Variant report

Variant	rs2273299
Chromosome Location	chr1:10218439-10218440
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 21 )
Associated
traits (count: 7 )

rSNPs within LD-proxies of this variant (count:18)

rs_ID	r²[population]
rs1074461	0.92[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs11121525	0.81[EUR][1000 genomes]
rs11806008	0.86[EUR][1000 genomes]
rs12074936	0.90[CEU][hapmap];0.92[TSI][hapmap];0.90[EUR][1000 genomes]
rs12092513	0.84[CHD][hapmap]
rs17034545	0.84[CHD][hapmap]
rs17034558	0.84[CHD][hapmap]
rs17034560	0.84[CHD][hapmap]
rs2273298	0.94[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];0.93[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35316894	0.98[AFR][1000 genomes];0.98[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs3762290	0.83[JPT][hapmap];0.80[AMR][1000 genomes]
rs4543799	0.94[ASW][hapmap];0.83[JPT][hapmap];0.86[LWK][hapmap];0.85[MEX][hapmap];0.94[MKK][hapmap];0.93[YRI][hapmap];0.89[AFR][1000 genomes];0.85[AMR][1000 genomes]
rs61782924	0.84[AMR][1000 genomes]
rs6659436	0.86[CHD][hapmap]
rs6667049	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.98[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6671289	0.81[CEU][hapmap];0.83[JPT][hapmap];0.82[AMR][1000 genomes]
rs6692491	0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9783053	0.89[CEU][hapmap];0.92[TSI][hapmap];0.88[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv3417409	chr1:9683992-10241703	Flanking Active TSS Enhancers Bivalent/Poised TSS Weak transcription Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Strong transcription Genic enhancers Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	52 gene(s)	inside rSNPs	diseases
2	nsv527217	chr1:10093457-10257167	Weak transcription Enhancers Flanking Active TSS Strong transcription Genic enhancers ZNF genes & repeats Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
3	nsv522629	chr1:10125765-10239197	Weak transcription Strong transcription Flanking Active TSS ZNF genes & repeats Enhancers Genic enhancers Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	8 gene(s)	inside rSNPs	diseases

mRNA abundance (count:7)

SNP	Gene	Cis/trans	Tissue	Source
rs2273299	LZIC	cis	lymphoblastoid	seeQTL
rs2273299	UBE4B	cis	parietal	SCAN
rs2273299	NOL9	cis	parietal	SCAN
rs2273299	KIF1B	cis	parietal	SCAN
rs2273299	LZIC	cis	Lymphoblastoid	GTEx
rs2273299	UBE4B	cis	cerebellum	SCAN
rs2273299	RERE	cis	parietal	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:10163400-10219000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
2	chr1:10164000-10227400	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
3	chr1:10182200-10231200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
4	chr1:10182400-10229400	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
5	chr1:10182800-10221000	Weak transcription	Fetal Brain Male	brain
6	chr1:10182800-10231400	Weak transcription	Pancreatic Islets	Pancreatic Islet
7	chr1:10184000-10235000	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
8	chr1:10191200-10225000	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
9	chr1:10191200-10239600	Weak transcription	Primary T helper naive cells from peripheral blood	blood
10	chr1:10193200-10231200	Weak transcription	Small Intestine	intestine
11	chr1:10194200-10232200	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
12	chr1:10195400-10219400	Weak transcription	Colonic Mucosa	Colon
13	chr1:10195600-10231200	Weak transcription	HUVEC	blood vessel
14	chr1:10197600-10225000	Weak transcription	NHEK	skin
15	chr1:10197800-10219800	Weak transcription	H9 Cell Line	embryonic stem cell
16	chr1:10197800-10220000	Weak transcription	Stomach Mucosa	stomach
17	chr1:10197800-10220000	Weak transcription	NH-A	brain
18	chr1:10197800-10224400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
19	chr1:10197800-10224800	Weak transcription	Esophagus	oesophagus
20	chr1:10201600-10231200	Weak transcription	HMEC	breast
21	chr1:10203400-10228000	Weak transcription	GM12878-XiMat	blood
22	chr1:10204200-10224800	Weak transcription	Primary T killer memory cells from peripheral blood	blood
23	chr1:10205600-10228000	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
24	chr1:10207200-10219800	Weak transcription	Pancreas	Pancrea
25	chr1:10207200-10224400	Weak transcription	Muscle Satellite Cultured Cells	--
26	chr1:10207400-10220800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
27	chr1:10207400-10224800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
28	chr1:10211200-10222000	Strong transcription	Breast Myoepithelial Primary Cells	Breast
29	chr1:10211200-10236400	Strong transcription	Fetal Stomach	stomach
30	chr1:10211800-10221000	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
31	chr1:10212000-10219800	Strong transcription	Fetal Intestine Small	intestine
32	chr1:10212000-10220800	Weak transcription	Gastric	stomach
33	chr1:10212000-10221200	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
34	chr1:10212000-10222600	Weak transcription	H1 Cell Line	embryonic stem cell
35	chr1:10212000-10224800	Weak transcription	iPS-15b Cell Line	embryonic stem cell
36	chr1:10212000-10224800	Weak transcription	Fetal Kidney	kidney
37	chr1:10212000-10225000	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
38	chr1:10212200-10220000	Weak transcription	Primary hematopoietic stem cells	blood
39	chr1:10212800-10221400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
40	chr1:10213000-10224400	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
41	chr1:10213200-10220000	Weak transcription	Dnd41	blood
42	chr1:10213200-10220000	Weak transcription	Hela-S3	cervix
43	chr1:10213200-10231000	Weak transcription	A549	lung
44	chr1:10213400-10220600	Weak transcription	Brain Substantia Nigra	brain
45	chr1:10213400-10222600	Weak transcription	Rectal Mucosa Donor 29	rectum
46	chr1:10213800-10236000	Strong transcription	Primary monocytes fromperipheralblood	blood
47	chr1:10214400-10219000	Strong transcription	HUES48 Cell Line	embryonic stem cell
48	chr1:10214600-10235600	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
49	chr1:10214600-10237000	Strong transcription	Monocytes-CD14+_RO01746	blood
50	chr1:10215000-10219000	Strong transcription	Primary T cells fromperipheralblood	blood

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links