	embryonic stem cell
14	chr4:675400-681800	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
15	chr4:675400-682400	Weak transcription	HUES64 Cell Line	embryonic stem cell
16	chr4:675800-679000	Weak transcription	H9 Cell Line	embryonic stem cell
17	chr4:675800-681600	Weak transcription	iPS-15b Cell Line	embryonic stem cell
18	chr4:676000-682000	Weak transcription	HUES48 Cell Line	embryonic stem cell
19	chr4:676200-680800	Weak transcription	HMEC	breast
20	chr4:676400-679000	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
21	chr4:676800-680400	Weak transcription	Breast Myoepithelial Primary Cells	Breast
22	chr4:677000-682400	Enhancers	Fetal Muscle Leg	muscle
23	chr4:677200-680600	Weak transcription	Duodenum Smooth Muscle	Duodenum
24	chr4:677200-680800	Weak transcription	Rectal Smooth Muscle	rectum
25	chr4:677400-679200	Genic enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
26	chr4:677600-678800	Enhancers	Fetal Lung	lung
27	chr4:677800-680400	Weak transcription	Liver	Liver
28	chr4:677800-680600	Weak transcription	Psoas Muscle	Psoas
29	chr4:677800-680600	Weak transcription	Right Atrium	heart
30	chr4:677800-682400	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
31	chr4:678000-678800	Enhancers	Foreskin Melanocyte Primary Cells skin01	Skin
32	chr4:678000-679000	Weak transcription	Adipose Nuclei	Adipose
33	chr4:678000-680400	Weak transcription	Left Ventricle	heart
34	chr4:678000-680600	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
35	chr4:678000-680600	Weak transcription	Sigmoid Colon	Sigmoid Colon
36	chr4:678000-681600	Weak transcription	Primary hematopoietic stem cells	blood
37	chr4:678000-681800	Weak transcription	Brain Anterior Caudate	brain
38	chr4:678000-682000	Weak transcription	Primary hematopoietic stem cells short term culture	blood
39	chr4:678200-678800	Flanking Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
40	chr4:678200-678800	Weak transcription	Right Ventricle	heart
41	chr4:678200-678800	Weak transcription	Monocytes-CD14+_RO01746	blood
42	chr4:678200-679000	Weak transcription	Colonic Mucosa	Colon
43	chr4:678200-679000	Weak transcription	Lung	lung
44	chr4:678200-679000	Weak transcription	Pancreas	Pancrea
45	chr4:678200-680200	Weak transcription	Skeletal Muscle Male	skeletal muscle
46	chr4:678200-680400	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
47	chr4:678200-680400	Weak transcription	Primary neutrophils fromperipheralblood	blood
48	chr4:678200-680400	Weak transcription	Esophagus	oesophagus
49	chr4:678200-680400	Strong transcription	Gastric	stomach
50	chr4:678200-680400	Weak transcription	Skeletal Muscle Female	skeletal muscle

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