Variant report

Variant	rs28696943
Chromosome Location	chr4:88310135-88310136
allele	A/G
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	MAFK	chr4:88310023-88310252	HepG2	liver:	n/a	n/a
2	IRF1	chr4:88310056-88310359	K562	blood:	n/a	chr4:88310246-88310257 chr4:88310244-88310257 chr4:88310244-88310257 chr4:88310244-88310257
3	CEBPB	chr4:88310063-88310391	K562	blood:	n/a	n/a
4	MAFF	chr4:88310040-88310228	HepG2	liver:	n/a	n/a
5	MAFK	chr4:88309970-88310239	Hela-S3	cervix:	n/a	n/a
6	MAFK	chr4:88310019-88310303	HepG2	liver:	n/a	n/a
7	IRF1	chr4:88309721-88310421	K562	blood:	n/a	chr4:88310246-88310257 chr4:88310244-88310257 chr4:88310244-88310257 chr4:88310244-88310257
8	MAX	chr4:88310042-88310407	NB4	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr4:88293477..88300868-chr4:88308814..88313684,7	K562	blood:
2	chr1:156186339..156187927-chr4:88309889..88311409,2	MCF-7	breast:
3	chr4:88309813..88313902-chr4:88342245..88346379,5	K562	blood:
4	chr4:88303180..88304947-chr4:88309411..88311690,2	K562	blood:
5	chr4:88309258..88311648-chr4:88320453..88322015,2	K562	blood:

Variant related genes	Relation type
RN7SL681P	TF binding region
ENSG00000198189	Chromatin interaction
ENSG00000170502	Chromatin interaction

Extended variants
information (count: 37 )
Associated
traits (count: 0)

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

rs_ID	r²[population]
rs10000196	0.83[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs10009948	0.88[ASN][1000 genomes]
rs10023606	0.82[AFR][1000 genomes];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs10024781	0.86[ASN][1000 genomes]
rs10030035	0.81[AMR][1000 genomes];0.93[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs10032122	0.88[ASN][1000 genomes]
rs10084883	0.89[ASN][1000 genomes]
rs12640451	0.88[ASN][1000 genomes]
rs12640894	0.90[ASN][1000 genomes]
rs12650763	0.89[ASN][1000 genomes]
rs12651034	0.89[ASN][1000 genomes]
rs28366407	0.83[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs28415220	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs28437709	0.88[ASN][1000 genomes]
rs28493315	0.81[AMR][1000 genomes];0.93[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs28493566	0.88[ASN][1000 genomes]
rs28529046	0.90[ASN][1000 genomes]
rs28535549	0.88[ASN][1000 genomes]
rs28712618	0.89[ASN][1000 genomes]
rs28718986	0.88[ASN][1000 genomes]
rs28762371	0.90[ASN][1000 genomes]
rs28805573	0.90[ASN][1000 genomes]
rs55824708	0.89[ASN][1000 genomes]
rs56153912	0.91[ASN][1000 genomes]
rs58192677	0.88[ASN][1000 genomes]
rs67121411	0.97[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs68045074	0.89[ASN][1000 genomes]
rs72652067	0.90[ASN][1000 genomes]
rs7665115	0.89[ASN][1000 genomes]
rs7673763	0.81[AMR][1000 genomes];0.93[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7677249	0.89[ASN][1000 genomes]
rs7680878	0.81[AMR][1000 genomes];0.93[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7690728	0.93[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs9995987	0.90[ASN][1000 genomes]
rs9998212	0.93[EUR][1000 genomes];0.91[ASN][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	nsv1004518	chr4:88218473-88354403	Weak transcription Active TSS Genic enhancers Flanking Active TSS Enhancers Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	13 gene(s)	inside rSNPs	diseases
2	nsv1002789	chr4:88239340-88606485	Strong transcription Enhancers Active TSS Weak transcription Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	18 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:103 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:88254800-88311800	Weak transcription	Placenta Amnion	Placenta Amnion
2	chr4:88256200-88310600	Weak transcription	Right Ventricle	heart
3	chr4:88257800-88311800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
4	chr4:88276200-88311400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
5	chr4:88293000-88311200	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
6	chr4:88293200-88311400	Weak transcription	H9 Cell Line	embryonic stem cell
7	chr4:88294000-88311000	Weak transcription	HSMM	muscle
8	chr4:88294200-88310800	Weak transcription	iPS-20b Cell Line	embryonic stem cell
9	chr4:88295400-88311200	Weak transcription	Aorta	Aorta
10	chr4:88297400-88310600	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
11	chr4:88297400-88310800	Weak transcription	Osteobl	bone
12	chr4:88302800-88312000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
13	chr4:88303600-88310400	Weak transcription	Fetal Muscle Trunk	muscle
14	chr4:88303600-88310400	Weak transcription	Placenta	Placenta
15	chr4:88307600-88310200	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
16	chr4:88307600-88310600	Enhancers	Primary T cells fromperipheralblood	blood
17	chr4:88307600-88310600	Enhancers	Primary T killer memory cells from peripheral blood	blood
18	chr4:88307600-88310800	Enhancers	Primary T killer naive cells fromperipheralblood	blood
19	chr4:88308000-88310600	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
20	chr4:88308200-88310800	Enhancers	Primary T helper cells fromperipheralblood	blood
21	chr4:88308200-88310800	Active TSS	GM12878-XiMat	blood
22	chr4:88308400-88311000	Enhancers	Primary B cells from peripheral blood	blood
23	chr4:88308400-88311400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
24	chr4:88308600-88310400	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
25	chr4:88308800-88310600	Active TSS	Rectal Mucosa Donor 31	rectum
26	chr4:88309000-88310600	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
27	chr4:88309000-88310600	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
28	chr4:88309000-88310600	Enhancers	Primary T cells effector/memory enriched fromperipheralblood	blood
29	chr4:88309000-88312400	Active TSS	Skeletal Muscle Female	skeletal muscle
30	chr4:88309000-88313200	Active TSS	Rectal Smooth Muscle	rectum
31	chr4:88309200-88310200	Flanking Active TSS	Primary neutrophils fromperipheralblood	blood
32	chr4:88309200-88311000	Transcr. at gene 5' and 3'	Dnd41	blood
33	chr4:88309400-88310200	ZNF genes & repeats	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
34	chr4:88309400-88310200	Flanking Active TSS	Primary T helper cells PMA-I stimulated	--
35	chr4:88309400-88310200	ZNF genes & repeats	Ganglion Eminence derived primary cultured neurospheres	brain
36	chr4:88309400-88310200	ZNF genes & repeats	Brain Substantia Nigra	brain
37	chr4:88309400-88310200	Flanking Active TSS	Hela-S3	cervix
38	chr4:88309400-88310600	Enhancers	Lung	lung
39	chr4:88309400-88310600	Weak transcription	Skeletal Muscle Male	skeletal muscle
40	chr4:88309400-88310600	Enhancers	Thymus	Thymus
41	chr4:88309400-88311200	Flanking Active TSS	Liver	Liver
42	chr4:88309400-88312800	Active TSS	Small Intestine	intestine
43	chr4:88309400-88313000	Active TSS	NHLF	lung
44	chr4:88309600-88310200	ZNF genes & repeats	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
45	chr4:88309600-88310200	ZNF genes & repeats	Brain Hippocampus Middle	brain
46	chr4:88309600-88310200	ZNF genes & repeats	A549	lung
47	chr4:88309600-88310400	Weak transcription	Spleen	Spleen
48	chr4:88309600-88310600	Weak transcription	Brain Inferior Temporal Lobe	brain
49	chr4:88309600-88310600	Enhancers	Ovary	ovary
50	chr4:88309600-88310800	Enhancers	Fetal Thymus	thymus

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