Variant report

Variant	rs10079000
Chromosome Location	chr5:114940200-114940201
allele	A/C
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	POLR2A	chr5:114940121-114940765	GM12892	blood:	n/a	n/a
2	POLR2A	chr5:114935210-114941425	K562	blood:	n/a	n/a
3	POLR2A	chr5:114940019-114940349	HepG2	liver:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr5:114936292..114939674-chr5:114939747..114944089,6	K562	blood:

Variant related genes	Relation type
TICAM2	TF binding region
ENSG00000249249	Chromatin interaction
ENSG00000243414	Chromatin interaction

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

rSNPs within LD-proxies of this variant (count:28)

rs_ID	r²[population]
rs10038493	0.82[CEU][hapmap];0.94[CHB][hapmap];0.94[JPT][hapmap];0.82[ASN][1000 genomes]
rs10043094	1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];0.90[GIH][hapmap];1.00[JPT][hapmap];0.93[TSI][hapmap];0.99[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs10053572	0.88[CHB][hapmap];0.95[JPT][hapmap]
rs10055339	1.00[CEU][hapmap];0.97[GIH][hapmap];0.85[LWK][hapmap];0.86[MKK][hapmap];0.97[TSI][hapmap];0.87[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs10069695	0.98[EUR][1000 genomes]
rs10073505	0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs10075869	0.80[AFR][1000 genomes];0.87[EUR][1000 genomes]
rs10077239	0.84[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs1015812	0.84[ASN][1000 genomes]
rs13153908	0.90[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs13184723	0.84[ASN][1000 genomes]
rs2032842	0.83[CHB][hapmap]
rs2052834	1.00[CEU][hapmap];0.97[GIH][hapmap];0.95[TSI][hapmap];0.98[EUR][1000 genomes]
rs2546484	0.88[CHB][hapmap];0.95[JPT][hapmap]
rs256938	0.88[CHB][hapmap];0.84[CHD][hapmap];0.95[JPT][hapmap]
rs256963	0.81[AFR][1000 genomes];0.84[AMR][1000 genomes]
rs256965	0.87[AMR][1000 genomes];0.81[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs256977	0.82[ASN][1000 genomes]
rs256989	0.87[AFR][1000 genomes];0.84[AMR][1000 genomes];0.84[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs256995	0.87[AFR][1000 genomes];0.87[AMR][1000 genomes];0.84[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs372702	0.88[CHB][hapmap];0.95[JPT][hapmap]
rs56104517	0.83[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs6860557	0.88[CHB][hapmap];0.94[JPT][hapmap]
rs6893854	0.88[CHB][hapmap];0.88[JPT][hapmap]
rs6894123	0.88[CHB][hapmap];0.89[JPT][hapmap]
rs746566	0.86[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[CHD][hapmap];0.82[GIH][hapmap];1.00[JPT][hapmap];0.96[MKK][hapmap];0.95[TSI][hapmap];0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs766454	0.84[ASN][1000 genomes]
rs9326970	0.91[AMR][1000 genomes];0.98[EUR][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	nsv916273	chr5:114656592-115089901	Enhancers Active TSS Weak transcription Flanking Active TSS Strong transcription Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	28 gene(s)	inside rSNPs	diseases
2	nsv868915	chr5:114723371-115252527	Enhancers Weak transcription Strong transcription Active TSS Flanking Active TSS Transcr. at gene 5' and 3' Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	41 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:121 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:114937800-114951600	Weak transcription	Primary T killer memory cells from peripheral blood	blood
2	chr5:114938200-114944400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
3	chr5:114938200-114957200	Weak transcription	Small Intestine	intestine
4	chr5:114938200-114958200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
5	chr5:114938200-114960200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
6	chr5:114938400-114944000	Strong transcription	Dnd41	blood
7	chr5:114938400-114951400	Weak transcription	HepG2	liver
8	chr5:114938600-114940200	Weak transcription	Liver	Liver
9	chr5:114938600-114940400	Enhancers	Primary monocytes fromperipheralblood	blood
10	chr5:114938600-114940600	Weak transcription	HMEC	breast
11	chr5:114938600-114943200	Weak transcription	Placenta	Placenta
12	chr5:114938600-114943600	Weak transcription	Left Ventricle	heart
13	chr5:114938600-114943800	Weak transcription	iPS-20b Cell Line	embryonic stem cell
14	chr5:114938600-114944000	Weak transcription	HUES64 Cell Line	embryonic stem cell
15	chr5:114938600-114944400	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
16	chr5:114938600-114948400	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
17	chr5:114938600-114949600	Weak transcription	H1 Cell Line	embryonic stem cell
18	chr5:114938600-114949600	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
19	chr5:114938600-114949800	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
20	chr5:114938600-114950000	Weak transcription	Fetal Intestine Large	intestine
21	chr5:114938600-114950000	Weak transcription	HSMMtube	muscle
22	chr5:114938600-114950200	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
23	chr5:114938600-114951600	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
24	chr5:114938600-114951800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
25	chr5:114938600-114951800	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
26	chr5:114938600-114951800	Weak transcription	Esophagus	oesophagus
27	chr5:114938600-114958000	Weak transcription	Ovary	ovary
28	chr5:114938600-114960000	Weak transcription	H9 Cell Line	embryonic stem cell
29	chr5:114938800-114940200	Weak transcription	A549	lung
30	chr5:114938800-114940400	Enhancers	Primary B cells from peripheral blood	blood
31	chr5:114938800-114940600	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
32	chr5:114938800-114940800	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
33	chr5:114938800-114943600	Weak transcription	Psoas Muscle	Psoas
34	chr5:114938800-114943800	Weak transcription	HUES48 Cell Line	embryonic stem cell
35	chr5:114938800-114945600	Weak transcription	Primary T cells fromperipheralblood	blood
36	chr5:114938800-114946000	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
37	chr5:114938800-114947600	Weak transcription	Primary T helper cells fromperipheralblood	blood
38	chr5:114938800-114948400	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
39	chr5:114938800-114948400	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
40	chr5:114938800-114949600	Weak transcription	Primary T helper cells PMA-I stimulated	--
41	chr5:114938800-114949600	Weak transcription	Hela-S3	cervix
42	chr5:114938800-114950000	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
43	chr5:114938800-114950200	Weak transcription	Primary T cells from cord blood	blood
44	chr5:114938800-114951600	Weak transcription	K562	blood
45	chr5:114938800-114951800	Weak transcription	Fetal Muscle Trunk	muscle
46	chr5:114938800-114951800	Weak transcription	Thymus	Thymus
47	chr5:114938800-114951800	Weak transcription	NHLF	lung
48	chr5:114938800-114952000	Weak transcription	Cortex derived primary cultured neurospheres	brain
49	chr5:114938800-114953800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
50	chr5:114938800-114954000	Weak transcription	Fetal Brain Female	brain

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