Variant report

Variant	rs228619
Chromosome Location	chr4:103569283-103569284
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr4:103563235..103566538-chr4:103568648..103571526,3	K562	blood:

Extended variants
information (count: 63 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:60)

rs_ID	r²[population]
rs1054029	0.82[CHB][hapmap]
rs1054037	0.82[CHB][hapmap];0.82[JPT][hapmap]
rs1077358	0.81[CHB][hapmap];0.81[JPT][hapmap]
rs11724614	0.82[CHB][hapmap];0.83[JPT][hapmap]
rs11727546	0.82[CHB][hapmap];0.82[JPT][hapmap]
rs12498722	0.82[CHB][hapmap];0.83[JPT][hapmap]
rs12644381	0.82[CHB][hapmap];0.83[JPT][hapmap]
rs12648696	0.80[CHB][hapmap]
rs13106304	0.82[CHB][hapmap];0.82[JPT][hapmap]
rs13106325	0.82[CHB][hapmap];0.82[JPT][hapmap]
rs1585214	0.82[JPT][hapmap]
rs1598856	0.81[JPT][hapmap]
rs17033015	0.83[CHB][hapmap];0.95[JPT][hapmap]
rs179195	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs2125211	0.82[CHB][hapmap];0.82[JPT][hapmap]
rs2272695	0.83[JPT][hapmap]
rs2272696	0.82[CHB][hapmap];0.83[JPT][hapmap]
rs2272697	0.82[CHB][hapmap];0.82[JPT][hapmap]
rs227276	0.96[CEU][hapmap];1.00[CHB][hapmap];0.96[JPT][hapmap]
rs227277	0.96[CEU][hapmap];1.00[CHB][hapmap];0.96[JPT][hapmap]
rs227361	0.88[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap]
rs228611	0.82[CHB][hapmap];0.82[JPT][hapmap]
rs228614	0.88[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap]
rs228617	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs228618	0.88[CEU][hapmap];0.87[CHB][hapmap];0.87[JPT][hapmap]
rs228623	0.84[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap]
rs230510	0.82[JPT][hapmap]
rs230530	0.81[JPT][hapmap]
rs2866407	0.82[CHB][hapmap];0.82[JPT][hapmap]
rs2866412	0.83[CHB][hapmap];0.83[JPT][hapmap]
rs2866413	0.82[CHB][hapmap];0.82[JPT][hapmap]
rs2866414	0.82[CHB][hapmap];0.82[JPT][hapmap]
rs2903283	0.84[JPT][hapmap]
rs3733202	0.82[CHB][hapmap];0.82[JPT][hapmap]
rs3774932	0.82[JPT][hapmap]
rs3774968	0.91[JPT][hapmap]
rs4013	0.82[CHB][hapmap];0.82[JPT][hapmap]
rs404574	0.84[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs434644	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs4496586	0.81[CEU][hapmap];0.82[CHB][hapmap];0.82[JPT][hapmap]
rs4547797	0.82[CHB][hapmap];0.82[JPT][hapmap]
rs4586937	0.82[JPT][hapmap]
rs5026472	0.82[CHB][hapmap];0.83[JPT][hapmap]
rs5026473	0.83[JPT][hapmap]
rs5026474	0.83[JPT][hapmap]
rs5026476	0.82[CHB][hapmap];0.83[JPT][hapmap]
rs6533020	0.82[CHB][hapmap];0.83[JPT][hapmap]
rs6533021	0.81[CHB][hapmap];0.85[JPT][hapmap]
rs6810869	0.81[CHB][hapmap];0.81[JPT][hapmap]
rs6812747	0.82[CHB][hapmap];0.83[JPT][hapmap]
rs6839064	0.83[CHB][hapmap];0.83[JPT][hapmap]
rs735403	0.82[CHB][hapmap];0.82[JPT][hapmap]
rs735404	0.82[CHB][hapmap];0.82[JPT][hapmap]
rs735405	0.82[CHB][hapmap];0.81[JPT][hapmap]
rs7674640	0.95[CHB][hapmap];0.83[JPT][hapmap]
rs7677509	0.83[CHB][hapmap];0.83[JPT][hapmap]
rs7699231	0.82[CHB][hapmap];0.83[JPT][hapmap]
rs7699678	0.82[CHB][hapmap];0.83[JPT][hapmap]
rs909349	0.82[CHB][hapmap];0.82[JPT][hapmap]
rs93059	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	esv1799158	chr4:103556316-103580296	Genic enhancers Weak transcription Enhancers Strong transcription Transcr. at gene 5' and 3' Flanking Active TSS ZNF genes & repeats Active TSS	TF binding region Chromatin interactive region	4 gene(s)	inside rSNPs	diseases
3	nsv1008110	chr4:103560583-103684526	Weak transcription Strong transcription Active TSS ZNF genes & repeats Flanking Active TSS Genic enhancers Enhancers Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs228619	MANBA	cis	multi-tissue	Pritchard
rs228619	KRT8P46	cis	lung	GTEx

Chromatin state (count:112 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:103536200-103595400	Weak transcription	Colonic Mucosa	Colon
2	chr4:103536600-103595800	Weak transcription	Placenta Amnion	Placenta Amnion
3	chr4:103541800-103571000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
4	chr4:103542400-103578800	Weak transcription	Psoas Muscle	Psoas
5	chr4:103542400-103594400	Weak transcription	K562	blood
6	chr4:103542400-103617400	Weak transcription	Rectal Smooth Muscle	rectum
7	chr4:103545200-103592000	Weak transcription	Fetal Muscle Trunk	muscle
8	chr4:103547000-103658200	Weak transcription	Small Intestine	intestine
9	chr4:103549000-103570400	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
10	chr4:103549800-103572000	Weak transcription	Placenta	Placenta
11	chr4:103550200-103582800	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
12	chr4:103550400-103573000	Weak transcription	Fetal Kidney	kidney
13	chr4:103551000-103607600	Strong transcription	Primary monocytes fromperipheralblood	blood
14	chr4:103551000-103607800	Strong transcription	Monocytes-CD14+_RO01746	blood
15	chr4:103552400-103579600	Weak transcription	Fetal Heart	heart
16	chr4:103553000-103651400	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
17	chr4:103553200-103591200	Weak transcription	H9 Cell Line	embryonic stem cell
18	chr4:103553400-103608200	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
19	chr4:103553400-103651400	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
20	chr4:103556000-103570400	Weak transcription	Fetal Brain Female	brain
21	chr4:103556000-103593800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
22	chr4:103556200-103571200	Weak transcription	iPS-18 Cell Line	embryonic stem cell
23	chr4:103556200-103572800	Weak transcription	Right Ventricle	heart
24	chr4:103556200-103581000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
25	chr4:103556200-103581000	Weak transcription	Gastric	stomach
26	chr4:103556200-103582200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
27	chr4:103556200-103588600	Weak transcription	Esophagus	oesophagus
28	chr4:103556200-103650400	Weak transcription	Pancreas	Pancrea
29	chr4:103556600-103569400	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
30	chr4:103557200-103573600	Weak transcription	A549	lung
31	chr4:103557600-103585200	Weak transcription	Skeletal Muscle Male	skeletal muscle
32	chr4:103557600-103626400	Weak transcription	Lung	lung
33	chr4:103558800-103569400	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
34	chr4:103558800-103569800	Weak transcription	Rectal Mucosa Donor 31	rectum
35	chr4:103559200-103571000	Weak transcription	HepG2	liver
36	chr4:103559200-103590000	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
37	chr4:103559600-103617200	Weak transcription	Fetal Stomach	stomach
38	chr4:103559800-103569800	Weak transcription	Fetal Lung	lung
39	chr4:103560000-103595400	Weak transcription	Primary T helper naive cells from peripheral blood	blood
40	chr4:103560400-103570800	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
41	chr4:103560600-103584000	Weak transcription	iPS-15b Cell Line	embryonic stem cell
42	chr4:103560800-103569600	Weak transcription	Fetal Intestine Large	intestine
43	chr4:103560800-103571200	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
44	chr4:103560800-103585200	Weak transcription	Sigmoid Colon	Sigmoid Colon
45	chr4:103560800-103587800	Weak transcription	Colon Smooth Muscle	Colon
46	chr4:103561000-103569800	Weak transcription	Stomach Smooth Muscle	stomach
47	chr4:103561000-103570000	Weak transcription	Duodenum Mucosa	Duodenum
48	chr4:103561000-103570200	Weak transcription	Dnd41	blood
49	chr4:103561000-103570400	Weak transcription	Left Ventricle	heart
50	chr4:103561000-103570400	Weak transcription	Ovary	ovary

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links