Variant report

Variant	rs10799329
Chromosome Location	chr1:226114499-226114500
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	SPI1	chr1:226114328-226114770	GM12891	blood:	n/a	n/a
2	EP300	chr1:226114263-226114863	K562	blood:	n/a	chr1:226114594-226114608
3	TBL1XR1	chr1:226114425-226114698	K562	blood:	n/a	n/a
4	SPI1	chr1:226114343-226114865	HL-60	blood:	n/a	n/a
5	SPI1	chr1:226114450-226114743	K562	blood:	n/a	n/a
6	GATA3	chr1:226114142-226114666	SK-N-SH	brain:	n/a	n/a
7	TEAD4	chr1:226114192-226114967	K562	blood:	n/a	n/a
8	SPI1	chr1:226114263-226114871	HL-60	blood:	n/a	n/a
9	MYC	chr1:226114404-226114727	K562	blood:	n/a	n/a
10	GTF2F1	chr1:226114423-226114818	K562	blood:	n/a	n/a
11	CBX3	chr1:226114127-226115460	K562	blood:	n/a	chr1:226114399-226114410
12	SPI1	chr1:226114441-226114729	K562	blood:	n/a	n/a
13	JUND	chr1:226114187-226114546	K562	blood:	n/a	chr1:226114294-226114304 chr1:226114295-226114303
14	SPI1	chr1:226114443-226114665	GM12891	blood:	n/a	n/a
15	MAZ	chr1:226114330-226114969	K562	blood:	n/a	n/a
16	SPI1	chr1:226114483-226114733	GM12878	blood:	n/a	n/a
17	GATA3	chr1:226114157-226114547	SK-N-SH	brain:	n/a	n/a
18	YY1	chr1:226114225-226114665	K562	blood:	n/a	chr1:226114379-226114387 chr1:226114376-226114386 chr1:226114376-226114398
19	MAFK	chr1:226114187-226114843	K562	blood:	n/a	chr1:226114654-226114669
20	NR2F2	chr1:226114053-226117256	K562	blood:	n/a	n/a
21	TBP	chr1:226114402-226114955	K562	blood:	n/a	n/a
22	ELF1	chr1:226114393-226115063	K562	blood:	n/a	chr1:226114946-226114955 chr1:226114945-226114954

No.	Distal block	Cell Line	Cell type
1	chr1:226108702..226117785-chr1:226183554..226190529,14	K562	blood:
2	chr1:226110464..226115809-chr1:226185735..226190763,7	K562	blood:
3	chr1:226113187..226115490-chr1:226126660..226128244,2	K562	blood:
4	chr1:226067470..226074101-chr1:226108823..226116408,13	MCF-7	breast:
5	chr1:226085907..226088745-chr1:226113166..226115980,2	K562	blood:
6	chr1:226070971..226073106-chr1:226113461..226115401,2	MCF-7	breast:
7	chr1:226112902..226114539-chr1:226249903..226252029,2	K562	blood:

Variant related genes	Relation type
PYCR2	TF binding region
ENSG00000255835	TF binding region
ENSG00000196187	Chromatin interaction
ENSG00000143751	Chromatin interaction
ENSG00000163041	Chromatin interaction
ENSG00000143768	Chromatin interaction

Extended variants
information (count: 12 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:3)

rs_ID	r²[population]
rs10915899	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs12746865	0.87[AFR][1000 genomes];0.92[ASN][1000 genomes]
rs360073	0.81[JPT][hapmap]

Variant overlapped rSNPs/rCNVs (count:9 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv1834948	chr1:225874059-226214882	Weak transcription Enhancers Strong transcription Flanking Active TSS Active TSS ZNF genes & repeats Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	60 gene(s)	inside rSNPs	diseases
2	nsv524126	chr1:225973777-226210653	Flanking Active TSS Weak transcription Flanking Bivalent TSS/Enh Active TSS Genic enhancers Strong transcription Enhancers ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	43 gene(s)	inside rSNPs	diseases
3	nsv873231	chr1:226019653-226134471	Enhancers Transcr. at gene 5' and 3' Strong transcription Weak transcription Genic enhancers Flanking Active TSS Active TSS Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	30 gene(s)	inside rSNPs	diseases
4	esv2762223	chr1:226025175-226201716	Weak transcription Strong transcription Enhancers Flanking Active TSS Genic enhancers Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	39 gene(s)	inside rSNPs	diseases
5	esv3335650	chr1:226074720-226125458	Bivalent Enhancer Flanking Active TSS Active TSS Enhancers Genic enhancers Weak transcription Strong transcription Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	19 gene(s)	inside rSNPs	diseases
6	esv3369235	chr1:226075748-226127738	Genic enhancers Weak transcription Flanking Active TSS Active TSS Enhancers Strong transcription Transcr. at gene 5' and 3' 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	19 gene(s)	inside rSNPs	diseases
7	nsv468216	chr1:226078915-226135132	Enhancers Genic enhancers Weak transcription Flanking Active TSS Active TSS Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	19 gene(s)	inside rSNPs	diseases
8	nsv549267	chr1:226078915-226135132	Genic enhancers Flanking Active TSS Transcr. at gene 5' and 3' Weak transcription Active TSS Enhancers Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	19 gene(s)	inside rSNPs	diseases
9	nsv535314	chr1:226087226-226128261	Enhancers Weak transcription Active TSS Transcr. at gene 5' and 3' Genic enhancers Flanking Active TSS Strong transcription ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	19 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs10799329	PSEN2	cis	lymphoblastoid	seeQTL
rs10799329	TMEM63A	cis	parietal	SCAN

Chromatin state (count:42 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:226112000-226114600	Weak transcription	Spleen	Spleen
2	chr1:226112000-226115800	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
3	chr1:226112600-226117400	Enhancers	Primary T cells from cord blood	blood
4	chr1:226112600-226125200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
5	chr1:226112600-226126800	Weak transcription	HUES48 Cell Line	embryonic stem cell
6	chr1:226112600-226126800	Weak transcription	HUES64 Cell Line	embryonic stem cell
7	chr1:226112800-226115800	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
8	chr1:226112800-226120800	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
9	chr1:226112800-226126800	Weak transcription	Right Atrium	heart
10	chr1:226113000-226116200	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
11	chr1:226113000-226116400	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
12	chr1:226113000-226124000	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
13	chr1:226113000-226124400	Weak transcription	H9 Cell Line	embryonic stem cell
14	chr1:226113200-226116000	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
15	chr1:226113200-226116200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
16	chr1:226113400-226115000	Enhancers	Primary neutrophils fromperipheralblood	blood
17	chr1:226113800-226115800	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
18	chr1:226113800-226118200	Enhancers	Primary T cells fromperipheralblood	blood
19	chr1:226114000-226114800	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
20	chr1:226114000-226114800	Enhancers	Muscle Satellite Cultured Cells	--
21	chr1:226114000-226114800	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
22	chr1:226114000-226115200	Enhancers	Primary T killer naive cells fromperipheralblood	blood
23	chr1:226114000-226116200	Enhancers	Primary hematopoietic stem cells	blood
24	chr1:226114000-226116800	Enhancers	Primary T helper naive cells fromperipheralblood	blood
25	chr1:226114200-226114600	Enhancers	Osteobl	bone
26	chr1:226114200-226115200	Enhancers	Primary T helper naive cells from peripheral blood	blood
27	chr1:226114200-226115200	Enhancers	Primary T helper cells PMA-I stimulated	--
28	chr1:226114200-226115200	Enhancers	Primary T helper cells fromperipheralblood	blood
29	chr1:226114200-226115200	Enhancers	Primary T killer memory cells from peripheral blood	blood
30	chr1:226114200-226117200	Enhancers	Fetal Thymus	thymus
31	chr1:226114200-226117400	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
32	chr1:226114400-226114600	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
33	chr1:226114400-226114600	Enhancers	iPS-18 Cell Line	embryonic stem cell
34	chr1:226114400-226114600	Flanking Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
35	chr1:226114400-226114600	Enhancers	HUVEC	blood vessel
36	chr1:226114400-226114800	Enhancers	ES-I3 Cell Line	embryonic stem cell
37	chr1:226114400-226114800	Enhancers	HUES6 Cell Line	embryonic stem cell
38	chr1:226114400-226114800	Flanking Active TSS	Primary hematopoietic stem cells short term culture	blood
39	chr1:226114400-226114800	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
40	chr1:226114400-226114800	Enhancers	Primary mononuclear cells fromperipheralblood	Blood
41	chr1:226114400-226115000	Enhancers	Esophagus	oesophagus
42	chr1:226114400-226115000	Flanking Active TSS	K562	blood

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