Variant report

Variant	rs4975148
Chromosome Location	chr4:79565004-79565005
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	RFX5	chr4:79564929-79567015	SK-N-SH	brain:	n/a	chr4:79566034-79566049 chr4:79566035-79566049 chr4:79566605-79566614 chr4:79566603-79566617 chr4:79566038-79566047 chr4:79566036-79566044

No.	Distal block	Cell Line	Cell type
1	chr4:79555903..79561750-chr4:79563110..79566277,7	K562	blood:
2	chr4:79563120..79566472-chr4:79698388..79700680,4	K562	blood:
3	chr4:79557761..79562686-chr4:79563110..79568703,4	K562	blood:
4	chr4:79549184..79553600-chr4:79560172..79565329,6	K562	blood:
5	chr4:79564649..79566835-chr4:79572826..79575093,2	K562	blood:
6	chr4:79564124..79566354-chr4:79779216..79781048,2	MCF-7	breast:
7	chr4:79563690..79568625-chr4:79568843..79572048,4	K562	blood:
8	chr4:79562196..79569044-chr4:79695847..79699797,11	MCF-7	breast:
9	chr4:79563449..79567560-chr4:79569303..79574487,6	K562	blood:
10	chr4:79562740..79566241-chr4:79702324..79704926,3	MCF-7	breast:
11	chr4:79564080..79567985-chr4:79696414..79698633,7	MCF-7	breast:

Variant related genes	Relation type
LINC01094	TF binding region
ENSG00000251019	Chromatin interaction
ENSG00000200998	Chromatin interaction
ENSG00000138756	Chromatin interaction
ENSG00000260278	Chromatin interaction
ENSG00000238816	Chromatin interaction

Extended variants
information (count: 72 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:71)

rs_ID	r²[population]
rs10001246	0.83[EUR][1000 genomes]
rs10007186	0.85[EUR][1000 genomes]
rs10019240	0.85[EUR][1000 genomes]
rs10212636	0.99[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs1107606	0.96[EUR][1000 genomes]
rs1108907	0.96[EUR][1000 genomes]
rs11724268	0.89[EUR][1000 genomes]
rs11724602	0.99[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs11728013	0.89[EUR][1000 genomes]
rs11731482	0.85[EUR][1000 genomes]
rs11733032	0.99[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs11733269	0.83[EUR][1000 genomes]
rs11736376	0.99[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs11736602	0.89[EUR][1000 genomes]
rs11942573	0.85[EUR][1000 genomes]
rs12233694	0.89[EUR][1000 genomes]
rs12233707	0.89[EUR][1000 genomes]
rs12643488	0.99[EUR][1000 genomes]
rs12646646	0.97[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs12650411	0.89[EUR][1000 genomes]
rs12711032	0.85[EUR][1000 genomes]
rs13120630	0.85[EUR][1000 genomes]
rs13138005	0.97[EUR][1000 genomes]
rs1972024	0.96[EUR][1000 genomes]
rs28597797	0.88[EUR][1000 genomes]
rs28833829	0.81[AFR][1000 genomes]
rs34325799	0.85[EUR][1000 genomes]
rs4073678	0.89[EUR][1000 genomes]
rs4073679	0.89[EUR][1000 genomes]
rs4074673	0.85[EUR][1000 genomes]
rs4074674	0.85[EUR][1000 genomes]
rs4075927	0.89[EUR][1000 genomes]
rs4077709	0.89[EUR][1000 genomes]
rs4270605	0.85[EUR][1000 genomes]
rs4306980	0.96[EUR][1000 genomes]
rs4353930	0.99[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs4632683	0.84[EUR][1000 genomes]
rs4643844	0.85[EUR][1000 genomes]
rs6533821	0.83[EUR][1000 genomes]
rs6533825	0.96[EUR][1000 genomes]
rs6533835	0.98[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs6533842	0.98[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs6811335	0.96[EUR][1000 genomes]
rs6812227	0.85[EUR][1000 genomes]
rs6812441	0.85[EUR][1000 genomes]
rs6814739	0.89[EUR][1000 genomes]
rs6819484	0.89[EUR][1000 genomes]
rs6824014	0.96[EUR][1000 genomes]
rs6829061	0.96[EUR][1000 genomes]
rs6829198	0.99[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs6834587	0.99[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs6835210	0.89[EUR][1000 genomes]
rs6835998	0.96[EUR][1000 genomes]
rs6836513	0.85[EUR][1000 genomes]
rs6838443	0.84[EUR][1000 genomes]
rs6840592	0.89[EUR][1000 genomes]
rs6845893	0.84[EUR][1000 genomes]
rs6846346	0.99[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs6851341	0.89[EUR][1000 genomes]
rs6854055	0.99[EUR][1000 genomes]
rs7317	0.96[EUR][1000 genomes]
rs7657082	0.96[EUR][1000 genomes]
rs7669674	0.87[EUR][1000 genomes]
rs7669866	0.93[EUR][1000 genomes]
rs7670506	1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];0.90[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs7680749	0.99[EUR][1000 genomes]
rs7680766	0.99[EUR][1000 genomes]
rs7682984	0.83[EUR][1000 genomes]
rs7689154	0.99[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs7697461	0.88[EUR][1000 genomes]
rs9998136	0.99[EUR][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	nsv1009633	chr4:78887573-79652236	Weak transcription Strong transcription Enhancers Flanking Active TSS Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	41 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:53 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:79551400-79578200	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
2	chr4:79555800-79566400	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
3	chr4:79557200-79568000	Enhancers	Primary B cells from cord blood	blood
4	chr4:79560200-79565200	Weak transcription	Primary T cells from cord blood	blood
5	chr4:79560200-79565400	Weak transcription	Primary T helper cells PMA-I stimulated	--
6	chr4:79560200-79565600	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
7	chr4:79561000-79565400	Weak transcription	NHEK	skin
8	chr4:79561600-79568000	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
9	chr4:79561800-79566800	Enhancers	K562	blood
10	chr4:79562000-79568000	Enhancers	Primary B cells from peripheral blood	blood
11	chr4:79562400-79566400	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
12	chr4:79562800-79567600	Enhancers	Primary hematopoietic stem cells	blood
13	chr4:79563000-79566000	Enhancers	Primary hematopoietic stem cells short term culture	blood
14	chr4:79563200-79568800	Enhancers	Primary monocytes fromperipheralblood	blood
15	chr4:79563400-79567200	Weak transcription	HUES6 Cell Line	embryonic stem cell
16	chr4:79563800-79566600	Enhancers	Hela-S3	cervix
17	chr4:79564000-79568000	Enhancers	Fetal Intestine Large	intestine
18	chr4:79564200-79566400	Enhancers	Monocytes-CD14+_RO01746	blood
19	chr4:79564200-79566400	Weak transcription	NHLF	lung
20	chr4:79564400-79565400	Weak transcription	HUVEC	blood vessel
21	chr4:79564400-79565600	Weak transcription	HMEC	breast
22	chr4:79564400-79566000	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
23	chr4:79564400-79566200	Weak transcription	Cortex derived primary cultured neurospheres	brain
24	chr4:79564400-79566400	Weak transcription	Brain Inferior Temporal Lobe	brain
25	chr4:79564400-79566400	Weak transcription	HSMM	muscle
26	chr4:79564400-79566600	Weak transcription	Rectal Mucosa Donor 29	rectum
27	chr4:79564400-79566800	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
28	chr4:79564400-79567000	Weak transcription	Left Ventricle	heart
29	chr4:79564400-79567000	Weak transcription	Spleen	Spleen
30	chr4:79564400-79571400	Weak transcription	Fetal Heart	heart
31	chr4:79564400-79577200	Weak transcription	Fetal Thymus	thymus
32	chr4:79564400-79589600	Weak transcription	Lung	lung
33	chr4:79564600-79565600	Weak transcription	Breast Myoepithelial Primary Cells	Breast
34	chr4:79564600-79566000	Weak transcription	Adipose Nuclei	Adipose
35	chr4:79564600-79566000	Weak transcription	NHDF-Ad	bronchial
36	chr4:79564600-79566400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
37	chr4:79564600-79566400	Weak transcription	Colon Smooth Muscle	Colon
38	chr4:79564600-79566400	Weak transcription	Duodenum Mucosa	Duodenum
39	chr4:79564600-79566600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
40	chr4:79564600-79566600	Weak transcription	Stomach Mucosa	stomach
41	chr4:79564600-79567000	Weak transcription	Esophagus	oesophagus
42	chr4:79564600-79567000	Weak transcription	Right Atrium	heart
43	chr4:79564800-79565600	Weak transcription	Brain Hippocampus Middle	brain
44	chr4:79564800-79566000	Weak transcription	Fetal Intestine Small	intestine
45	chr4:79564800-79566400	Weak transcription	Rectal Mucosa Donor 31	rectum
46	chr4:79564800-79566600	Weak transcription	HSMMtube	muscle
47	chr4:79564800-79567200	Weak transcription	Sigmoid Colon	Sigmoid Colon
48	chr4:79564800-79567600	Enhancers	GM12878-XiMat	blood
49	chr4:79565000-79565400	Weak transcription	Brain Anterior Caudate	brain
50	chr4:79565000-79565400	Weak transcription	A549	lung

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