Variant report

Variant	rs2615799
Chromosome Location	chr1:226412230-226412231
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	POLR2A	chr1:226411665-226412293	K562	blood:	n/a	n/a

Variant related genes	Relation type
MIXL1	TF binding region

Extended variants
information (count: 38 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:33)

rs_ID	r²[population]
rs10127753	0.85[AMR][1000 genomes];0.89[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs10127776	0.95[CEU][hapmap];0.89[EUR][1000 genomes]
rs10127970	1.00[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.85[AMR][1000 genomes];0.89[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs10753416	1.00[CEU][hapmap];0.81[CHB][hapmap];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs10799341	0.93[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs10799343	0.85[EUR][1000 genomes]
rs10799344	1.00[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.87[AMR][1000 genomes];0.88[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs10799345	0.81[JPT][hapmap]
rs10799346	0.86[EUR][1000 genomes]
rs10799347	0.95[CEU][hapmap];0.94[CHB][hapmap];0.93[JPT][hapmap];1.00[YRI][hapmap];0.85[AMR][1000 genomes];0.89[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs10915962	0.92[EUR][1000 genomes]
rs10915964	0.85[AMR][1000 genomes];0.89[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs10915970	0.85[EUR][1000 genomes]
rs12022311	0.87[JPT][hapmap]
rs1219658	1.00[CEU][hapmap];0.89[CHB][hapmap];0.93[JPT][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1417766	0.82[AFR][1000 genomes];0.85[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs1813323	0.95[CEU][hapmap];0.82[EUR][1000 genomes]
rs2126573	0.87[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs2126577	0.80[AMR][1000 genomes];0.85[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2126578	0.82[AFR][1000 genomes];0.84[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs2169567	1.00[CEU][hapmap];0.89[CHB][hapmap];0.93[JPT][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2254723	1.00[CEU][hapmap];0.89[CHB][hapmap];0.81[JPT][hapmap];1.00[YRI][hapmap];0.80[AMR][1000 genomes];0.86[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2377026	0.95[CEU][hapmap];0.85[CHB][hapmap];0.88[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs2377028	1.00[CEU][hapmap];0.84[CHB][hapmap];0.93[JPT][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2377029	0.97[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2615803	1.00[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.80[AMR][1000 genomes];0.83[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2666429	0.95[CEU][hapmap];0.94[CHB][hapmap];0.90[YRI][hapmap];0.83[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs2889537	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.93[AFR][1000 genomes];0.94[AMR][1000 genomes];0.93[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2927338	0.94[AFR][1000 genomes];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4612598	0.81[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs6605032	1.00[CEU][hapmap];0.94[CHB][hapmap];0.93[JPT][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7552015	0.87[AMR][1000 genomes];0.89[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs9725097	0.83[EUR][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	nsv832759	chr1:226303760-226504170	Weak transcription Genic enhancers Enhancers Active TSS Bivalent Enhancer Flanking Active TSS Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	42 gene(s)	inside rSNPs	diseases
2	esv2829936	chr1:226375267-226488826	Enhancers Weak transcription Strong transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Flanking Active TSS Transcr. at gene 5' and 3' Active TSS Bivalent/Poised TSS Bivalent Enhancer Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	11 gene(s)	inside rSNPs	diseases
3	nsv517107	chr1:226375267-226508645	Transcr. at gene 5' and 3' Enhancers Active TSS Weak transcription Bivalent Enhancer Flanking Active TSS Strong transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	19 gene(s)	inside rSNPs	diseases
4	nsv873233	chr1:226385623-226508645	Weak transcription Flanking Active TSS Enhancers Active TSS Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	17 gene(s)	inside rSNPs	diseases
5	esv3425958	chr1:226410154-226412702	Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Flanking Active TSS Active TSS Weak transcription Enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs2615799	ACBD3	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:53 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:226410600-226412400	Bivalent/Poised TSS	ES-I3 Cell Line	embryonic stem cell
2	chr1:226410600-226412800	Active TSS	HUES6 Cell Line	embryonic stem cell
3	chr1:226410800-226412400	Bivalent/Poised TSS	HUES48 Cell Line	embryonic stem cell
4	chr1:226410800-226412400	Bivalent/Poised TSS	HUES64 Cell Line	embryonic stem cell
5	chr1:226410800-226412400	Bivalent/Poised TSS	iPS-20b Cell Line	embryonic stem cell
6	chr1:226410800-226412400	Bivalent/Poised TSS	Primary T cells from cord blood	blood
7	chr1:226410800-226412800	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
8	chr1:226411000-226412800	Active TSS	HepG2	liver
9	chr1:226411200-226413200	Active TSS	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
10	chr1:226411600-226412400	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
11	chr1:226411800-226416200	Weak transcription	Dnd41	blood
12	chr1:226412000-226412400	Bivalent Enhancer	Primary T helper cells fromperipheralblood	blood
13	chr1:226412000-226412400	Bivalent Enhancer	Primary Natural Killer cells fromperipheralblood	blood
14	chr1:226412000-226412400	Bivalent Enhancer	Primary T killer memory cells from peripheral blood	blood
15	chr1:226412000-226415800	Weak transcription	Right Atrium	heart
16	chr1:226412000-226416400	Weak transcription	K562	blood
17	chr1:226412000-226417400	Weak transcription	Left Ventricle	heart
18	chr1:226412000-226417800	Weak transcription	Breast Myoepithelial Primary Cells	Breast
19	chr1:226412000-226417800	Weak transcription	Right Ventricle	heart
20	chr1:226412000-226417800	Weak transcription	HSMM	muscle
21	chr1:226412000-226418200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
22	chr1:226412000-226424200	Weak transcription	Psoas Muscle	Psoas
23	chr1:226412000-226426200	Weak transcription	Lung	lung
24	chr1:226412000-226427600	Weak transcription	Spleen	Spleen
25	chr1:226412000-226428000	Weak transcription	Pancreas	Pancrea
26	chr1:226412000-226429400	Weak transcription	Gastric	stomach
27	chr1:226412000-226431200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
28	chr1:226412000-226449600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
29	chr1:226412000-226455400	Weak transcription	Ovary	ovary
30	chr1:226412000-226456200	Weak transcription	NH-A	brain
31	chr1:226412000-226460600	Weak transcription	Aorta	Aorta
32	chr1:226412200-226412400	Enhancers	Primary hematopoietic stem cells	blood
33	chr1:226412200-226412400	Bivalent Enhancer	Primary T helper cells PMA-I stimulated	--
34	chr1:226412200-226412400	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
35	chr1:226412200-226412800	Bivalent Enhancer	Primary B cells from peripheral blood	blood
36	chr1:226412200-226412800	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
37	chr1:226412200-226413600	Enhancers	Fetal Heart	heart
38	chr1:226412200-226414000	Weak transcription	GM12878-XiMat	blood
39	chr1:226412200-226417200	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
40	chr1:226412200-226417200	Weak transcription	Primary hematopoietic stem cells short term culture	blood
41	chr1:226412200-226417600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
42	chr1:226412200-226417800	Weak transcription	Duodenum Mucosa	Duodenum
43	chr1:226412200-226417800	Weak transcription	HUVEC	blood vessel
44	chr1:226412200-226424000	Weak transcription	NHEK	skin
45	chr1:226412200-226424400	Weak transcription	A549	lung
46	chr1:226412200-226424400	Weak transcription	HMEC	breast
47	chr1:226412200-226425800	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
48	chr1:226412200-226426000	Weak transcription	Brain Substantia Nigra	brain
49	chr1:226412200-226428000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
50	chr1:226412200-226437200	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin

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