Variant report

Variant	rs2289189
Chromosome Location	chr1:220331205-220331206
allele	C/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	chr1:220331096-220331367	H1-neurons	neurons:	n/a	n/a
2	POLR2A	chr1:220331102-220331345	H1-neurons	neurons:	n/a	n/a
3	REST	chr1:220330938-220331575	H1-neurons	neurons:	n/a	n/a
4	REST	chr1:220330814-220331655	H1-neurons	neurons:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr1:220326376..220329361-chr1:220330815..220332940,2	MCF-7	breast:
2	chr1:220322576..220325762-chr1:220328423..220332016,4	K562	blood:
3	chr1:220327833..220330003-chr1:220331080..220333776,2	MCF-7	breast:
4	chr1:220324262..220326114-chr1:220329198..220331900,2	K562	blood:

Variant related genes	Relation type
RAB3GAP2	TF binding region
ENSG00000118873	Chromatin interaction

Extended variants
information (count: 11 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:10)

rs_ID	r²[population]
rs1059140	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AFR][1000 genomes];0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11547779	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12032345	1.00[AFR][1000 genomes];0.92[AMR][1000 genomes];0.89[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2289191	0.83[AMR][1000 genomes]
rs2292418	1.00[AFR][1000 genomes];0.91[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs2577165	1.00[JPT][hapmap]
rs3767655	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs41274790	0.80[AMR][1000 genomes]
rs41274794	0.84[AMR][1000 genomes]
rs41303055	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]

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

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv427930	chr1:220120379-220333434	Weak transcription Flanking Active TSS Enhancers Strong transcription Active TSS Genic enhancers Bivalent Enhancer 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 miRNA target site	744 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs2289189	RAB3GAP2	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:126 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:220298800-220334600	Strong transcription	Fetal Thymus	thymus
2	chr1:220303800-220331600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
3	chr1:220304800-220335600	Strong transcription	Placenta	Placenta
4	chr1:220305400-220331800	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
5	chr1:220305400-220347000	Strong transcription	Dnd41	blood
6	chr1:220305400-220376600	Strong transcription	Monocytes-CD14+_RO01746	blood
7	chr1:220305600-220347600	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
8	chr1:220305800-220347000	Strong transcription	Primary monocytes fromperipheralblood	blood
9	chr1:220306600-220336600	Strong transcription	HUES6 Cell Line	embryonic stem cell
10	chr1:220306600-220346600	Strong transcription	HUES48 Cell Line	embryonic stem cell
11	chr1:220306600-220348200	Strong transcription	HUES64 Cell Line	embryonic stem cell
12	chr1:220308400-220339600	Weak transcription	Psoas Muscle	Psoas
13	chr1:220311200-220343400	Weak transcription	Pancreatic Islets	Pancreatic Islet
14	chr1:220311600-220335000	Strong transcription	Primary hematopoietic stem cells short term culture	blood
15	chr1:220312200-220347400	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
16	chr1:220318600-220335400	Strong transcription	iPS-20b Cell Line	embryonic stem cell
17	chr1:220319000-220341400	Strong transcription	Primary neutrophils fromperipheralblood	blood
18	chr1:220320400-220341800	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
19	chr1:220320600-220336600	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
20	chr1:220320800-220331600	Strong transcription	NHLF	lung
21	chr1:220322800-220334600	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
22	chr1:220323000-220335000	Strong transcription	Fetal Muscle Trunk	muscle
23	chr1:220323000-220341000	Strong transcription	HSMM	muscle
24	chr1:220323200-220334800	Strong transcription	NH-A	brain
25	chr1:220323200-220335000	Strong transcription	Skeletal Muscle Female	skeletal muscle
26	chr1:220323400-220331800	Strong transcription	Primary T cells from cord blood	blood
27	chr1:220323400-220333800	Strong transcription	Fetal Stomach	stomach
28	chr1:220323800-220331400	Strong transcription	A549	lung
29	chr1:220323800-220332400	Strong transcription	H1 Cell Line	embryonic stem cell
30	chr1:220323800-220333200	Strong transcription	Primary T cells fromperipheralblood	blood
31	chr1:220323800-220336600	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
32	chr1:220323800-220348000	Strong transcription	Primary B cells from cord blood	blood
33	chr1:220324000-220331400	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
34	chr1:220324000-220331400	Strong transcription	Fetal Intestine Large	intestine
35	chr1:220324000-220331600	Strong transcription	Thymus	Thymus
36	chr1:220324000-220331800	Strong transcription	Rectal Mucosa Donor 29	rectum
37	chr1:220324000-220334800	Strong transcription	Fetal Muscle Leg	muscle
38	chr1:220324000-220335800	Strong transcription	Primary B cells from peripheral blood	blood
39	chr1:220324000-220347000	Strong transcription	HMEC	breast
40	chr1:220324200-220331400	Strong transcription	Rectal Mucosa Donor 31	rectum
41	chr1:220324200-220331400	Strong transcription	GM12878-XiMat	blood
42	chr1:220324400-220332800	Strong transcription	iPS-18 Cell Line	embryonic stem cell
43	chr1:220324600-220331400	Strong transcription	Skeletal Muscle Male	skeletal muscle
44	chr1:220324600-220332400	Strong transcription	Fetal Brain Female	brain
45	chr1:220324600-220332600	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
46	chr1:220324600-220335200	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
47	chr1:220324800-220331400	Strong transcription	Sigmoid Colon	Sigmoid Colon
48	chr1:220324800-220331800	Strong transcription	Brain Inferior Temporal Lobe	brain
49	chr1:220325000-220331400	Weak transcription	Stomach Mucosa	stomach
50	chr1:220325000-220398400	Weak transcription	ES-WA7 Cell Line	embryonic stem cell

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