Variant report

Variant	rs1939798
Chromosome Location	chr11:105972014-105972015
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr11:105947655..105949809-chr11:105969558..105972572,3	MCF-7	breast:
2	chr11:105939028..105941380-chr11:105969620..105972203,2	K562	blood:

Variant related genes	Relation type
ENSG00000149313	Chromatin interaction
ENSG00000182359	Chromatin interaction

Extended variants
information (count: 32 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:31)

rs_ID	r²[population]
rs10791780	0.90[CHB][hapmap]
rs10895899	0.82[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs10895900	0.84[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap]
rs10895904	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11226915	0.84[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.94[YRI][hapmap];0.88[AFR][1000 genomes];0.89[AMR][1000 genomes];0.83[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11226920	0.85[CHB][hapmap]
rs11226922	0.95[CEU][hapmap];0.90[CHB][hapmap];0.95[JPT][hapmap];0.86[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11226931	0.86[ASN][1000 genomes]
rs12365489	0.90[CHB][hapmap]
rs17105049	0.85[CHB][hapmap]
rs1893174	0.91[CHB][hapmap];0.85[JPT][hapmap]
rs1939799	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1940772	0.89[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2155340	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2186731	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2277278	0.82[ASN][1000 genomes]
rs3740869	0.81[CHB][hapmap]
rs4237618	0.84[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap];0.83[YRI][hapmap];0.87[AMR][1000 genomes];0.83[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4440991	0.84[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[YRI][hapmap];0.85[AMR][1000 genomes];0.83[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4474407	0.91[CHB][hapmap]
rs4565867	0.89[AMR][1000 genomes];0.83[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4754141	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs60606604	0.82[ASN][1000 genomes]
rs7108636	0.86[CHB][hapmap]
rs7130759	0.89[AMR][1000 genomes];0.92[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7131047	0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs754562	0.89[CEU][hapmap];0.90[CHB][hapmap];0.95[JPT][hapmap]
rs7554	0.90[CHB][hapmap]
rs766717	0.89[CEU][hapmap];0.90[CHB][hapmap];0.95[JPT][hapmap]
rs9651674	0.90[CHB][hapmap];0.82[JPT][hapmap]
rs9943677	0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[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	nsv1048381	chr11:105945117-106561574	Weak transcription Enhancers Active TSS Genic enhancers Strong transcription Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	13 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs1939798	AASDHPPT	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:53 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:105949000-105973400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
2	chr11:105957200-105976600	Weak transcription	Pancreas	Pancrea
3	chr11:105957200-105976800	Weak transcription	Aorta	Aorta
4	chr11:105963000-105972400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
5	chr11:105963200-105972200	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
6	chr11:105966800-105972400	Weak transcription	Stomach Smooth Muscle	stomach
7	chr11:105968400-105972200	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
8	chr11:105968400-105972800	Weak transcription	Brain Angular Gyrus	brain
9	chr11:105968400-105975400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
10	chr11:105968600-105972400	Weak transcription	Osteobl	bone
11	chr11:105968600-105972800	Weak transcription	Primary hematopoietic stem cells	blood
12	chr11:105968600-105973600	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
13	chr11:105968600-105975200	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
14	chr11:105968600-105975200	Weak transcription	Psoas Muscle	Psoas
15	chr11:105968800-105973200	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
16	chr11:105968800-105978000	Weak transcription	Ovary	ovary
17	chr11:105969000-105972400	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
18	chr11:105969000-105972800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
19	chr11:105969000-105973800	Weak transcription	Fetal Muscle Trunk	muscle
20	chr11:105969200-105972200	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
21	chr11:105969200-105972400	Weak transcription	NH-A	brain
22	chr11:105969200-105973000	Weak transcription	Fetal Thymus	thymus
23	chr11:105969200-105974000	Weak transcription	GM12878-XiMat	blood
24	chr11:105969600-105974000	Weak transcription	Primary T cells fromperipheralblood	blood
25	chr11:105970000-105972200	Weak transcription	HUVEC	blood vessel
26	chr11:105970000-105975000	Weak transcription	A549	lung
27	chr11:105970200-105972400	Weak transcription	Monocytes-CD14+_RO01746	blood
28	chr11:105970200-105973600	Weak transcription	Skeletal Muscle Male	skeletal muscle
29	chr11:105970400-105972200	Weak transcription	Primary monocytes fromperipheralblood	blood
30	chr11:105970400-105972200	Weak transcription	Liver	Liver
31	chr11:105970400-105972400	Weak transcription	Primary hematopoietic stem cells short term culture	blood
32	chr11:105970400-105972600	Weak transcription	Primary B cells from cord blood	blood
33	chr11:105970400-105972800	Weak transcription	Cortex derived primary cultured neurospheres	brain
34	chr11:105970400-105973000	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
35	chr11:105970400-105973200	Weak transcription	Skeletal Muscle Female	skeletal muscle
36	chr11:105970400-105973400	Weak transcription	Breast Myoepithelial Primary Cells	Breast
37	chr11:105970600-105972200	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
38	chr11:105970600-105972200	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
39	chr11:105970600-105972200	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
40	chr11:105970800-105972400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
41	chr11:105970800-105973000	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
42	chr11:105970800-105973000	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
43	chr11:105971000-105973200	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
44	chr11:105971200-105972400	Enhancers	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
45	chr11:105971200-105972800	Enhancers	iPS-15b Cell Line	embryonic stem cell
46	chr11:105971600-105972200	Weak transcription	HSMM	muscle
47	chr11:105971800-105972400	Enhancers	HUES6 Cell Line	embryonic stem cell
48	chr11:105971800-105972400	Enhancers	HUES64 Cell Line	embryonic stem cell
49	chr11:105971800-105972400	Enhancers	iPS-18 Cell Line	embryonic stem cell
50	chr11:105971800-105972600	Enhancers	HUES48 Cell Line	embryonic stem cell

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links