Variant report

Variant	rs3772551
Chromosome Location	chr3:105258452-105258453
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 23 )
Associated
traits (count: 1 )

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

rs_ID	r²[population]
rs1438548	0.83[CHB][hapmap]
rs17189452	1.00[CEU][hapmap];0.82[YRI][hapmap];0.83[AFR][1000 genomes];0.99[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs1898656	0.90[CHB][hapmap]
rs3772554	0.90[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.97[TSI][hapmap];0.91[YRI][hapmap];0.81[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs478259	1.00[ASW][hapmap];1.00[CEU][hapmap];0.95[CHD][hapmap];0.81[GIH][hapmap];0.82[LWK][hapmap];0.90[MKK][hapmap];0.84[TSI][hapmap];0.82[AFR][1000 genomes];0.99[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs485922	0.90[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.97[TSI][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4894832	1.00[CEU][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];0.99[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs490029	0.91[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs503321	0.90[MEX][hapmap]
rs519016	0.82[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.87[MKK][hapmap];0.97[TSI][hapmap];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs526375	0.80[AFR][1000 genomes];0.97[AMR][1000 genomes]
rs526963	0.86[AFR][1000 genomes];0.99[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs562960	1.00[ASW][hapmap];1.00[CEU][hapmap];0.95[MEX][hapmap];0.91[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs577295	1.00[CEU][hapmap];0.97[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs610047	1.00[ASW][hapmap];1.00[CEU][hapmap];0.95[CHD][hapmap];0.88[GIH][hapmap];0.95[MEX][hapmap];0.93[MKK][hapmap];0.83[TSI][hapmap];0.80[AFR][1000 genomes];0.94[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs629187	0.90[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.97[TSI][hapmap];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs66875175	0.82[AFR][1000 genomes]
rs7652866	0.83[CHB][hapmap]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv525071	chr3:105004853-105409321	Enhancers Strong transcription Weak transcription ZNF genes & repeats Active TSS Flanking Active TSS Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	6 gene(s)	inside rSNPs	diseases
2	nsv534224	chr3:105141696-105404293	Weak transcription Strong transcription Enhancers ZNF genes & repeats Genic enhancers Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	2 gene(s)	inside rSNPs	diseases
3	nsv829651	chr3:105203424-105402136	Weak transcription Strong transcription Enhancers Genic enhancers ZNF genes & repeats Flanking Active TSS Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	2 gene(s)	inside rSNPs	diseases
4	nsv460811	chr3:105212993-105316769	Strong transcription Weak transcription Genic enhancers Enhancers Active TSS ZNF genes & repeats Flanking Active TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	1 gene(s)	inside rSNPs	diseases
5	nsv591240	chr3:105212993-105316769	Enhancers Weak transcription Strong transcription Genic enhancers Flanking Active TSS Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	1 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs3772551	ALCAM	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:85 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:105221400-105300400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
2	chr3:105222200-105260600	Weak transcription	Fetal Kidney	kidney
3	chr3:105223800-105274800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
4	chr3:105229600-105260400	Weak transcription	H1 Cell Line	embryonic stem cell
5	chr3:105230200-105262600	Weak transcription	H9 Cell Line	embryonic stem cell
6	chr3:105232200-105274000	Weak transcription	HSMMtube	muscle
7	chr3:105234200-105260400	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
8	chr3:105234600-105260600	Weak transcription	iPS-20b Cell Line	embryonic stem cell
9	chr3:105234600-105261000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
10	chr3:105234600-105274600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
11	chr3:105237800-105259000	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
12	chr3:105237800-105274600	Weak transcription	HUES6 Cell Line	embryonic stem cell
13	chr3:105237800-105275800	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
14	chr3:105241000-105260400	Weak transcription	Pancreas	Pancrea
15	chr3:105241600-105260200	Weak transcription	HepG2	liver
16	chr3:105241800-105259000	Weak transcription	Primary hematopoietic stem cells	blood
17	chr3:105242000-105259800	Weak transcription	Primary neutrophils fromperipheralblood	blood
18	chr3:105242000-105293600	Weak transcription	Lung	lung
19	chr3:105242200-105259000	Weak transcription	Ovary	ovary
20	chr3:105242400-105280400	Weak transcription	Rectal Mucosa Donor 31	rectum
21	chr3:105242800-105266800	Weak transcription	Duodenum Smooth Muscle	Duodenum
22	chr3:105243200-105259000	Weak transcription	Primary monocytes fromperipheralblood	blood
23	chr3:105244800-105275800	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
24	chr3:105245000-105258800	Weak transcription	Primary B cells from cord blood	blood
25	chr3:105245200-105259200	Weak transcription	HUES64 Cell Line	embryonic stem cell
26	chr3:105245600-105260400	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
27	chr3:105245800-105260600	Weak transcription	iPS-18 Cell Line	embryonic stem cell
28	chr3:105245800-105268000	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
29	chr3:105246600-105284400	Weak transcription	Cortex derived primary cultured neurospheres	brain
30	chr3:105247400-105260400	Weak transcription	Brain Anterior Caudate	brain
31	chr3:105247800-105259200	Weak transcription	Brain Angular Gyrus	brain
32	chr3:105248000-105281200	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
33	chr3:105248200-105258800	Weak transcription	Brain Substantia Nigra	brain
34	chr3:105248200-105262800	Weak transcription	NHLF	lung
35	chr3:105248400-105291200	Weak transcription	Brain Cingulate Gyrus	brain
36	chr3:105249400-105278600	Weak transcription	Small Intestine	intestine
37	chr3:105249800-105261200	Weak transcription	Fetal Intestine Small	intestine
38	chr3:105249800-105263400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
39	chr3:105249800-105284000	Weak transcription	Fetal Stomach	stomach
40	chr3:105249800-105285200	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
41	chr3:105250600-105262600	Weak transcription	iPS-15b Cell Line	embryonic stem cell
42	chr3:105250600-105270400	Weak transcription	Pancreatic Islets	Pancreatic Islet
43	chr3:105251200-105266400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
44	chr3:105251400-105258800	Weak transcription	Primary hematopoietic stem cells short term culture	blood
45	chr3:105251800-105274400	Weak transcription	Dnd41	blood
46	chr3:105252600-105263400	Weak transcription	Left Ventricle	heart
47	chr3:105253000-105259400	Weak transcription	Stomach Smooth Muscle	stomach
48	chr3:105253200-105273000	Weak transcription	Gastric	stomach
49	chr3:105253600-105260400	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
50	chr3:105253600-105260400	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links