Variant report

Variant	rs3770688
Chromosome Location	chr2:211334073-211334074
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr2:211332522..211338097-chr2:211338673..211343444,12	K562	blood:
2	chr2:211333118..211336164-chr2:211339980..211343181,4	MCF-7	breast:
3	chr2:211333367..211335513-chr2:211340157..211342892,2	MCF-7	breast:
4	chr2:211331221..211336571-chr2:211337651..211341435,6	K562	blood:

Variant related genes	Relation type
ENSG00000021826	Chromatin interaction
ENSG00000115365	Chromatin interaction

Extended variants
information (count: 37 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:35)

rs_ID	r²[population]
rs10184506	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10195425	1.00[CEU][hapmap];0.92[CHB][hapmap];1.00[JPT][hapmap];0.82[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10932340	1.00[CEU][hapmap]
rs12694198	0.97[ASN][1000 genomes]
rs12694200	0.80[EUR][1000 genomes]
rs13005638	0.85[EUR][1000 genomes]
rs13013076	0.85[CEU][hapmap]
rs13420747	0.85[JPT][hapmap]
rs1509816	1.00[CEU][hapmap];0.83[EUR][1000 genomes]
rs1858194	0.83[EUR][1000 genomes]
rs1858195	1.00[CEU][hapmap];0.83[EUR][1000 genomes]
rs2160851	1.00[CEU][hapmap];0.80[EUR][1000 genomes]
rs2287426	1.00[CEU][hapmap];0.92[CHB][hapmap];1.00[JPT][hapmap];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2287427	1.00[CEU][hapmap];0.92[CHB][hapmap];1.00[JPT][hapmap];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2370962	1.00[CEU][hapmap];0.80[EUR][1000 genomes]
rs2664239	1.00[CEU][hapmap];0.80[EUR][1000 genomes]
rs34374637	0.82[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs35003355	0.89[AMR][1000 genomes];0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs3732058	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs3755185	0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs3755186	1.00[CEU][hapmap];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs3755187	1.00[CEU][hapmap];0.92[CHB][hapmap];1.00[JPT][hapmap];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs3770686	0.82[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3770693	1.00[CEU][hapmap];0.92[CHB][hapmap];1.00[JPT][hapmap];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs3770696	1.00[CEU][hapmap];0.92[CHB][hapmap];1.00[JPT][hapmap];0.92[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs3845634	0.87[CEU][hapmap]
rs4672580	0.82[EUR][1000 genomes]
rs4672581	0.82[EUR][1000 genomes]
rs4672582	0.82[EUR][1000 genomes]
rs57718949	0.94[AMR][1000 genomes]
rs6749711	1.00[CEU][hapmap];0.83[EUR][1000 genomes]
rs7590759	1.00[CEU][hapmap];0.80[EUR][1000 genomes]
rs759688	1.00[CEU][hapmap];0.83[EUR][1000 genomes]
rs918234	1.00[CEU][hapmap]
rs9941507	1.00[CEU][hapmap]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv875767	chr2:211119233-211334647	Weak transcription Enhancers Genic enhancers ZNF genes & repeats Strong transcription Flanking Active TSS Active TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	5 gene(s)	inside rSNPs	diseases
2	esv3398091	chr2:211315261-211634200	Active TSS Flanking Active TSS Weak transcription Strong transcription Enhancers Genic enhancers ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs3770688	LANCL1	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:124 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:211293800-211335400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
2	chr2:211295000-211336000	Weak transcription	Colonic Mucosa	Colon
3	chr2:211295000-211340600	Weak transcription	HUVEC	blood vessel
4	chr2:211296000-211340200	Weak transcription	Small Intestine	intestine
5	chr2:211296400-211341000	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
6	chr2:211297800-211336200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
7	chr2:211301200-211340200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
8	chr2:211301200-211340600	Weak transcription	Fetal Intestine Small	intestine
9	chr2:211301200-211340800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
10	chr2:211301400-211334400	Weak transcription	NHEK	skin
11	chr2:211301400-211336000	Weak transcription	Primary T killer memory cells from peripheral blood	blood
12	chr2:211315400-211340000	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
13	chr2:211315600-211337800	Strong transcription	Fetal Thymus	thymus
14	chr2:211315600-211339600	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
15	chr2:211315800-211337200	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
16	chr2:211315800-211337800	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
17	chr2:211316000-211338000	Strong transcription	Primary T helper cells fromperipheralblood	blood
18	chr2:211316200-211337800	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
19	chr2:211316200-211337800	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
20	chr2:211316600-211339000	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
21	chr2:211316800-211338800	Strong transcription	Dnd41	blood
22	chr2:211318000-211337800	Strong transcription	Stomach Smooth Muscle	stomach
23	chr2:211321000-211334200	Strong transcription	Primary T helper cells PMA-I stimulated	--
24	chr2:211321200-211337600	Strong transcription	Primary hematopoietic stem cells short term culture	blood
25	chr2:211322400-211340400	Weak transcription	iPS-15b Cell Line	embryonic stem cell
26	chr2:211322600-211340400	Weak transcription	K562	blood
27	chr2:211323400-211336000	Weak transcription	H9 Cell Line	embryonic stem cell
28	chr2:211323400-211340200	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
29	chr2:211324200-211336000	Strong transcription	Breast Myoepithelial Primary Cells	Breast
30	chr2:211324800-211339000	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
31	chr2:211325800-211340800	Weak transcription	Primary neutrophils fromperipheralblood	blood
32	chr2:211326800-211338800	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
33	chr2:211326800-211339800	Weak transcription	Pancreatic Islets	Pancreatic Islet
34	chr2:211327200-211338000	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
35	chr2:211327400-211339000	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
36	chr2:211327600-211339000	Strong transcription	HUES64 Cell Line	embryonic stem cell
37	chr2:211328000-211334200	Strong transcription	Brain Germinal Matrix	brain
38	chr2:211328200-211337800	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
39	chr2:211328600-211337000	Strong transcription	HUES48 Cell Line	embryonic stem cell
40	chr2:211329400-211334400	Strong transcription	Fetal Brain Female	brain
41	chr2:211329400-211336600	Strong transcription	Primary T helper 17 cells PMA-I stimulated	--
42	chr2:211329600-211336800	Strong transcription	Left Ventricle	heart
43	chr2:211329600-211337200	Strong transcription	Primary T cells from cord blood	blood
44	chr2:211329800-211334200	Strong transcription	Brain Hippocampus Middle	brain
45	chr2:211329800-211334200	Strong transcription	Brain Inferior Temporal Lobe	brain
46	chr2:211329800-211334400	Strong transcription	Cortex derived primary cultured neurospheres	brain
47	chr2:211329800-211334600	Strong transcription	Primary hematopoietic stem cells	blood
48	chr2:211329800-211334600	Strong transcription	Fetal Lung	lung
49	chr2:211329800-211334600	Strong transcription	Monocytes-CD14+_RO01746	blood
50	chr2:211329800-211335000	Strong transcription	Brain Dorsolateral Prefrontal Cortex	brain

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