Variant report

Variant	rs6830518
Chromosome Location	chr4:57306795-57306796
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr4:57268050..57270580-chr4:57305183..57307241,2	K562	blood:
2	chr4:57298117..57310780-chr4:57324651..57337770,39	MCF-7	breast:
3	chr4:57306221..57310097-chr4:57330857..57334001,4	MCF-7	breast:

Variant related genes	Relation type
ENSG00000174780	Chromatin interaction
ENSG00000270109	Chromatin interaction

Extended variants
information (count: 61 )
Associated
traits (count: 5 )

rSNPs within LD-proxies of this variant (count:57)

rs_ID	r²[population]
rs10009543	0.87[EUR][1000 genomes]
rs10015221	1.00[CEU][hapmap];0.87[EUR][1000 genomes]
rs10518	0.81[LWK][hapmap]
rs1060472	0.88[MEX][hapmap]
rs10866433	0.90[YRI][hapmap];0.83[AFR][1000 genomes]
rs11133439	0.91[JPT][hapmap]
rs11133442	0.88[MEX][hapmap]
rs11610	0.87[ASW][hapmap];0.91[CHB][hapmap];1.00[CHD][hapmap];0.83[GIH][hapmap];1.00[JPT][hapmap];0.93[LWK][hapmap];0.88[MEX][hapmap];0.80[TSI][hapmap];1.00[YRI][hapmap];0.93[AFR][1000 genomes];0.85[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs11724302	0.95[JPT][hapmap]
rs12498340	0.80[MEX][hapmap]
rs12504291	0.80[CEU][hapmap];0.80[JPT][hapmap]
rs12646703	1.00[ASW][hapmap];0.94[CEU][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];1.00[GIH][hapmap];0.95[JPT][hapmap];0.98[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];0.94[TSI][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12648503	0.85[AFR][1000 genomes];0.88[ASN][1000 genomes]
rs13141793	0.91[JPT][hapmap]
rs1356787	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.98[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs17051687	1.00[CEU][hapmap];0.92[TSI][hapmap]
rs17086696	0.80[MEX][hapmap]
rs17086793	0.96[AFR][1000 genomes];0.85[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs17086803	0.90[YRI][hapmap];0.83[AFR][1000 genomes]
rs17086883	0.86[AFR][1000 genomes];0.93[ASN][1000 genomes]
rs17086887	0.86[AFR][1000 genomes];0.93[ASN][1000 genomes]
rs1967559	0.84[MEX][hapmap]
rs2049087	0.89[TSI][hapmap]
rs2292985	0.95[JPT][hapmap]
rs4383672	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4524447	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4615235	0.95[AFR][1000 genomes];0.85[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs4616819	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4865090	0.95[JPT][hapmap]
rs4865102	0.87[EUR][1000 genomes]
rs4865104	0.81[AFR][1000 genomes]
rs4865105	0.84[AFR][1000 genomes];0.83[AMR][1000 genomes]
rs4865110	0.83[AFR][1000 genomes];0.92[ASN][1000 genomes]
rs57523479	0.90[ASN][1000 genomes]
rs58975286	0.84[AFR][1000 genomes];0.86[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs6554348	0.95[JPT][hapmap]
rs6554349	0.95[JPT][hapmap]
rs6584	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.98[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs66599079	0.86[AFR][1000 genomes];0.93[ASN][1000 genomes]
rs68101565	0.85[AFR][1000 genomes];0.92[ASN][1000 genomes]
rs6811482	0.86[AFR][1000 genomes];0.93[ASN][1000 genomes]
rs6816268	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6818715	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6819534	1.00[CEU][hapmap];0.92[TSI][hapmap];0.88[EUR][1000 genomes]
rs6820417	0.87[ASN][1000 genomes]
rs6832168	0.96[AFR][1000 genomes];0.85[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs6842307	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6848187	0.94[ASW][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];0.95[LWK][hapmap];0.88[MEX][hapmap];0.80[TSI][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];0.87[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs7664841	0.80[MEX][hapmap]
rs7670198	0.85[AFR][1000 genomes];0.94[ASN][1000 genomes]
rs7689163	1.00[CHB][hapmap];0.95[JPT][hapmap];1.00[YRI][hapmap];0.84[AFR][1000 genomes];0.88[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs7692073	0.87[EUR][1000 genomes]
rs7692385	0.95[JPT][hapmap]
rs7693137	0.95[JPT][hapmap]
rs7694047	0.90[EUR][1000 genomes]
rs8340	0.80[MEX][hapmap]
rs9996593	0.89[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	nsv999639	chr4:56942917-57401310	Weak transcription Flanking Active TSS Bivalent/Poised TSS Active TSS Strong transcription Enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	50 gene(s)	inside rSNPs	diseases
2	nsv1014045	chr4:56942917-57404511	Weak transcription Strong transcription Enhancers Active TSS ZNF genes & repeats Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	50 gene(s)	inside rSNPs	diseases
3	nsv868815	chr4:57114268-58084688	Weak transcription Bivalent Enhancer Flanking Active TSS Active TSS Enhancers Strong transcription Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	88 gene(s)	inside rSNPs	diseases
4	nsv530121	chr4:57167367-57695576	Flanking Bivalent TSS/Enh Enhancers Flanking Active TSS Weak transcription Active TSS Genic enhancers Strong transcription Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	59 gene(s)	inside rSNPs	diseases

mRNA abundance (count:5)

SNP	Gene	Cis/trans	Tissue	Source
rs6830518	SRP72	cis	cerebellum	SCAN
rs6830518	PAICS	cis	cerebellum	SCAN
rs6830518	AASDH	cis	cerebellum	SCAN
rs6830518	SRP72	cis	multi-tissue	Pritchard
rs6830518	AASDH	cis	parietal	SCAN

Chromatin state (count:121 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:57303000-57309000	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
2	chr4:57303400-57330800	Weak transcription	Spleen	Spleen
3	chr4:57303800-57308400	Weak transcription	Sigmoid Colon	Sigmoid Colon
4	chr4:57303800-57326000	Weak transcription	Gastric	stomach
5	chr4:57303800-57331000	Weak transcription	Stomach Mucosa	stomach
6	chr4:57303800-57332000	Weak transcription	Small Intestine	intestine
7	chr4:57304000-57306800	Enhancers	Liver	Liver
8	chr4:57304000-57312000	Weak transcription	Left Ventricle	heart
9	chr4:57304000-57315800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
10	chr4:57304000-57330000	Weak transcription	Pancreas	Pancrea
11	chr4:57304000-57330000	Weak transcription	Right Ventricle	heart
12	chr4:57304000-57331800	Weak transcription	Esophagus	oesophagus
13	chr4:57304200-57307800	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
14	chr4:57304200-57307800	Weak transcription	Fetal Muscle Trunk	muscle
15	chr4:57304200-57308000	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
16	chr4:57304200-57308000	Weak transcription	Placenta	Placenta
17	chr4:57304200-57308200	Weak transcription	Brain Hippocampus Middle	brain
18	chr4:57304200-57314600	Weak transcription	Skeletal Muscle Male	skeletal muscle
19	chr4:57304200-57314800	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
20	chr4:57304200-57317400	Weak transcription	Thymus	Thymus
21	chr4:57304200-57318800	Weak transcription	Colon Smooth Muscle	Colon
22	chr4:57304200-57319200	Weak transcription	Stomach Smooth Muscle	stomach
23	chr4:57304200-57331800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
24	chr4:57304400-57307000	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
25	chr4:57304400-57307000	Weak transcription	Primary T helper cells fromperipheralblood	blood
26	chr4:57304400-57307000	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
27	chr4:57304400-57307200	Weak transcription	Primary T cells from cord blood	blood
28	chr4:57304400-57307400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
29	chr4:57304400-57307600	Weak transcription	Primary hematopoietic stem cells	blood
30	chr4:57304400-57307800	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
31	chr4:57304400-57307800	Weak transcription	Fetal Brain Male	brain
32	chr4:57304400-57307800	Weak transcription	Fetal Lung	lung
33	chr4:57304400-57307800	Weak transcription	HSMM	muscle
34	chr4:57304400-57307800	Weak transcription	NHDF-Ad	bronchial
35	chr4:57304400-57308000	Weak transcription	Placenta Amnion	Placenta Amnion
36	chr4:57304400-57308000	Weak transcription	Rectal Mucosa Donor 29	rectum
37	chr4:57304400-57308000	Weak transcription	Osteobl	bone
38	chr4:57304400-57308200	Weak transcription	Primary B cells from peripheral blood	blood
39	chr4:57304400-57308200	Weak transcription	Skeletal Muscle Female	skeletal muscle
40	chr4:57304400-57308400	Weak transcription	Primary monocytes fromperipheralblood	blood
41	chr4:57304400-57308600	Weak transcription	Brain Anterior Caudate	brain
42	chr4:57304400-57308600	Weak transcription	Fetal Kidney	kidney
43	chr4:57304400-57310400	Weak transcription	NHLF	lung
44	chr4:57304400-57312600	Weak transcription	Rectal Mucosa Donor 31	rectum
45	chr4:57304400-57314000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
46	chr4:57304400-57314000	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
47	chr4:57304400-57314600	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
48	chr4:57304400-57314600	Weak transcription	Duodenum Smooth Muscle	Duodenum
49	chr4:57304400-57314600	Weak transcription	Fetal Brain Female	brain
50	chr4:57304400-57314600	Weak transcription	Monocytes-CD14+_RO01746	blood

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links