Variant report

Variant	rs729925
Chromosome Location	chr6:35256934-35256935
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr6:35251015..35257008-chr6:35259512..35261942,5	K562	blood:
2	chr6:35246027..35248636-chr6:35256362..35259895,3	K562	blood:
3	chr6:35246027..35248404-chr6:35256900..35259895,2	K562	blood:

Variant related genes	Relation type
ENSG00000065029	Chromatin interaction
ENSG00000217004	Chromatin interaction

Extended variants
information (count: 35 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:33)

rs_ID	r²[population]
rs11552398	1.00[GIH][hapmap]
rs16871749	1.00[GIH][hapmap]
rs16871814	1.00[GIH][hapmap]
rs1929846	0.81[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1929848	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.82[MEX][hapmap];0.95[TSI][hapmap];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2234044	1.00[GIH][hapmap]
rs2395617	0.83[CEU][hapmap];1.00[CHB][hapmap];1.00[GIH][hapmap];0.91[MKK][hapmap];0.91[TSI][hapmap];0.83[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3756856	1.00[GIH][hapmap]
rs4713842	1.00[MEX][hapmap];0.81[EUR][1000 genomes]
rs4713843	1.00[MEX][hapmap];0.81[EUR][1000 genomes]
rs4713844	0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6457815	1.00[CHB][hapmap]
rs6906666	1.00[GIH][hapmap]
rs6919534	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.82[MEX][hapmap];0.95[TSI][hapmap];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6931442	0.92[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6937124	1.00[CHB][hapmap]
rs707969	0.82[MEX][hapmap]
rs734538	0.86[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];0.93[MKK][hapmap];1.00[TSI][hapmap];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs763155	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.82[LWK][hapmap];1.00[MEX][hapmap];0.93[MKK][hapmap];1.00[TSI][hapmap];0.87[YRI][hapmap];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs763157	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7751726	1.00[CHB][hapmap]
rs7767150	0.84[AFR][1000 genomes];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7770619	1.00[CHB][hapmap]
rs9394282	0.86[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.82[LWK][hapmap];1.00[MEX][hapmap];0.93[MKK][hapmap];1.00[TSI][hapmap];0.94[YRI][hapmap];0.86[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9462081	1.00[CHB][hapmap];1.00[CHD][hapmap]
rs9658077	1.00[CHB][hapmap]
rs9658081	1.00[CHB][hapmap]
rs9658085	1.00[CHB][hapmap]
rs9658089	1.00[CHD][hapmap]
rs9658118	1.00[CHD][hapmap]
rs9658119	1.00[CHB][hapmap];1.00[CHD][hapmap]
rs9658136	1.00[CHD][hapmap]
rs9658151	1.00[CHB][hapmap];1.00[CHD][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	esv2758047	chr6:35168116-35291002	Enhancers Flanking Bivalent TSS/Enh Flanking Active TSS Strong transcription Active TSS Weak transcription Bivalent/Poised TSS Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	26 gene(s)	inside rSNPs	diseases
2	esv2759419	chr6:35168116-35291002	Weak transcription Flanking Active TSS Active TSS Enhancers Genic enhancers Strong transcription Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	26 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs729925	TCP11	cis	lymphoblastoid	seeQTL
rs729925	TPM2	trans	lymphoblastoid	seeQTL

Chromatin state (count:125 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:35232600-35265200	Weak transcription	Stomach Mucosa	stomach
2	chr6:35233800-35258400	Weak transcription	Small Intestine	intestine
3	chr6:35237800-35264800	Weak transcription	K562	blood
4	chr6:35243400-35265000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
5	chr6:35247800-35264600	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
6	chr6:35248000-35264800	Strong transcription	Stomach Smooth Muscle	stomach
7	chr6:35248400-35262200	Strong transcription	Primary T cells fromperipheralblood	blood
8	chr6:35248400-35263400	Strong transcription	Rectal Smooth Muscle	rectum
9	chr6:35248400-35264400	Strong transcription	Primary T helper 17 cells PMA-I stimulated	--
10	chr6:35248600-35264200	Strong transcription	Primary monocytes fromperipheralblood	blood
11	chr6:35248600-35264200	Strong transcription	Fetal Thymus	thymus
12	chr6:35248600-35264400	Strong transcription	Monocytes-CD14+_RO01746	blood
13	chr6:35248800-35257000	Strong transcription	Breast Myoepithelial Primary Cells	Breast
14	chr6:35248800-35260000	Strong transcription	Primary B cells from peripheral blood	blood
15	chr6:35248800-35260200	Strong transcription	Primary B cells from cord blood	blood
16	chr6:35248800-35261200	Weak transcription	A549	lung
17	chr6:35248800-35262000	Strong transcription	Primary T helper cells PMA-I stimulated	--
18	chr6:35248800-35263600	Strong transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
19	chr6:35248800-35263600	Strong transcription	Duodenum Mucosa	Duodenum
20	chr6:35248800-35263800	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
21	chr6:35248800-35264000	Strong transcription	Duodenum Smooth Muscle	Duodenum
22	chr6:35248800-35264000	Strong transcription	Sigmoid Colon	Sigmoid Colon
23	chr6:35248800-35264000	Strong transcription	Dnd41	blood
24	chr6:35248800-35264200	Strong transcription	Primary T helper naive cells fromperipheralblood	blood
25	chr6:35248800-35264400	Strong transcription	Primary hematopoietic stem cells short term culture	blood
26	chr6:35248800-35264400	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
27	chr6:35248800-35264400	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
28	chr6:35248800-35264400	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
29	chr6:35248800-35264600	Strong transcription	Primary T cells from cord blood	blood
30	chr6:35248800-35264600	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
31	chr6:35248800-35264800	Strong transcription	Primary T helper cells fromperipheralblood	blood
32	chr6:35248800-35264800	Strong transcription	Thymus	Thymus
33	chr6:35248800-35265000	Strong transcription	Fetal Intestine Small	intestine
34	chr6:35248800-35265000	Strong transcription	Fetal Stomach	stomach
35	chr6:35248800-35265400	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
36	chr6:35248800-35265800	Strong transcription	Brain Inferior Temporal Lobe	brain
37	chr6:35249000-35263400	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
38	chr6:35249000-35264200	Strong transcription	Rectal Mucosa Donor 29	rectum
39	chr6:35249000-35264600	Strong transcription	Brain Anterior Caudate	brain
40	chr6:35249000-35264600	Strong transcription	Brain Cingulate Gyrus	brain
41	chr6:35249000-35264600	Strong transcription	Fetal Intestine Large	intestine
42	chr6:35249000-35265000	Strong transcription	Liver	Liver
43	chr6:35249000-35265200	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
44	chr6:35249000-35265200	Strong transcription	Osteobl	bone
45	chr6:35249000-35265400	Weak transcription	Right Atrium	heart
46	chr6:35249000-35266800	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
47	chr6:35249200-35264400	Strong transcription	Placenta	Placenta
48	chr6:35249200-35265400	Strong transcription	Fetal Brain Female	brain
49	chr6:35249400-35263600	Strong transcription	Aorta	Aorta
50	chr6:35250000-35263400	Strong transcription	Brain Angular Gyrus	brain

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links