Variant report

Variant	rs2959101
Chromosome Location	chr11:46018139-46018140
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr11:45937806..45941201-chr11:46015490..46019535,4	K562	blood:
2	chr11:45937806..45940023-chr11:46017253..46018800,2	K562	blood:
3	chr11:46000949..46006706-chr11:46011674..46018213,17	K562	blood:

Variant related genes	Relation type
ENSG00000121680	Chromatin interaction

Extended variants
information (count: 22 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:21)

rs_ID	r²[population]
rs10769187	1.00[LWK][hapmap];1.00[MKK][hapmap];1.00[YRI][hapmap]
rs11038720	0.85[CHD][hapmap]
rs1125290	0.80[ASN][1000 genomes]
rs11600515	1.00[YRI][hapmap]
rs12418498	1.00[YRI][hapmap]
rs2945999	0.84[MEX][hapmap]
rs2959087	0.82[CHD][hapmap];0.88[MEX][hapmap]
rs2959098	0.80[ASN][1000 genomes]
rs2959099	0.80[ASN][1000 genomes]
rs2959100	0.96[CEU][hapmap];0.86[CHB][hapmap];0.92[JPT][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs4144718	0.89[CHD][hapmap];0.83[MEX][hapmap]
rs4237660	0.89[CHD][hapmap]
rs4505038	1.00[YRI][hapmap]
rs7108186	0.89[CHD][hapmap];0.80[MEX][hapmap]
rs7112677	0.85[JPT][hapmap];1.00[YRI][hapmap]
rs7128184	0.89[CHD][hapmap]
rs7926314	0.89[CHD][hapmap]
rs7948502	0.89[CHD][hapmap]
rs7950336	0.86[CHD][hapmap]
rs7950391	0.89[CHD][hapmap]
rs939107	0.89[CHD][hapmap]

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	nsv523952	chr11:45983385-46028281	Enhancers Weak transcription Active TSS Strong transcription Genic enhancers Flanking Active TSS	TF binding region CpG island Chromatin interactive region	8 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs2959101	MADD	cis	parietal	SCAN
rs2959101	PHF21A	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:78 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:46001400-46070400	Weak transcription	Primary hematopoietic stem cells	blood
2	chr11:46001600-46021000	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
3	chr11:46002000-46025000	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
4	chr11:46002000-46042400	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
5	chr11:46002000-46056200	Weak transcription	Primary T helper cells fromperipheralblood	blood
6	chr11:46002200-46024800	Weak transcription	Primary neutrophils fromperipheralblood	blood
7	chr11:46002200-46025000	Weak transcription	Primary monocytes fromperipheralblood	blood
8	chr11:46002600-46023200	Weak transcription	Primary B cells from peripheral blood	blood
9	chr11:46006200-46025200	Weak transcription	Monocytes-CD14+_RO01746	blood
10	chr11:46006800-46021400	Weak transcription	Primary B cells from cord blood	blood
11	chr11:46012000-46018400	Enhancers	Fetal Brain Male	brain
12	chr11:46012800-46031000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
13	chr11:46012800-46062800	Weak transcription	GM12878-XiMat	blood
14	chr11:46013400-46021200	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
15	chr11:46014200-46018200	Enhancers	Brain Germinal Matrix	brain
16	chr11:46014400-46019800	Enhancers	ES-I3 Cell Line	embryonic stem cell
17	chr11:46014400-46020000	Enhancers	HUES48 Cell Line	embryonic stem cell
18	chr11:46014800-46018200	Enhancers	H1 Cell Line	embryonic stem cell
19	chr11:46014800-46020000	Enhancers	iPS-20b Cell Line	embryonic stem cell
20	chr11:46015000-46018400	Flanking Active TSS	K562	blood
21	chr11:46015000-46019800	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
22	chr11:46015200-46018400	Enhancers	iPS-15b Cell Line	embryonic stem cell
23	chr11:46015400-46018600	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
24	chr11:46015400-46019000	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
25	chr11:46015400-46022600	Weak transcription	HSMM	muscle
26	chr11:46015600-46022800	Weak transcription	Brain Inferior Temporal Lobe	brain
27	chr11:46015600-46026400	Weak transcription	Stomach Mucosa	stomach
28	chr11:46016200-46018200	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
29	chr11:46016200-46018200	Enhancers	Fetal Brain Female	brain
30	chr11:46016200-46019000	Weak transcription	Pancreas	Pancrea
31	chr11:46016200-46019400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
32	chr11:46016200-46020000	Enhancers	Cortex derived primary cultured neurospheres	brain
33	chr11:46016200-46020200	Weak transcription	Fetal Muscle Trunk	muscle
34	chr11:46016200-46021000	Weak transcription	Placenta Amnion	Placenta Amnion
35	chr11:46016200-46022600	Weak transcription	HSMMtube	muscle
36	chr11:46016200-46022800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
37	chr11:46016200-46048200	Weak transcription	Esophagus	oesophagus
38	chr11:46016400-46019000	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
39	chr11:46016400-46019200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
40	chr11:46016400-46019200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
41	chr11:46016400-46020000	Enhancers	iPS-18 Cell Line	embryonic stem cell
42	chr11:46016400-46020000	Enhancers	Pancreatic Islets	Pancreatic Islet
43	chr11:46016400-46022800	Weak transcription	Brain Substantia Nigra	brain
44	chr11:46016400-46022800	Weak transcription	Ovary	ovary
45	chr11:46016400-46023000	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
46	chr11:46016400-46025200	Weak transcription	Right Atrium	heart
47	chr11:46016600-46019200	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
48	chr11:46016600-46019800	Enhancers	Fetal Heart	heart
49	chr11:46016600-46022800	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
50	chr11:46016600-46023000	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links