Variant report

Variant	rs230542
Chromosome Location	chr4:103498455-103498456
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr4:103495819..103498669-chr4:103504146..103506135,2	MCF-7	breast:
2	chr4:103489104..103492778-chr4:103495068..103498574,4	MCF-7	breast:
3	chr4:103419957..103425638-chr4:103495824..103504548,11	MCF-7	breast:

Variant related genes	Relation type
ENSG00000109320	Chromatin interaction
ENSG00000260651	Chromatin interaction

Extended variants
information (count: 79 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:75)

rs_ID	r²[population]
rs1005819	1.00[JPT][hapmap]
rs1020759	0.90[JPT][hapmap]
rs1020760	1.00[JPT][hapmap]
rs11722146	0.88[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap]
rs11723120	0.87[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs118882	1.00[CEU][hapmap];0.95[CHB][hapmap];0.95[CHD][hapmap];0.90[GIH][hapmap];0.91[JPT][hapmap];0.96[MEX][hapmap];0.95[TSI][hapmap]
rs12509517	0.88[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap]
rs12648696	0.94[CHB][hapmap]
rs1585213	0.91[JPT][hapmap];0.92[MEX][hapmap];0.83[TSI][hapmap]
rs1585215	1.00[CEU][hapmap];0.86[CHB][hapmap];0.91[JPT][hapmap];1.00[YRI][hapmap]
rs1598859	0.88[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.96[MEX][hapmap];0.92[TSI][hapmap]
rs1599961	0.91[JPT][hapmap];0.92[MEX][hapmap];0.81[TSI][hapmap]
rs1609798	0.82[CHB][hapmap];0.82[CHD][hapmap];0.80[GIH][hapmap]
rs17032683	1.00[YRI][hapmap]
rs17032705	0.91[JPT][hapmap];0.92[MEX][hapmap];0.83[TSI][hapmap]
rs170731	1.00[CEU][hapmap];0.95[CHB][hapmap];0.90[JPT][hapmap]
rs1801	0.88[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs2085549	1.00[YRI][hapmap]
rs2168805	0.86[JPT][hapmap]
rs230491	0.92[CEU][hapmap];0.95[CHB][hapmap];0.91[JPT][hapmap]
rs230492	1.00[CEU][hapmap];0.95[CHB][hapmap];0.90[JPT][hapmap];1.00[YRI][hapmap]
rs230493	0.92[CEU][hapmap];0.95[CHB][hapmap];0.90[CHD][hapmap];0.92[GIH][hapmap];0.91[JPT][hapmap];0.87[MEX][hapmap];0.92[TSI][hapmap]
rs230495	0.90[JPT][hapmap]
rs230496	0.90[JPT][hapmap]
rs230498	0.88[CEU][hapmap];0.95[CHB][hapmap];0.95[CHD][hapmap];1.00[GIH][hapmap];0.91[JPT][hapmap];0.92[MEX][hapmap];0.92[TSI][hapmap]
rs230500	0.88[CEU][hapmap];0.95[CHB][hapmap];0.95[CHD][hapmap];1.00[GIH][hapmap];0.91[JPT][hapmap];0.92[MEX][hapmap];0.92[TSI][hapmap]
rs230504	0.92[CEU][hapmap];0.95[CHB][hapmap];0.95[CHD][hapmap];0.90[GIH][hapmap];0.91[JPT][hapmap];0.96[MEX][hapmap];0.95[TSI][hapmap]
rs230505	0.84[CHD][hapmap];0.91[JPT][hapmap];0.88[MEX][hapmap]
rs230509	1.00[CEU][hapmap];0.95[CHB][hapmap];0.91[JPT][hapmap];1.00[YRI][hapmap]
rs230511	1.00[CEU][hapmap]
rs230514	1.00[CEU][hapmap];0.95[CHB][hapmap];0.91[JPT][hapmap]
rs230515	1.00[CEU][hapmap];0.94[CHB][hapmap];0.89[JPT][hapmap]
rs230516	1.00[CEU][hapmap];0.95[CHB][hapmap];0.89[JPT][hapmap]
rs230519	1.00[CEU][hapmap];0.95[CHB][hapmap];0.95[CHD][hapmap];0.90[GIH][hapmap];0.91[JPT][hapmap];1.00[MEX][hapmap];0.97[TSI][hapmap]
rs230520	1.00[ASW][hapmap];1.00[CEU][hapmap];0.95[CHB][hapmap];0.95[CHD][hapmap];0.90[GIH][hapmap];0.91[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap]
rs230521	0.91[JPT][hapmap]
rs230525	0.96[CEU][hapmap];0.95[CHB][hapmap];0.95[CHD][hapmap];0.84[GIH][hapmap];0.91[JPT][hapmap];0.95[TSI][hapmap]
rs230526	0.83[CHD][hapmap];0.91[JPT][hapmap];0.88[MEX][hapmap]
rs230528	0.84[CHD][hapmap];0.91[JPT][hapmap];0.88[MEX][hapmap]
rs230529	0.84[CHD][hapmap];0.91[JPT][hapmap];0.88[MEX][hapmap]
rs230531	1.00[CEU][hapmap];0.95[CHB][hapmap];0.95[CHD][hapmap];0.90[GIH][hapmap];0.91[JPT][hapmap];0.95[MEX][hapmap];0.97[TSI][hapmap]
rs230532	1.00[CEU][hapmap];0.95[CHB][hapmap];0.95[CHD][hapmap];0.90[GIH][hapmap];0.91[JPT][hapmap];1.00[MEX][hapmap];0.97[TSI][hapmap]
rs230533	0.92[CEU][hapmap];0.95[CHB][hapmap];0.91[JPT][hapmap]
rs230534	1.00[CEU][hapmap];0.95[CHB][hapmap];0.90[JPT][hapmap];1.00[YRI][hapmap]
rs230535	0.96[CEU][hapmap];0.95[CHB][hapmap];0.95[CHD][hapmap];0.90[GIH][hapmap];0.91[JPT][hapmap];1.00[MEX][hapmap];0.97[TSI][hapmap]
rs230539	1.00[CEU][hapmap];1.00[CHB][hapmap];0.86[JPT][hapmap];1.00[YRI][hapmap]
rs230540	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap]
rs230541	0.89[CHD][hapmap];0.86[GIH][hapmap];1.00[JPT][hapmap];0.87[MEX][hapmap]
rs2903281	1.00[YRI][hapmap]
rs3755867	0.95[CHB][hapmap];1.00[JPT][hapmap]
rs3774933	0.90[JPT][hapmap]
rs3774936	1.00[CEU][hapmap];0.86[CHB][hapmap];0.91[JPT][hapmap]
rs3774937	1.00[ASW][hapmap];1.00[CEU][hapmap];0.86[CHB][hapmap];0.90[GIH][hapmap];0.91[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap]
rs3774938	0.91[JPT][hapmap]
rs3774956	1.00[JPT][hapmap]
rs3774959	0.88[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.80[MEX][hapmap];0.92[TSI][hapmap]
rs3774963	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs3774964	0.89[CHD][hapmap];0.83[GIH][hapmap];1.00[JPT][hapmap]
rs3817685	1.00[JPT][hapmap]
rs3821958	1.00[JPT][hapmap]
rs4235404	1.00[CEU][hapmap];0.85[CHB][hapmap];0.91[JPT][hapmap];1.00[YRI][hapmap]
rs4456957	1.00[YRI][hapmap]
rs4648011	0.83[CHD][hapmap];0.91[JPT][hapmap];0.92[MEX][hapmap]
rs4648055	0.84[ASW][hapmap];0.88[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MKK][hapmap];0.84[TSI][hapmap];1.00[YRI][hapmap]
rs4648058	0.80[CHB][hapmap];1.00[JPT][hapmap]
rs4648068	1.00[CHB][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap]
rs4648085	1.00[YRI][hapmap]
rs4648133	0.88[CEU][hapmap];0.86[CHB][hapmap];0.80[GIH][hapmap];0.81[TSI][hapmap]
rs4698858	1.00[JPT][hapmap]
rs4698861	0.83[CEU][hapmap];0.81[JPT][hapmap]
rs4698863	0.81[JPT][hapmap]
rs4699030	0.89[CHD][hapmap];0.86[GIH][hapmap];1.00[JPT][hapmap];0.88[MEX][hapmap]
rs747559	0.91[JPT][hapmap];0.84[MEX][hapmap];0.81[TSI][hapmap]
rs9790601	0.91[CHB][hapmap];1.00[JPT][hapmap]
rs980455	0.91[JPT][hapmap];0.84[MEX][hapmap];0.83[TSI][hapmap]

Variant overlapped rSNPs/rCNVs (count:4 , 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	nsv1003490	chr4:103391483-103521772	Weak transcription Genic enhancers Enhancers Flanking Active TSS Active TSS Strong transcription Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	25 gene(s)	inside rSNPs	diseases
3	nsv1004030	chr4:103419352-103504042	Weak transcription Strong transcription Flanking Active TSS Active TSS Genic enhancers Enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	24 gene(s)	inside rSNPs	diseases
4	nsv537203	chr4:103419352-103504042	Active TSS Flanking Active TSS Enhancers Strong transcription Weak transcription Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	24 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs230542	MANBA	cis	parietal	SCAN
rs230542	ADH7	cis	cerebellum	SCAN
rs230542	CISD2	cis	parietal	SCAN

Chromatin state (count:110 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:103466800-103498600	Weak transcription	Placenta	Placenta
2	chr4:103473400-103524600	Weak transcription	Fetal Brain Male	brain
3	chr4:103478200-103511800	Weak transcription	Pancreatic Islets	Pancreatic Islet
4	chr4:103482200-103498800	Weak transcription	Brain Cingulate Gyrus	brain
5	chr4:103482400-103498600	Weak transcription	Duodenum Smooth Muscle	Duodenum
6	chr4:103483000-103518600	Weak transcription	Small Intestine	intestine
7	chr4:103483200-103516600	Weak transcription	Brain Angular Gyrus	brain
8	chr4:103483400-103541600	Weak transcription	K562	blood
9	chr4:103488200-103520000	Weak transcription	Fetal Kidney	kidney
10	chr4:103488400-103498800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
11	chr4:103488600-103498800	Weak transcription	Fetal Heart	heart
12	chr4:103488600-103498800	Weak transcription	Psoas Muscle	Psoas
13	chr4:103489000-103498800	Weak transcription	HSMM	muscle
14	chr4:103490800-103519200	Weak transcription	Stomach Mucosa	stomach
15	chr4:103491000-103498800	Weak transcription	Muscle Satellite Cultured Cells	--
16	chr4:103495800-103511800	Strong transcription	Primary B cells from cord blood	blood
17	chr4:103495800-103516400	Weak transcription	NHLF	lung
18	chr4:103496000-103500000	Genic enhancers	Primary T helper cells PMA-I stimulated	--
19	chr4:103496200-103513200	Strong transcription	Monocytes-CD14+_RO01746	blood
20	chr4:103496400-103510000	Strong transcription	Primary hematopoietic stem cells short term culture	blood
21	chr4:103496800-103499200	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
22	chr4:103497000-103498800	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
23	chr4:103497000-103498800	Weak transcription	Primary T killer memory cells from peripheral blood	blood
24	chr4:103497000-103499600	Weak transcription	A549	lung
25	chr4:103497000-103499800	Weak transcription	HUES48 Cell Line	embryonic stem cell
26	chr4:103497000-103500000	Weak transcription	Hela-S3	cervix
27	chr4:103497000-103504000	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
28	chr4:103497000-103516600	Weak transcription	Brain Substantia Nigra	brain
29	chr4:103497200-103498800	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
30	chr4:103497200-103498800	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
31	chr4:103497200-103498800	Weak transcription	Primary T helper naive cells from peripheral blood	blood
32	chr4:103497200-103499600	Weak transcription	Cortex derived primary cultured neurospheres	brain
33	chr4:103497200-103499800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
34	chr4:103497200-103499800	Strong transcription	GM12878-XiMat	blood
35	chr4:103497400-103499200	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
36	chr4:103497400-103513000	Strong transcription	Primary monocytes fromperipheralblood	blood
37	chr4:103497600-103500000	Strong transcription	Primary T cells from cord blood	blood
38	chr4:103497600-103504800	Strong transcription	Stomach Smooth Muscle	stomach
39	chr4:103497600-103505200	Strong transcription	Primary hematopoietic stem cells	blood
40	chr4:103497600-103505400	Strong transcription	Breast Myoepithelial Primary Cells	Breast
41	chr4:103497600-103506600	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
42	chr4:103497600-103507000	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
43	chr4:103497600-103533400	Strong transcription	Primary B cells from peripheral blood	blood
44	chr4:103497800-103499000	Strong transcription	Primary T helper naive cells fromperipheralblood	blood
45	chr4:103497800-103499200	Strong transcription	Primary T helper 17 cells PMA-I stimulated	--
46	chr4:103497800-103500000	Strong transcription	Colon Smooth Muscle	Colon
47	chr4:103497800-103500400	Strong transcription	Brain Inferior Temporal Lobe	brain
48	chr4:103497800-103501400	Strong transcription	Fetal Intestine Large	intestine
49	chr4:103497800-103505800	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
50	chr4:103497800-103505800	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin

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