Variant report

Variant	rs11097640
Chromosome Location	chr4:99848701-99848702
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:1)
CpG islands
(count:0)
Chromatin interactive
region (count:14)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

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

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	MXI1	chr4:99848648-99851624	SK-N-SH	brain:	n/a	chr4:99850350-99850359 chr4:99850501-99850510

No data

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

No.	Distal block	Cell Line	Cell type
1	chr4:99848351..99851753-chr4:99915675..99920876,6	MCF-7	breast:
2	chr4:99821499..99832064-chr4:99845860..99851281,12	MCF-7	breast:
3	chr4:99846410..99852563-chr4:99914756..99918771,11	MCF-7	breast:
4	chr4:99181196..99182841-chr4:99847002..99849754,2	MCF-7	breast:
5	chr4:99848192..99852255-chr4:100007586..100012546,7	K562	blood:
6	chr4:99828711..99830237-chr4:99846843..99849645,2	MCF-7	breast:
7	chr4:99811621..99813284-chr4:99847831..99850392,2	MCF-7	breast:
8	chr4:99848589..99851336-chr4:100870396..100872880,2	MCF-7	breast:
9	chr4:99764627..99767221-chr4:99848476..99850008,2	K562	blood:
10	chr4:99805865..99807821-chr4:99847875..99849598,2	MCF-7	breast:
11	chr4:99847842..99851448-chr4:99963294..99966988,3	K562	blood:
12	chr4:99842136..99852937-chr4:99913200..99922220,39	K562	blood:
13	chr4:99844460..99852883-chr4:99909835..99921707,41	K562	blood:
14	chr4:99848578..99852948-chr4:99876464..99882582,7	K562	blood:

No data

Variant related genes	Relation type
ENSG00000263923	TF binding region
ENSG00000138698	Chromatin interaction
ENSG00000197894	Chromatin interaction
ENSG00000246090	Chromatin interaction
ENSG00000164024	Chromatin interaction
ENSG00000245322	Chromatin interaction
ENSG00000214886	Chromatin interaction
ENSG00000214559	Chromatin interaction
ENSG00000249055	Chromatin interaction
ENSG00000164032	Chromatin interaction
ENSG00000265213	Chromatin interaction
ENSG00000151247	Chromatin interaction

Extended variants
information (count: 29 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:27)

rs_ID	r²[population]
rs10004975	0.88[AFR][1000 genomes];0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10023577	0.84[AFR][1000 genomes];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs10433890	0.87[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11725932	0.84[EUR][1000 genomes]
rs11729285	0.88[AFR][1000 genomes];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12498533	0.88[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12644580	0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs17028293	0.87[EUR][1000 genomes]
rs2100426	0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs28494580	0.94[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs28577966	0.83[EUR][1000 genomes]
rs2924581	0.85[AMR][1000 genomes];0.92[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs34830689	0.94[AFR][1000 genomes];0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs35447189	0.87[EUR][1000 genomes]
rs4264834	0.94[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4699688	0.88[AFR][1000 genomes];0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4699693	0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6810489	0.85[EUR][1000 genomes]
rs6811070	0.97[AMR][1000 genomes];0.91[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6830125	0.84[EUR][1000 genomes]
rs6852715	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7660937	0.84[EUR][1000 genomes]
rs7661487	0.87[EUR][1000 genomes]
rs7664964	0.84[EUR][1000 genomes]
rs7665587	0.97[AMR][1000 genomes];0.92[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs7665590	0.97[AMR][1000 genomes];0.92[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs9996959	0.85[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1009017	chr4:99669441-100406394	Active TSS Enhancers Flanking Active TSS Weak transcription Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	57 gene(s)	inside rSNPs	diseases
2	nsv879654	chr4:99748988-99877402	Weak transcription Enhancers Strong transcription Active TSS Flanking Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	31 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:125 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:99802800-99849000	Weak transcription	Aorta	Aorta
2	chr4:99804400-99848800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
3	chr4:99807200-99849000	Weak transcription	Colonic Mucosa	Colon
4	chr4:99808600-99849000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
5	chr4:99823000-99848800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
6	chr4:99823000-99849000	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
7	chr4:99823000-99849200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
8	chr4:99823200-99848800	Weak transcription	Placenta	Placenta
9	chr4:99831000-99849200	Weak transcription	Gastric	stomach
10	chr4:99831400-99848800	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
11	chr4:99832200-99848800	Weak transcription	Rectal Smooth Muscle	rectum
12	chr4:99832400-99849000	Weak transcription	Right Atrium	heart
13	chr4:99832600-99849200	Weak transcription	Spleen	Spleen
14	chr4:99838400-99848800	Weak transcription	Adipose Nuclei	Adipose
15	chr4:99838800-99848800	Weak transcription	Rectal Mucosa Donor 29	rectum
16	chr4:99838800-99848800	Weak transcription	Small Intestine	intestine
17	chr4:99839000-99849200	Weak transcription	Ovary	ovary
18	chr4:99839200-99849400	Weak transcription	Sigmoid Colon	Sigmoid Colon
19	chr4:99839400-99849200	Weak transcription	Lung	lung
20	chr4:99840400-99848800	Weak transcription	HSMMtube	muscle
21	chr4:99841000-99849200	Weak transcription	Pancreas	Pancrea
22	chr4:99841600-99849200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
23	chr4:99843400-99848800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
24	chr4:99845600-99848800	Weak transcription	Monocytes-CD14+_RO01746	blood
25	chr4:99846400-99848800	Weak transcription	H9 Cell Line	embryonic stem cell
26	chr4:99846400-99848800	Enhancers	Primary T helper naive cells fromperipheralblood	blood
27	chr4:99846400-99849000	Enhancers	Primary T killer naive cells fromperipheralblood	blood
28	chr4:99847000-99848800	Enhancers	Primary T cells fromperipheralblood	blood
29	chr4:99847200-99848800	Enhancers	Fetal Brain Male	brain
30	chr4:99847400-99848800	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
31	chr4:99847400-99848800	Enhancers	Primary T helper naive cells from peripheral blood	blood
32	chr4:99847400-99848800	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
33	chr4:99847400-99849000	Weak transcription	Left Ventricle	heart
34	chr4:99847800-99848800	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
35	chr4:99847800-99848800	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
36	chr4:99847800-99848800	Enhancers	Cortex derived primary cultured neurospheres	brain
37	chr4:99847800-99848800	Enhancers	Brain Angular Gyrus	brain
38	chr4:99847800-99848800	Enhancers	Brain Cingulate Gyrus	brain
39	chr4:99847800-99848800	Enhancers	Brain Inferior Temporal Lobe	brain
40	chr4:99847800-99848800	Enhancers	Brain Substantia Nigra	brain
41	chr4:99847800-99849000	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
42	chr4:99847800-99849000	Enhancers	Fetal Heart	heart
43	chr4:99847800-99849000	Enhancers	Skeletal Muscle Female	skeletal muscle
44	chr4:99847800-99850800	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
45	chr4:99847800-99850800	Active TSS	NH-A	brain
46	chr4:99847800-99851400	Active TSS	Hela-S3	cervix
47	chr4:99847800-99851600	Active TSS	Psoas Muscle	Psoas
48	chr4:99848000-99848800	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
49	chr4:99848000-99848800	Enhancers	Primary neutrophils fromperipheralblood	blood
50	chr4:99848000-99848800	Enhancers	Brain Germinal Matrix	brain

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