Variant report

Variant	rs7536099
Chromosome Location	chr1:70821757-70821758
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

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

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

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	RCOR1	chr1:70821596-70821955	K562	blood:	n/a	n/a
2	CEBPB	chr1:70821728-70822035	IMR90	lung:	n/a	n/a
3	SPI1	chr1:70821582-70822031	HL-60	blood:	n/a	chr1:70821769-70821776
4	TBP	chr1:70821489-70821818	K562	blood:	n/a	n/a
5	CEBPB	chr1:70821687-70822129	K562	blood:	n/a	n/a
6	CEBPB	chr1:70821676-70822117	HepG2	liver:	n/a	n/a

No data

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

No.	Distal block	Cell Line	Cell type
1	chr1:70686799..70688622-chr1:70819236..70822047,3	K562	blood:
2	chr1:70670191..70673421-chr1:70819814..70822311,3	K562	blood:
3	chr1:70819013..70822302-chr1:70824014..70829303,9	MCF-7	breast:
4	chr1:70685799..70687948-chr1:70819964..70821804,2	MCF-7	breast:
5	chr1:70814842..70821925-chr1:70874223..70879265,8	K562	blood:
6	chr1:70818087..70822177-chr1:70874224..70879265,8	K562	blood:

No data

Variant related genes	Relation type
ANKRD13C	TF binding region
ENSG00000116754	Chromatin interaction
ENSG00000226088	Chromatin interaction
ENSG00000066557	Chromatin interaction
ENSG00000228988	Chromatin interaction
ENSG00000116761	Chromatin interaction

Extended variants
information (count: 7 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:2)

rs_ID	r²[population]
rs12140479	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];0.88[GIH][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs12732737	0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv999219	chr1:70730556-71014911	Enhancers Weak transcription Flanking Active TSS Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Active TSS Genic enhancers Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	49 gene(s)	inside rSNPs	diseases
2	nsv1012563	chr1:70753332-70832118	Weak transcription Flanking Active TSS Strong transcription Bivalent/Poised TSS Enhancers Active TSS Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	29 gene(s)	inside rSNPs	diseases
3	esv1801665	chr1:70755511-70832053	Active TSS Strong transcription Flanking Active TSS Weak transcription Enhancers Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	29 gene(s)	inside rSNPs	diseases
4	nsv830137	chr1:70765921-70958718	Active TSS Weak transcription Flanking Active TSS Enhancers Strong transcription ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	48 gene(s)	inside rSNPs	diseases
5	esv11736	chr1:70820591-70825114	Flanking Active TSS Active TSS Enhancers Weak transcription Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	27 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs7536099	HHLA3	cis	parietal	SCAN
rs7536099	HHLA3	Cis_1M	lymphoblastoid	RTeQTL
rs7536099	HHLA3	cis	brain	BrainEAC
rs7536099	HHLA3	cis	Esophagus Muscularis	GTEx

Chromatin state (count:60 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:70817600-70822000	Active TSS	ES-I3 Cell Line	embryonic stem cell
2	chr1:70818000-70821800	Active TSS	HUES6 Cell Line	embryonic stem cell
3	chr1:70821000-70822000	Enhancers	Primary T regulatory cells fromperipheralblood	blood
4	chr1:70821000-70822400	Enhancers	Primary monocytes fromperipheralblood	blood
5	chr1:70821000-70824000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
6	chr1:70821000-70827600	Weak transcription	HSMM	muscle
7	chr1:70821000-70835200	Weak transcription	Pancreas	Pancrea
8	chr1:70821000-70836400	Weak transcription	Left Ventricle	heart
9	chr1:70821000-70838400	Weak transcription	Lung	lung
10	chr1:70821200-70821800	Enhancers	Primary neutrophils fromperipheralblood	blood
11	chr1:70821200-70821800	Enhancers	Primary T cells fromperipheralblood	blood
12	chr1:70821200-70821800	Enhancers	Primary T helper naive cells from peripheral blood	blood
13	chr1:70821200-70822000	Enhancers	Primary T killer naive cells fromperipheralblood	blood
14	chr1:70821200-70822000	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
15	chr1:70821200-70822000	Enhancers	Brain Substantia Nigra	brain
16	chr1:70821200-70822000	Enhancers	Fetal Heart	heart
17	chr1:70821200-70822400	Enhancers	Monocytes-CD14+_RO01746	blood
18	chr1:70821200-70823800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
19	chr1:70821200-70824200	Weak transcription	HMEC	breast
20	chr1:70821200-70824200	Weak transcription	NHLF	lung
21	chr1:70821200-70824400	Weak transcription	NHEK	skin
22	chr1:70821200-70824600	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
23	chr1:70821200-70827600	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
24	chr1:70821200-70828000	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
25	chr1:70821200-70829600	Weak transcription	Fetal Intestine Small	intestine
26	chr1:70821200-70832000	Weak transcription	H1 Cell Line	embryonic stem cell
27	chr1:70821200-70833600	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
28	chr1:70821200-70835200	Weak transcription	iPS-20b Cell Line	embryonic stem cell
29	chr1:70821200-70836800	Weak transcription	Fetal Stomach	stomach
30	chr1:70821200-70841400	Weak transcription	Brain Cingulate Gyrus	brain
31	chr1:70821400-70821800	Weak transcription	HUES48 Cell Line	embryonic stem cell
32	chr1:70821400-70821800	Active TSS	K562	blood
33	chr1:70821400-70822000	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
34	chr1:70821400-70822000	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
35	chr1:70821400-70822000	Enhancers	Brain Anterior Caudate	brain
36	chr1:70821400-70822000	Enhancers	Brain Inferior Temporal Lobe	brain
37	chr1:70821400-70822000	Enhancers	Dnd41	blood
38	chr1:70821400-70822000	Enhancers	GM12878-XiMat	blood
39	chr1:70821400-70822000	Enhancers	Hela-S3	cervix
40	chr1:70821400-70822200	Enhancers	HepG2	liver
41	chr1:70821400-70822400	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
42	chr1:70821400-70822400	Weak transcription	NH-A	brain
43	chr1:70821400-70823000	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
44	chr1:70821400-70824600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
45	chr1:70821400-70827000	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
46	chr1:70821400-70827400	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
47	chr1:70821400-70827400	Weak transcription	Cortex derived primary cultured neurospheres	brain
48	chr1:70821400-70827600	Weak transcription	H9 Cell Line	embryonic stem cell
49	chr1:70821400-70827600	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
50	chr1:70821400-70827600	Weak transcription	Fetal Lung	lung

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