Variant report

Variant	rs7684459
Chromosome Location	chr4:110739753-110739754
allele	C/T
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:9)
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	PAX5	chr4:110739735-110739908	GM12878	blood:	n/a	n/a
2	PAX5	chr4:110739744-110739951	GM12878	blood:	n/a	n/a

No data

(count:9 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr4:110739041..110741927-chr4:110742062..110743764,2	MCF-7	breast:
2	chr4:109570584..109572425-chr4:110736914..110740419,3	K562	blood:
3	chr4:110650210..110652125-chr4:110738761..110740839,2	K562	blood:
4	chr4:110683032..110685527-chr4:110738470..110740917,2	K562	blood:
5	chr4:110739567..110741609-chr4:110748053..110749745,2	MCF-7	breast:
6	chr4:110736593..110738765-chr4:110738981..110740675,2	MCF-7	breast:
7	chr4:110739239..110741975-chr4:110896217..110899898,3	MCF-7	breast:
8	chr4:110684027..110686689-chr4:110739417..110742962,3	K562	blood:
9	chr4:110736073..110738614-chr4:110739183..110744192,10	MCF-7	breast:

No data

Variant related genes	Relation type
ENSG00000272795	TF binding region
ENSG00000109534	Chromatin interaction
ENSG00000180245	Chromatin interaction
ENSG00000272795	Chromatin interaction
ENSG00000205403	Chromatin interaction
ENSG00000198856	Chromatin interaction
ENSG00000138798	Chromatin interaction
ENSG00000123739	Chromatin interaction

Extended variants
information (count: 36 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:35)

rs_ID	r²[population]
rs10020617	0.94[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10022841	0.98[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12500239	0.94[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs12504835	0.94[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs12510851	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12513108	0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12643147	0.94[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs12644142	0.94[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs13109228	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs13112387	0.88[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs13129185	0.89[AFR][1000 genomes];0.93[AMR][1000 genomes];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs13140289	0.94[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs13141065	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs13150454	0.82[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1860130	0.88[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs34378309	0.92[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs34706258	0.92[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs34717063	0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs34734592	0.82[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs35426158	0.88[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs36101562	0.82[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs3775961	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4353905	0.94[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs4422417	0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4610335	0.94[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs4698749	0.81[AFR][1000 genomes];0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4698750	0.87[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs6814743	0.84[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs6842245	0.85[AMR][1000 genomes];0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6858351	0.84[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs7442158	0.83[AMR][1000 genomes];0.93[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7657133	0.85[AMR][1000 genomes];0.98[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7678178	0.88[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs7698794	0.88[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs9993509	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]

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

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv530156	chr4:110721397-110911297	Weak transcription Active TSS Enhancers Strong transcription Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:123 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:110737600-110743400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
2	chr4:110737600-110745400	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
3	chr4:110737600-110745800	Weak transcription	Spleen	Spleen
4	chr4:110737600-110770600	Weak transcription	Aorta	Aorta
5	chr4:110737800-110740000	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
6	chr4:110737800-110740600	Weak transcription	Left Ventricle	heart
7	chr4:110737800-110741800	Weak transcription	Primary neutrophils fromperipheralblood	blood
8	chr4:110737800-110743400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
9	chr4:110737800-110746400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
10	chr4:110737800-110746600	Weak transcription	Esophagus	oesophagus
11	chr4:110737800-110748000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
12	chr4:110737800-110753200	Weak transcription	Lung	lung
13	chr4:110738000-110739800	Weak transcription	Primary T cells fromperipheralblood	blood
14	chr4:110738000-110741400	Weak transcription	Primary B cells from cord blood	blood
15	chr4:110738000-110741800	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
16	chr4:110738000-110743400	Weak transcription	Fetal Stomach	stomach
17	chr4:110738000-110747200	Weak transcription	Gastric	stomach
18	chr4:110738000-110748400	Weak transcription	Small Intestine	intestine
19	chr4:110738000-110760800	Weak transcription	Brain Cingulate Gyrus	brain
20	chr4:110738200-110739800	Weak transcription	Placenta Amnion	Placenta Amnion
21	chr4:110738200-110742200	Weak transcription	Stomach Smooth Muscle	stomach
22	chr4:110738200-110743400	Weak transcription	Rectal Smooth Muscle	rectum
23	chr4:110738200-110743400	Weak transcription	Thymus	Thymus
24	chr4:110738200-110746400	Weak transcription	Colonic Mucosa	Colon
25	chr4:110738200-110747800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
26	chr4:110738400-110739800	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
27	chr4:110738400-110740000	Weak transcription	Colon Smooth Muscle	Colon
28	chr4:110738400-110740000	Weak transcription	Fetal Lung	lung
29	chr4:110738400-110740000	Weak transcription	Hela-S3	cervix
30	chr4:110738400-110740200	Weak transcription	Primary T helper naive cells from peripheral blood	blood
31	chr4:110738400-110740200	Weak transcription	Duodenum Mucosa	Duodenum
32	chr4:110738400-110740200	Weak transcription	Fetal Kidney	kidney
33	chr4:110738400-110740400	Weak transcription	Primary hematopoietic stem cells	blood
34	chr4:110738400-110740400	Weak transcription	Skeletal Muscle Male	skeletal muscle
35	chr4:110738400-110740400	Weak transcription	NHDF-Ad	bronchial
36	chr4:110738400-110740600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
37	chr4:110738400-110740800	Weak transcription	Cortex derived primary cultured neurospheres	brain
38	chr4:110738400-110741000	Weak transcription	H9 Cell Line	embryonic stem cell
39	chr4:110738400-110741200	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
40	chr4:110738400-110741800	Weak transcription	Brain Hippocampus Middle	brain
41	chr4:110738400-110742000	Weak transcription	HSMMtube	muscle
42	chr4:110738400-110743200	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
43	chr4:110738400-110743400	Weak transcription	Pancreas	Pancrea
44	chr4:110738400-110743400	Weak transcription	Sigmoid Colon	Sigmoid Colon
45	chr4:110738400-110748000	Weak transcription	Primary T killer memory cells from peripheral blood	blood
46	chr4:110738400-110748000	Weak transcription	Ovary	ovary
47	chr4:110738400-110748400	Weak transcription	Right Ventricle	heart
48	chr4:110738400-110748600	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
49	chr4:110738400-110757200	Weak transcription	Brain Inferior Temporal Lobe	brain
50	chr4:110738600-110740200	Weak transcription	Duodenum Smooth Muscle	Duodenum

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