Variant report

Variant	rs13098087
Chromosome Location	chr3:49209987-49209988
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	MXI1	chr3:49208067-49212337	SK-N-SH	brain:	n/a	chr3:49211019-49211034 chr3:49211021-49211036
2	POLR2A	chr3:49208217-49210067	K562	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr3:49064349..49066955-chr3:49207317..49210098,3	MCF-7	breast:
2	chr3:49208330..49210147-chr3:49711158..49712878,2	K562	blood:
3	chr3:49059138..49060690-chr3:49207989..49210294,2	K562	blood:
4	chr3:49207667..49210496-chr3:49210545..49213014,4	K562	blood:
5	chr3:49207629..49210061-chr3:49211282..49215140,3	MCF-7	breast:
6	chr3:49195402..49201533-chr3:49207296..49212401,9	MCF-7	breast:
7	chr3:49156732..49159393-chr3:49207552..49211410,3	K562	blood:

Variant related genes	Relation type
KLHDC8B	TF binding region
ENSG00000178057	Chromatin interaction
ENSG00000272434	Chromatin interaction
ENSG00000164062	Chromatin interaction
ENSG00000270441	Chromatin interaction
ENSG00000185909	Chromatin interaction
ENSG00000178149	Chromatin interaction
ENSG00000172037	Chromatin interaction
ENSG00000172046	Chromatin interaction
ENSG00000178035	Chromatin interaction

Extended variants
information (count: 7 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:4)

rs_ID	r²[population]
rs33942096	1.00[MKK][hapmap]
rs35202395	1.00[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs35867420	1.00[MKK][hapmap]
rs71324958	1.00[AMR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv876764	chr3:49040462-49245645	Active TSS Transcr. at gene 5' and 3' Weak transcription Flanking Active TSS Strong transcription Enhancers Genic enhancers Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	279 gene(s)	inside rSNPs	diseases
2	nsv834686	chr3:49106047-49270556	Weak transcription Active TSS Flanking Active TSS Strong transcription Enhancers Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	53 gene(s)	inside rSNPs	diseases
3	nsv1008750	chr3:49208815-49362401	Weak transcription Genic enhancers Strong transcription Active TSS Enhancers Transcr. at gene 5' and 3' Flanking Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA	22 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:115 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:49208200-49210000	Flanking Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
2	chr3:49208200-49210200	Flanking Active TSS	Primary hematopoietic stem cells	blood
3	chr3:49208200-49210400	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
4	chr3:49208200-49211200	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
5	chr3:49208200-49211400	Flanking Active TSS	Adipose Nuclei	Adipose
6	chr3:49208200-49212000	Flanking Active TSS	Brain Germinal Matrix	brain
7	chr3:49208400-49210000	Active TSS	HUES64 Cell Line	embryonic stem cell
8	chr3:49208400-49210000	Active TSS	Pancreatic Islets	Pancreatic Islet
9	chr3:49208400-49210000	Active TSS	Ovary	ovary
10	chr3:49208400-49210200	Flanking Active TSS	Primary hematopoietic stem cells short term culture	blood
11	chr3:49208400-49210200	Flanking Active TSS	Liver	Liver
12	chr3:49208400-49210200	Active TSS	Small Intestine	intestine
13	chr3:49208400-49210400	Active TSS	iPS-20b Cell Line	embryonic stem cell
14	chr3:49208400-49210600	Active TSS	Fetal Kidney	kidney
15	chr3:49208600-49210000	Active TSS	ES-I3 Cell Line	embryonic stem cell
16	chr3:49208600-49210000	Active TSS	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
17	chr3:49208600-49210000	Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
18	chr3:49208600-49210000	Active TSS	Rectal Smooth Muscle	rectum
19	chr3:49208600-49210000	Active TSS	Right Atrium	heart
20	chr3:49208600-49210000	Active TSS	Sigmoid Colon	Sigmoid Colon
21	chr3:49208600-49210400	Flanking Active TSS	Colonic Mucosa	Colon
22	chr3:49208600-49210400	Active TSS	Colon Smooth Muscle	Colon
23	chr3:49208800-49210000	Active TSS	Fetal Heart	heart
24	chr3:49208800-49210200	Active TSS	Rectal Mucosa Donor 29	rectum
25	chr3:49208800-49210400	Transcr. at gene 5' and 3'	Skeletal Muscle Male	skeletal muscle
26	chr3:49209000-49210200	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
27	chr3:49209200-49210000	Flanking Active TSS	Primary T helper naive cells fromperipheralblood	blood
28	chr3:49209200-49210000	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
29	chr3:49209200-49210000	Flanking Active TSS	Cortex derived primary cultured neurospheres	brain
30	chr3:49209200-49210000	Flanking Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
31	chr3:49209200-49210200	Flanking Active TSS	HUES6 Cell Line	embryonic stem cell
32	chr3:49209200-49210600	Flanking Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
33	chr3:49209200-49210600	Weak transcription	Hela-S3	cervix
34	chr3:49209200-49211800	Flanking Active TSS	H9 Derived Neuron Cultured Cells	ES cell derived
35	chr3:49209200-49212000	Flanking Active TSS	Fetal Brain Female	brain
36	chr3:49209200-49212400	Flanking Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
37	chr3:49209400-49210000	Flanking Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
38	chr3:49209400-49210000	Flanking Active TSS	Fetal Muscle Trunk	muscle
39	chr3:49209400-49210000	Flanking Active TSS	Pancreas	Pancrea
40	chr3:49209400-49210000	Active TSS	Thymus	Thymus
41	chr3:49209400-49210000	Flanking Active TSS	HUVEC	blood vessel
42	chr3:49209400-49210000	Flanking Active TSS	Osteobl	bone
43	chr3:49209400-49210200	Flanking Active TSS	IMR90 fetal lung fibroblasts Cell Line	lung
44	chr3:49209400-49210200	Enhancers	Primary T killer naive cells fromperipheralblood	blood
45	chr3:49209400-49210400	Enhancers	Primary T killer memory cells from peripheral blood	blood
46	chr3:49209400-49210400	Flanking Active TSS	Muscle Satellite Cultured Cells	--
47	chr3:49209400-49210400	Flanking Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
48	chr3:49209400-49211200	Flanking Active TSS	Skeletal Muscle Female	skeletal muscle
49	chr3:49209400-49211200	Flanking Active TSS	K562	blood
50	chr3:49209400-49211400	Flanking Active TSS	HepG2	liver

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