Variant report

Variant	rs4698861
Chromosome Location	chr4:103545487-103545488
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr4:103545322..103548006-chr4:103788328..103790591,2	MCF-7	breast:
2	chr4:103544609..103545517-chr4:103930008..103930946,3	MCF-7	breast:
3	chr4:103543864..103546409-chr4:103549438..103551075,2	K562	blood:
4	chr4:103534750..103537170-chr4:103544463..103546367,2	K562	blood:

Variant related genes	Relation type
ENSG00000145354	Chromatin interaction
ENSG00000109332	Chromatin interaction

Extended variants
information (count: 43 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:40)

rs_ID	r²[population]
rs1005819	0.81[JPT][hapmap]
rs1020760	0.81[JPT][hapmap]
rs11722146	0.92[CEU][hapmap];0.81[CHB][hapmap];0.81[JPT][hapmap]
rs118882	0.83[CEU][hapmap]
rs12509403	0.84[CEU][hapmap]
rs12509517	0.92[CEU][hapmap];0.81[CHB][hapmap];0.81[JPT][hapmap]
rs12648696	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs1585215	0.83[CEU][hapmap]
rs1598859	0.81[JPT][hapmap]
rs1609798	0.91[CEU][hapmap];0.95[CHB][hapmap];0.90[CHD][hapmap];0.90[GIH][hapmap];0.81[JPT][hapmap];0.89[TSI][hapmap]
rs170731	0.83[CEU][hapmap]
rs1801	0.81[JPT][hapmap]
rs230492	0.81[CEU][hapmap]
rs230509	0.82[CEU][hapmap]
rs230511	0.83[CEU][hapmap]
rs230514	0.83[CEU][hapmap]
rs230516	0.81[CEU][hapmap]
rs230519	0.83[CEU][hapmap]
rs230520	0.83[CEU][hapmap]
rs230531	0.83[CEU][hapmap]
rs230532	0.83[CEU][hapmap]
rs230534	0.82[CEU][hapmap]
rs230539	0.83[CEU][hapmap]
rs230540	0.83[CEU][hapmap];0.81[JPT][hapmap]
rs230541	0.81[JPT][hapmap]
rs230542	0.83[CEU][hapmap];0.81[JPT][hapmap]
rs3755867	0.87[CEU][hapmap];0.81[CHB][hapmap];0.81[JPT][hapmap]
rs3774936	0.83[CEU][hapmap]
rs3774937	0.83[CEU][hapmap]
rs3774959	0.81[JPT][hapmap]
rs3774963	0.87[CEU][hapmap]
rs3821958	0.81[JPT][hapmap]
rs4235404	0.82[CEU][hapmap]
rs4648055	0.92[CEU][hapmap];0.81[JPT][hapmap]
rs4648068	0.87[CEU][hapmap];0.81[JPT][hapmap]
rs4648133	0.92[CEU][hapmap];0.90[CHB][hapmap];0.85[GIH][hapmap];0.83[TSI][hapmap]
rs4698858	0.82[JPT][hapmap]
rs4698863	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap]
rs4699030	0.81[JPT][hapmap]
rs9790601	0.87[CEU][hapmap];0.85[CHB][hapmap];0.81[JPT][hapmap]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv830020	chr4:103387343-103581284	Strong transcription Weak transcription Genic enhancers Enhancers Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh 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	29 gene(s)	inside rSNPs	diseases
2	nsv1003618	chr4:103530465-103562161	Enhancers Weak transcription Strong transcription Flanking Active TSS Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats Active TSS	Chromatin interactive region miRNA target site	10 gene(s)	inside rSNPs	diseases
3	esv3350888	chr4:103541304-103545802	Weak transcription Enhancers Flanking Active TSS Active TSS	Chromatin interactive region	7 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs4698861	MANBA	cis	multi-tissue	Pritchard
rs4698861	ADH6	cis	cerebellum	SCAN
rs4698861	COL9A2	trans	multi-tissue	Pritchard

Chromatin state (count:107 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:103521400-103554400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
2	chr4:103534000-103546200	Weak transcription	Small Intestine	intestine
3	chr4:103536200-103552800	Weak transcription	Ovary	ovary
4	chr4:103536200-103595400	Weak transcription	Colonic Mucosa	Colon
5	chr4:103536400-103553400	Weak transcription	Fetal Brain Female	brain
6	chr4:103536600-103550800	Weak transcription	Thymus	Thymus
7	chr4:103536600-103562600	Weak transcription	Brain Germinal Matrix	brain
8	chr4:103536600-103595800	Weak transcription	Placenta Amnion	Placenta Amnion
9	chr4:103537800-103546200	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
10	chr4:103538000-103545600	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
11	chr4:103538000-103546600	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
12	chr4:103538000-103552800	Weak transcription	Spleen	Spleen
13	chr4:103538200-103546200	Weak transcription	Primary T helper naive cells from peripheral blood	blood
14	chr4:103538200-103549400	Weak transcription	Fetal Lung	lung
15	chr4:103538200-103550800	Weak transcription	Lung	lung
16	chr4:103538200-103552400	Weak transcription	Primary hematopoietic stem cells	blood
17	chr4:103538200-103555600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
18	chr4:103538200-103555600	Weak transcription	Gastric	stomach
19	chr4:103538200-103555800	Weak transcription	Esophagus	oesophagus
20	chr4:103538600-103546600	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
21	chr4:103538600-103552800	Weak transcription	HUES48 Cell Line	embryonic stem cell
22	chr4:103538800-103546000	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
23	chr4:103538800-103546200	Weak transcription	Primary monocytes fromperipheralblood	blood
24	chr4:103538800-103546200	Weak transcription	Primary T cells fromperipheralblood	blood
25	chr4:103538800-103546200	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
26	chr4:103538800-103546200	Weak transcription	Dnd41	blood
27	chr4:103538800-103546400	Weak transcription	Primary T killer memory cells from peripheral blood	blood
28	chr4:103538800-103546400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
29	chr4:103538800-103546400	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
30	chr4:103538800-103546600	Weak transcription	Primary B cells from peripheral blood	blood
31	chr4:103538800-103552800	Weak transcription	H1 Cell Line	embryonic stem cell
32	chr4:103538800-103552800	Weak transcription	H9 Cell Line	embryonic stem cell
33	chr4:103538800-103552800	Weak transcription	Adipose Nuclei	Adipose
34	chr4:103538800-103555600	Weak transcription	Right Ventricle	heart
35	chr4:103538800-103555800	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
36	chr4:103539000-103546200	Weak transcription	Primary neutrophils fromperipheralblood	blood
37	chr4:103539000-103546200	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
38	chr4:103539000-103546200	Weak transcription	Monocytes-CD14+_RO01746	blood
39	chr4:103539000-103546600	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
40	chr4:103540000-103546400	Weak transcription	Primary B cells from cord blood	blood
41	chr4:103540200-103546600	Weak transcription	GM12878-XiMat	blood
42	chr4:103541800-103562400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
43	chr4:103541800-103571000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
44	chr4:103542000-103547400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
45	chr4:103542000-103552400	Weak transcription	iPS-20b Cell Line	embryonic stem cell
46	chr4:103542200-103546200	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
47	chr4:103542200-103546200	Weak transcription	Primary T helper cells fromperipheralblood	blood
48	chr4:103542200-103552000	Weak transcription	Stomach Smooth Muscle	stomach
49	chr4:103542200-103552800	Weak transcription	iPS-18 Cell Line	embryonic stem cell
50	chr4:103542200-103552800	Weak transcription	Colon Smooth Muscle	Colon

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links