Variant report

Variant	rs2303554
Chromosome Location	chr2:182792984-182792985
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr2:182792823..182795162-chr2:182816712..182819215,2	MCF-7	breast:
2	chr2:182789974..182793109-chr2:182797646..182800395,3	K562	blood:
3	chr2:182792850..182795214-chr2:182884772..182886542,2	MCF-7	breast:
4	chr2:182792682..182794662-chr2:182800438..182802896,2	MCF-7	breast:
5	chr2:182791877..182794695-chr2:182814477..182817975,3	MCF-7	breast:
6	chr2:182780096..182784341-chr2:182791692..182796761,4	MCF-7	breast:
7	chr2:182792632..182794412-chr2:182945840..182948376,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000138434	Chromatin interaction
ENSG00000150722	Chromatin interaction

Extended variants
information (count: 70 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:66)

rs_ID	r²[population]
rs10165936	1.00[CEU][hapmap]
rs10166975	0.80[EUR][1000 genomes]
rs10173114	1.00[CEU][hapmap]
rs10176061	1.00[CEU][hapmap]
rs10176613	1.00[CEU][hapmap]
rs10176757	1.00[CEU][hapmap]
rs10179363	1.00[CEU][hapmap]
rs10179547	1.00[CEU][hapmap]
rs10189187	0.84[EUR][1000 genomes]
rs10191082	0.80[EUR][1000 genomes]
rs10197254	0.87[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs10199645	1.00[CEU][hapmap]
rs10200243	1.00[CEU][hapmap]
rs10201303	1.00[CEU][hapmap];0.84[EUR][1000 genomes]
rs10210215	1.00[CEU][hapmap]
rs10221891	1.00[CEU][hapmap]
rs13389121	0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13401364	0.84[EUR][1000 genomes]
rs13404156	1.00[CEU][hapmap]
rs13425734	1.00[CEU][hapmap]
rs1528024	1.00[CEU][hapmap];0.80[EUR][1000 genomes]
rs1528025	1.00[CEU][hapmap];0.80[EUR][1000 genomes]
rs1528026	0.80[EUR][1000 genomes]
rs1528027	1.00[CEU][hapmap];0.80[EUR][1000 genomes]
rs16867498	1.00[CEU][hapmap];0.84[EUR][1000 genomes]
rs16867509	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs17456384	0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1881158	1.00[CEU][hapmap]
rs1881159	1.00[CEU][hapmap]
rs2059702	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2288330	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2368224	1.00[CEU][hapmap]
rs2368235	0.84[EUR][1000 genomes]
rs3731693	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[AFR][1000 genomes];0.81[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs3815877	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs3815878	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4597477	0.80[EUR][1000 genomes]
rs55732891	0.81[AFR][1000 genomes];0.81[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs55758877	0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6433943	1.00[CEU][hapmap]
rs6707164	1.00[CEU][hapmap];0.80[EUR][1000 genomes]
rs6707654	0.80[EUR][1000 genomes]
rs6720109	1.00[CEU][hapmap];0.80[EUR][1000 genomes]
rs6720702	1.00[CEU][hapmap]
rs6723011	0.80[EUR][1000 genomes]
rs6735322	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6736341	0.80[EUR][1000 genomes]
rs6736766	1.00[CEU][hapmap];0.80[EUR][1000 genomes]
rs6739707	0.80[EUR][1000 genomes]
rs6744556	1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6748354	1.00[CEU][hapmap]
rs6751464	0.80[EUR][1000 genomes]
rs6751685	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[AFR][1000 genomes];0.87[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6754192	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6754819	0.80[EUR][1000 genomes]
rs6755017	1.00[CEU][hapmap];1.00[EUR][1000 genomes]
rs73032623	0.84[EUR][1000 genomes]
rs7557969	1.00[CEU][hapmap]
rs7562680	1.00[CEU][hapmap]
rs7563333	0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7580410	1.00[CEU][hapmap]
rs7603721	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7606321	0.92[AFR][1000 genomes];0.87[AMR][1000 genomes];0.84[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7608942	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.80[YRI][hapmap];0.81[AMR][1000 genomes];0.84[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs9807949	1.00[CEU][hapmap]
rs9808112	1.00[CEU][hapmap]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1005870	chr2:181968637-182921439	Enhancers Strong transcription Weak transcription Bivalent/Poised TSS Flanking Active TSS Flanking Bivalent TSS/Enh Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	39 gene(s)	inside rSNPs	diseases
2	nsv536063	chr2:181968637-182921439	Enhancers Active TSS Weak transcription Strong transcription Bivalent/Poised TSS Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	39 gene(s)	inside rSNPs	diseases
3	nsv834478	chr2:182654811-182843201	Enhancers Weak transcription Active TSS Strong transcription Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	19 gene(s)	inside rSNPs	diseases
4	nsv834479	chr2:182738483-182905444	Enhancers Strong transcription Transcr. at gene 5' and 3' Weak transcription Active TSS Flanking Active TSS Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	19 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs2303554	LOC647288///LOC730587	trans	lymphoblastoid	RTeQTL

Chromatin state (count:97 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:182760000-182794800	Strong transcription	Fetal Thymus	thymus
2	chr2:182761400-182795800	Strong transcription	Placenta	Placenta
3	chr2:182769400-182795600	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
4	chr2:182769600-182795800	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
5	chr2:182769600-182795800	Strong transcription	Dnd41	blood
6	chr2:182774600-182795200	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
7	chr2:182775800-182795800	Strong transcription	Primary monocytes fromperipheralblood	blood
8	chr2:182775800-182795800	Strong transcription	Monocytes-CD14+_RO01746	blood
9	chr2:182776000-182795800	Strong transcription	Hela-S3	cervix
10	chr2:182776200-182793200	Strong transcription	Primary hematopoietic stem cells short term culture	blood
11	chr2:182779600-182796000	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
12	chr2:182779800-182795200	Weak transcription	Primary T killer memory cells from peripheral blood	blood
13	chr2:182781000-182796000	Weak transcription	Psoas Muscle	Psoas
14	chr2:182781000-182796400	Weak transcription	Esophagus	oesophagus
15	chr2:182781200-182795400	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
16	chr2:182781400-182793200	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
17	chr2:182781400-182794200	Weak transcription	iPS-18 Cell Line	embryonic stem cell
18	chr2:182781600-182793200	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
19	chr2:182781800-182796000	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
20	chr2:182781800-182797000	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
21	chr2:182782400-182795600	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
22	chr2:182782600-182795800	Weak transcription	Fetal Brain Female	brain
23	chr2:182782600-182812800	Weak transcription	Aorta	Aorta
24	chr2:182784200-182796000	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
25	chr2:182784400-182795000	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
26	chr2:182785200-182794200	Weak transcription	Brain Cingulate Gyrus	brain
27	chr2:182787200-182796200	Weak transcription	iPS-20b Cell Line	embryonic stem cell
28	chr2:182787200-182796400	Weak transcription	Colonic Mucosa	Colon
29	chr2:182787400-182796400	Weak transcription	HUES6 Cell Line	embryonic stem cell
30	chr2:182787600-182796800	Weak transcription	Primary T cells fromperipheralblood	blood
31	chr2:182787600-182806200	Weak transcription	Placenta Amnion	Placenta Amnion
32	chr2:182788000-182794000	Weak transcription	Primary T helper cells PMA-I stimulated	--
33	chr2:182788000-182796400	Weak transcription	Stomach Smooth Muscle	stomach
34	chr2:182788200-182793600	Weak transcription	Skeletal Muscle Male	skeletal muscle
35	chr2:182788200-182795800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
36	chr2:182788200-182797800	Weak transcription	HUES64 Cell Line	embryonic stem cell
37	chr2:182789400-182793200	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
38	chr2:182789400-182795800	Strong transcription	Liver	Liver
39	chr2:182789600-182795800	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
40	chr2:182790000-182796000	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
41	chr2:182790000-182799400	Weak transcription	Brain Anterior Caudate	brain
42	chr2:182790200-182795800	Strong transcription	Cortex derived primary cultured neurospheres	brain
43	chr2:182790400-182799000	Weak transcription	Colon Smooth Muscle	Colon
44	chr2:182790600-182793600	Weak transcription	Gastric	stomach
45	chr2:182790600-182794000	Weak transcription	NHDF-Ad	bronchial
46	chr2:182790600-182794200	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
47	chr2:182790600-182794200	Weak transcription	Brain Hippocampus Middle	brain
48	chr2:182790600-182795800	Weak transcription	Fetal Heart	heart
49	chr2:182790600-182796000	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
50	chr2:182790600-182796600	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--

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