Variant report

Variant	rs486172
Chromosome Location	chr4:75022563-75022564
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:4)
CpG islands
(count:0)
Chromatin interactive
region (count:6)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:4 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr4:75022387-75025140	MCF10A-Er-Src	breast:	n/a	n/a
2	POLR2A	chr4:75022256-75036597	K562	blood:	n/a	n/a
3	POLR2A	chr4:75022369-75024468	IMR90	lung:	n/a	n/a
4	POLR2A	chr4:75022348-75024497	MCF10A-Er-Src	breast:	n/a	n/a

No data

(count:6 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr4:74964506..74967065-chr4:75022087..75025561,3	K562	blood:
2	chr4:75022222..75023752-chr4:75142957..75145413,2	K562	blood:
3	chr4:75021911..75023462-chr4:75229589..75232447,2	K562	blood:
4	chr4:75000738..75003533-chr4:75021528..75023491,2	K562	blood:
5	chr4:75001823..75003533-chr4:75021528..75023480,2	K562	blood:
6	chr4:74964506..74968474-chr4:75022087..75025768,6	K562	blood:

No data

Variant related genes	Relation type
MTHFD2L	TF binding region
ENSG00000124882	Chromatin interaction
ENSG00000081041	Chromatin interaction

Extended variants
information (count: 30 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:22)

rs_ID	r²[population]
rs476893	1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs477628	1.00[AMR][1000 genomes]
rs480956	0.82[YRI][hapmap];1.00[AMR][1000 genomes]
rs481763	1.00[AMR][1000 genomes]
rs487335	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs490645	1.00[YRI][hapmap];1.00[AMR][1000 genomes]
rs493135	1.00[YRI][hapmap];1.00[AMR][1000 genomes]
rs493800	1.00[AMR][1000 genomes]
rs495740	1.00[AMR][1000 genomes]
rs513726	1.00[AMR][1000 genomes]
rs514044	1.00[AMR][1000 genomes]
rs515780	1.00[AMR][1000 genomes]
rs516508	1.00[AMR][1000 genomes]
rs530096	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs531683	1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs557131	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs567157	1.00[AMR][1000 genomes]
rs568187	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs577889	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs579228	1.00[AMR][1000 genomes]
rs6825147	1.00[AMR][1000 genomes]
rs6840665	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:8 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv525980	chr4:74731526-75382209	Strong transcription Weak transcription Enhancers Bivalent/Poised TSS Flanking Active TSS Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	40 gene(s)	inside rSNPs	diseases
2	nsv1004768	chr4:74774372-75109579	Weak transcription Enhancers Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Strong transcription ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	25 gene(s)	inside rSNPs	diseases
3	nsv1006218	chr4:74782324-75105424	Enhancers Weak transcription Flanking Active TSS Active TSS Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	25 gene(s)	inside rSNPs	diseases
4	nsv594683	chr4:75013441-75106485	Enhancers Active TSS Weak transcription Strong transcription Flanking Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Genic enhancers Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases
5	nsv1013260	chr4:75013441-75121643	Weak transcription Active TSS Enhancers Strong transcription Flanking Active TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases
6	nsv1002907	chr4:75013441-75131443	Weak transcription Enhancers Flanking Active TSS Active TSS Strong transcription ZNF genes & repeats Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases
7	nsv1004706	chr4:75014770-75121643	Enhancers Weak transcription Genic enhancers Flanking Active TSS Strong transcription Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases
8	nsv594684	chr4:75015750-75106485	Weak transcription Enhancers Strong transcription ZNF genes & repeats Flanking Active TSS Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:34 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:75013200-75023200	Weak transcription	Psoas Muscle	Psoas
2	chr4:75015800-75022600	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
3	chr4:75019000-75022600	Weak transcription	Cortex derived primary cultured neurospheres	brain
4	chr4:75019000-75022800	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
5	chr4:75019000-75023000	Weak transcription	Colon Smooth Muscle	Colon
6	chr4:75019000-75023000	Weak transcription	Fetal Brain Male	brain
7	chr4:75021800-75022600	Enhancers	HUVEC	blood vessel
8	chr4:75021800-75023000	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
9	chr4:75021800-75023000	Enhancers	Rectal Mucosa Donor 31	rectum
10	chr4:75022000-75022600	Flanking Active TSS	K562	blood
11	chr4:75022000-75022600	Enhancers	NHLF	lung
12	chr4:75022000-75022800	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
13	chr4:75022000-75022800	Enhancers	Muscle Satellite Cultured Cells	--
14	chr4:75022000-75022800	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
15	chr4:75022000-75022800	Enhancers	Rectal Mucosa Donor 29	rectum
16	chr4:75022000-75022800	Enhancers	Hela-S3	cervix
17	chr4:75022000-75022800	Enhancers	HMEC	breast
18	chr4:75022000-75022800	Enhancers	NHDF-Ad	bronchial
19	chr4:75022200-75022600	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
20	chr4:75022200-75022600	Enhancers	NHEK	skin
21	chr4:75022200-75022800	Enhancers	Primary hematopoietic stem cells short term culture	blood
22	chr4:75022200-75022800	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
23	chr4:75022200-75022800	Enhancers	Fetal Adrenal Gland	Adrenal Gland
24	chr4:75022200-75022800	Enhancers	Fetal Heart	heart
25	chr4:75022200-75022800	Enhancers	Fetal Intestine Small	intestine
26	chr4:75022200-75023000	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
27	chr4:75022400-75022600	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
28	chr4:75022400-75022800	Flanking Active TSS	H9 Derived Neuron Cultured Cells	ES cell derived
29	chr4:75022400-75022800	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
30	chr4:75022400-75022800	Enhancers	Osteobl	bone
31	chr4:75022400-75023000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
32	chr4:75022400-75023000	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
33	chr4:75022400-75023000	Enhancers	Fetal Intestine Large	intestine
34	chr4:75022400-75023000	Enhancers	NH-A	brain

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