Variant report

Variant	rs2272022
Chromosome Location	chr3:112063850-112063851
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 17 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:16)

rs_ID	r²[population]
rs10511311	0.87[ASW][hapmap];1.00[CEU][hapmap];0.91[CHB][hapmap];0.96[GIH][hapmap];0.81[JPT][hapmap];1.00[MEX][hapmap];0.87[MKK][hapmap];0.86[TSI][hapmap];0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs12106673	0.84[CEU][hapmap];0.81[MEX][hapmap]
rs12106967	0.84[CEU][hapmap]
rs12491166	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13072567	0.86[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs13084367	0.81[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs13090468	0.83[CEU][hapmap]
rs13093633	0.85[JPT][hapmap]
rs13098589	1.00[ASW][hapmap];1.00[CEU][hapmap];0.91[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.92[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];0.81[YRI][hapmap];0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1317243	0.81[CEU][hapmap]
rs1343852	1.00[CEU][hapmap];0.89[CHB][hapmap];1.00[JPT][hapmap];0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2276772	0.88[AMR][1000 genomes];0.94[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2399416	0.87[ASW][hapmap];1.00[CEU][hapmap];0.91[CHB][hapmap];1.00[GIH][hapmap];0.81[JPT][hapmap];1.00[MEX][hapmap];0.89[MKK][hapmap];0.93[TSI][hapmap];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs34345145	0.83[AFR][1000 genomes];0.99[EUR][1000 genomes]
rs4682399	0.80[CEU][hapmap];0.84[MEX][hapmap]
rs7647411	1.00[ASW][hapmap];1.00[CEU][hapmap];0.91[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.92[JPT][hapmap];0.92[LWK][hapmap];1.00[MEX][hapmap];0.98[MKK][hapmap];1.00[TSI][hapmap];0.81[YRI][hapmap];0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[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	nsv10307	chr3:111903974-112087686	Enhancers Active TSS Weak transcription Flanking Active TSS Strong transcription Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs2272022	CD200	cis	parietal	SCAN
rs2272022	ZNF80	cis	cerebellum	SCAN
rs2272022	CD200	cis	cerebellum	SCAN

Chromatin state (count:77 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:112052600-112066400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
2	chr3:112052800-112076200	Weak transcription	Right Ventricle	heart
3	chr3:112053200-112066400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
4	chr3:112053200-112076400	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
5	chr3:112053800-112064200	Weak transcription	Fetal Intestine Large	intestine
6	chr3:112054000-112065800	Weak transcription	Fetal Kidney	kidney
7	chr3:112054000-112068600	Weak transcription	Duodenum Smooth Muscle	Duodenum
8	chr3:112054200-112064000	Weak transcription	Rectal Mucosa Donor 29	rectum
9	chr3:112054800-112066400	Weak transcription	Rectal Smooth Muscle	rectum
10	chr3:112054800-112076800	Weak transcription	Lung	lung
11	chr3:112054800-112083000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
12	chr3:112055200-112068800	Weak transcription	Fetal Intestine Small	intestine
13	chr3:112055600-112080200	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
14	chr3:112055800-112076400	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
15	chr3:112056200-112065400	Weak transcription	Colon Smooth Muscle	Colon
16	chr3:112056400-112064000	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
17	chr3:112056600-112064600	Weak transcription	Rectal Mucosa Donor 31	rectum
18	chr3:112056600-112076400	Weak transcription	Primary T helper cells fromperipheralblood	blood
19	chr3:112057800-112067000	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
20	chr3:112057800-112068800	Strong transcription	HUES6 Cell Line	embryonic stem cell
21	chr3:112058600-112067400	Strong transcription	iPS-20b Cell Line	embryonic stem cell
22	chr3:112058800-112064000	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
23	chr3:112058800-112069800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
24	chr3:112059000-112066600	Strong transcription	HUES64 Cell Line	embryonic stem cell
25	chr3:112059200-112069000	Strong transcription	H1 Cell Line	embryonic stem cell
26	chr3:112059600-112066600	Weak transcription	Brain Substantia Nigra	brain
27	chr3:112059600-112075000	Strong transcription	Fetal Thymus	thymus
28	chr3:112059800-112065600	ZNF genes & repeats	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
29	chr3:112060200-112064200	Weak transcription	Placenta	Placenta
30	chr3:112060800-112064000	Weak transcription	Brain Angular Gyrus	brain
31	chr3:112061200-112083000	Weak transcription	Colonic Mucosa	Colon
32	chr3:112061400-112076000	Strong transcription	Primary hematopoietic stem cells	blood
33	chr3:112061600-112064400	ZNF genes & repeats	Primary hematopoietic stem cells short term culture	blood
34	chr3:112061800-112067400	Strong transcription	HUES48 Cell Line	embryonic stem cell
35	chr3:112062200-112066200	Strong transcription	iPS-18 Cell Line	embryonic stem cell
36	chr3:112062200-112066600	Strong transcription	Fetal Lung	lung
37	chr3:112062200-112067800	Strong transcription	Primary T helper 17 cells PMA-I stimulated	--
38	chr3:112062400-112064400	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
39	chr3:112062400-112069000	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
40	chr3:112062400-112083000	Weak transcription	Sigmoid Colon	Sigmoid Colon
41	chr3:112062600-112064000	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
42	chr3:112062600-112064600	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
43	chr3:112062600-112076600	Strong transcription	Primary B cells from cord blood	blood
44	chr3:112062800-112074600	Strong transcription	Primary B cells from peripheral blood	blood
45	chr3:112063000-112065600	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
46	chr3:112063000-112066800	Strong transcription	Brain Anterior Caudate	brain
47	chr3:112063200-112064000	ZNF genes & repeats	Left Ventricle	heart
48	chr3:112063200-112064200	Genic enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
49	chr3:112063200-112064400	Genic enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
50	chr3:112063200-112064800	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast

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