Variant report

Variant	rs2399416
Chromosome Location	chr3:112059213-112059214
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 18 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:17)

rs_ID	r²[population]
rs10511311	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.96[GIH][hapmap];1.00[JPT][hapmap];0.95[LWK][hapmap];1.00[MEX][hapmap];0.98[MKK][hapmap];0.93[TSI][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12106673	0.84[CEU][hapmap];0.81[MEX][hapmap]
rs12106967	0.84[CEU][hapmap]
rs12491166	0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs13072567	0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs13090468	0.83[CEU][hapmap]
rs13098589	0.87[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[GIH][hapmap];0.81[JPT][hapmap];1.00[MEX][hapmap];0.89[MKK][hapmap];0.91[TSI][hapmap];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1317243	0.81[CEU][hapmap]
rs1343852	1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2272022	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]
rs2276772	0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2399412	0.84[AMR][1000 genomes]
rs2399413	0.84[ASW][hapmap]
rs34345145	0.96[EUR][1000 genomes]
rs4682103	0.83[CHB][hapmap];0.82[JPT][hapmap]
rs4682399	0.80[CEU][hapmap];0.84[MEX][hapmap];0.81[TSI][hapmap];0.84[AMR][1000 genomes]
rs7647411	0.87[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];0.87[MKK][hapmap];0.91[TSI][hapmap];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.92[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:2)

SNP	Gene	Cis/trans	Tissue	Source
rs2399416	CD200	cis	parietal	SCAN
rs2399416	CD200	cis	cerebellum	SCAN

Chromatin state (count:74 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:112052600-112062400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
2	chr3:112052600-112066400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
3	chr3:112052800-112076200	Weak transcription	Right Ventricle	heart
4	chr3:112053200-112062200	Weak transcription	Sigmoid Colon	Sigmoid Colon
5	chr3:112053200-112066400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
6	chr3:112053200-112076400	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
7	chr3:112053800-112063800	Weak transcription	Cortex derived primary cultured neurospheres	brain
8	chr3:112053800-112064200	Weak transcription	Fetal Intestine Large	intestine
9	chr3:112054000-112065800	Weak transcription	Fetal Kidney	kidney
10	chr3:112054000-112068600	Weak transcription	Duodenum Smooth Muscle	Duodenum
11	chr3:112054200-112063800	Weak transcription	Fetal Muscle Trunk	muscle
12	chr3:112054200-112064000	Weak transcription	Rectal Mucosa Donor 29	rectum
13	chr3:112054600-112059600	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
14	chr3:112054600-112059600	Weak transcription	Fetal Muscle Leg	muscle
15	chr3:112054800-112059400	Weak transcription	Right Atrium	heart
16	chr3:112054800-112059600	Weak transcription	Primary B cells from cord blood	blood
17	chr3:112054800-112060800	Enhancers	Brain Angular Gyrus	brain
18	chr3:112054800-112061800	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
19	chr3:112054800-112063400	Weak transcription	Ovary	ovary
20	chr3:112054800-112063800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
21	chr3:112054800-112066400	Weak transcription	Rectal Smooth Muscle	rectum
22	chr3:112054800-112076800	Weak transcription	Lung	lung
23	chr3:112054800-112083000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
24	chr3:112055000-112059400	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
25	chr3:112055000-112063400	Weak transcription	Brain Germinal Matrix	brain
26	chr3:112055200-112068800	Weak transcription	Fetal Intestine Small	intestine
27	chr3:112055400-112059600	Weak transcription	Fetal Thymus	thymus
28	chr3:112055400-112062200	Weak transcription	Fetal Lung	lung
29	chr3:112055400-112063800	Weak transcription	Fetal Stomach	stomach
30	chr3:112055600-112080200	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
31	chr3:112055800-112076400	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
32	chr3:112056000-112063800	Weak transcription	Thymus	Thymus
33	chr3:112056200-112065400	Weak transcription	Colon Smooth Muscle	Colon
34	chr3:112056400-112059400	Genic enhancers	Primary hematopoietic stem cells short term culture	blood
35	chr3:112056400-112059800	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
36	chr3:112056400-112064000	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
37	chr3:112056600-112060000	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
38	chr3:112056600-112064600	Weak transcription	Rectal Mucosa Donor 31	rectum
39	chr3:112056600-112076400	Weak transcription	Primary T helper cells fromperipheralblood	blood
40	chr3:112057400-112059800	Transcr. at gene 5' and 3'	Breast Myoepithelial Primary Cells	Breast
41	chr3:112057600-112063200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
42	chr3:112057800-112059600	Weak transcription	H9 Cell Line	embryonic stem cell
43	chr3:112057800-112063200	Weak transcription	Fetal Brain Male	brain
44	chr3:112057800-112067000	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
45	chr3:112057800-112068800	Strong transcription	HUES6 Cell Line	embryonic stem cell
46	chr3:112058000-112060200	Genic enhancers	iPS-18 Cell Line	embryonic stem cell
47	chr3:112058200-112060200	Enhancers	Pancreatic Islets	Pancreatic Islet
48	chr3:112058400-112059600	Weak transcription	Primary hematopoietic stem cells	blood
49	chr3:112058400-112060800	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
50	chr3:112058600-112060600	Weak transcription	Fetal Brain Female	brain

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links