Variant report

Variant	rs228611
Chromosome Location	chr4:103561709-103561710
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	chr4:103559305..103561876-chr4:103747638..103749966,2	K562	blood:

Variant related genes	Relation type
ENSG00000246560	Chromatin interaction
ENSG00000109332	Chromatin interaction

Extended variants
information (count: 56 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:52)

rs_ID	r²[population]
rs1054029	0.92[CEU][hapmap];0.91[CHB][hapmap];0.88[CHD][hapmap];0.93[GIH][hapmap];0.85[JPT][hapmap];0.85[MEX][hapmap];0.85[TSI][hapmap]
rs1054037	0.88[CEU][hapmap];0.91[CHB][hapmap];0.88[CHD][hapmap];0.93[GIH][hapmap];0.91[JPT][hapmap];0.85[TSI][hapmap]
rs1077358	0.91[CEU][hapmap];0.90[CHB][hapmap];0.90[JPT][hapmap]
rs11724614	0.88[CEU][hapmap];0.91[CHB][hapmap];0.91[JPT][hapmap]
rs11727546	0.92[CEU][hapmap];0.86[CHB][hapmap];0.90[JPT][hapmap]
rs12498722	0.92[CEU][hapmap];0.91[CHB][hapmap];0.91[JPT][hapmap]
rs12644381	0.88[CEU][hapmap];0.91[CHB][hapmap];0.91[JPT][hapmap]
rs13106304	0.92[CEU][hapmap];0.91[CHB][hapmap];0.90[JPT][hapmap]
rs13106325	0.92[CEU][hapmap];0.91[CHB][hapmap];0.90[JPT][hapmap]
rs17033015	0.80[JPT][hapmap]
rs179195	0.82[CHB][hapmap];0.83[GIH][hapmap];0.82[JPT][hapmap];0.85[TSI][hapmap]
rs2125211	0.96[CEU][hapmap];0.91[CHB][hapmap];0.88[GIH][hapmap];0.91[JPT][hapmap]
rs2272695	0.92[CEU][hapmap];0.87[CHB][hapmap];0.91[JPT][hapmap]
rs2272696	0.92[CEU][hapmap];0.91[CHB][hapmap];0.91[JPT][hapmap]
rs2272697	0.92[CEU][hapmap];0.91[CHB][hapmap];0.88[CHD][hapmap];0.93[GIH][hapmap];0.91[JPT][hapmap];0.81[MEX][hapmap];0.85[TSI][hapmap]
rs227276	0.82[CHB][hapmap]
rs227277	0.82[CHB][hapmap]
rs227361	0.89[CEU][hapmap];0.82[CHB][hapmap];0.85[GIH][hapmap];0.82[JPT][hapmap];0.84[MEX][hapmap];0.93[TSI][hapmap]
rs228614	0.89[CEU][hapmap];0.82[CHB][hapmap];0.85[GIH][hapmap];0.82[JPT][hapmap];0.84[MEX][hapmap];0.93[TSI][hapmap]
rs228617	0.82[CHB][hapmap];0.80[GIH][hapmap];0.82[JPT][hapmap];0.85[TSI][hapmap]
rs228618	0.89[CEU][hapmap];0.87[CHB][hapmap];0.84[CHD][hapmap];0.83[GIH][hapmap];0.95[JPT][hapmap];0.84[MEX][hapmap];0.96[TSI][hapmap]
rs228619	0.82[CHB][hapmap];0.82[JPT][hapmap]
rs228623	0.85[CEU][hapmap];0.86[CHB][hapmap];0.82[GIH][hapmap];0.91[TSI][hapmap]
rs2866407	0.92[CEU][hapmap];0.91[CHB][hapmap];0.90[JPT][hapmap]
rs2866412	0.92[CEU][hapmap];0.91[CHB][hapmap];0.91[JPT][hapmap]
rs2866413	0.92[CEU][hapmap];0.91[CHB][hapmap];0.91[CHD][hapmap];0.93[GIH][hapmap];0.91[JPT][hapmap];0.81[MEX][hapmap];0.85[TSI][hapmap]
rs2866414	0.92[CEU][hapmap];0.91[CHB][hapmap];0.91[CHD][hapmap];0.93[GIH][hapmap];0.91[JPT][hapmap];0.81[MEX][hapmap];0.85[TSI][hapmap]
rs2903283	0.91[CEU][hapmap];0.90[CHB][hapmap];0.89[JPT][hapmap]
rs3733202	0.89[CEU][hapmap];0.91[CHB][hapmap];0.91[CHD][hapmap];0.93[GIH][hapmap];0.91[JPT][hapmap];0.85[TSI][hapmap]
rs4013	0.88[CEU][hapmap];0.91[CHB][hapmap];0.88[CHD][hapmap];0.93[GIH][hapmap];0.91[JPT][hapmap];0.81[MEX][hapmap];0.85[TSI][hapmap]
rs404574	0.87[CEU][hapmap];0.84[CHB][hapmap];0.83[JPT][hapmap]
rs434644	0.81[CHB][hapmap];0.80[JPT][hapmap]
rs4496586	0.82[CEU][hapmap];0.91[CHB][hapmap];0.90[JPT][hapmap]
rs4547797	0.92[CEU][hapmap];0.91[CHB][hapmap];0.91[CHD][hapmap];0.93[GIH][hapmap];0.91[JPT][hapmap];0.81[MEX][hapmap];0.85[TSI][hapmap]
rs4586937	0.92[CEU][hapmap];0.86[CHB][hapmap];0.88[CHD][hapmap];0.91[JPT][hapmap];0.85[TSI][hapmap]
rs5026472	0.92[CEU][hapmap];0.91[CHB][hapmap];0.91[JPT][hapmap]
rs5026473	0.92[CEU][hapmap];0.91[CHB][hapmap];0.91[JPT][hapmap]
rs5026474	0.92[CEU][hapmap];0.91[CHB][hapmap];0.91[JPT][hapmap]
rs5026476	0.92[CEU][hapmap];0.91[CHB][hapmap];0.91[JPT][hapmap]
rs6533020	0.92[CEU][hapmap];0.91[CHB][hapmap];0.91[JPT][hapmap]
rs6533021	0.92[CEU][hapmap];0.85[CHB][hapmap];0.89[JPT][hapmap]
rs6810869	0.88[CEU][hapmap];0.90[CHB][hapmap];0.90[JPT][hapmap]
rs6812747	0.92[CEU][hapmap];0.91[CHB][hapmap];0.91[JPT][hapmap]
rs6839064	0.92[CEU][hapmap];0.91[CHB][hapmap];0.91[JPT][hapmap]
rs735403	0.92[CEU][hapmap];0.91[CHB][hapmap];0.88[CHD][hapmap];0.93[GIH][hapmap];0.91[JPT][hapmap];0.81[MEX][hapmap];0.85[TSI][hapmap]
rs735404	0.92[CEU][hapmap];0.91[CHB][hapmap];0.88[CHD][hapmap];0.93[GIH][hapmap];0.91[JPT][hapmap];0.81[MEX][hapmap];0.85[TSI][hapmap]
rs735405	0.92[CEU][hapmap];0.91[CHB][hapmap];0.90[JPT][hapmap]
rs7674640	0.84[CHB][hapmap]
rs7677509	0.88[CEU][hapmap];0.91[CHB][hapmap];0.91[JPT][hapmap]
rs7699231	0.88[CEU][hapmap];0.91[CHB][hapmap];0.91[JPT][hapmap]
rs7699678	0.88[CEU][hapmap];0.91[CHB][hapmap];0.91[JPT][hapmap]
rs909349	0.92[CEU][hapmap];0.91[CHB][hapmap];0.88[CHD][hapmap];0.93[GIH][hapmap];0.91[JPT][hapmap];0.81[MEX][hapmap];0.85[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	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	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
4	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:4)

SNP	Gene	Cis/trans	Tissue	Source
rs228611	MANBA	cis	parietal	SCAN
rs228611	CISD2	cis	parietal	SCAN
rs228611	MANBA	cis	multi-tissue	Pritchard
rs228611	CISD2	cis	lymphoblastoid	seeQTL

Chromatin state (count:119 , 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	chr4:103536600-103562600	Weak transcription	Brain Germinal Matrix	brain
3	chr4:103536600-103595800	Weak transcription	Placenta Amnion	Placenta Amnion
4	chr4:103541800-103562400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
5	chr4:103541800-103571000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
6	chr4:103542400-103562200	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
7	chr4:103542400-103578800	Weak transcription	Psoas Muscle	Psoas
8	chr4:103542400-103594400	Weak transcription	K562	blood
9	chr4:103542400-103617400	Weak transcription	Rectal Smooth Muscle	rectum
10	chr4:103542800-103563800	Weak transcription	Pancreatic Islets	Pancreatic Islet
11	chr4:103545200-103592000	Weak transcription	Fetal Muscle Trunk	muscle
12	chr4:103547000-103658200	Weak transcription	Small Intestine	intestine
13	chr4:103549000-103570400	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
14	chr4:103549800-103572000	Weak transcription	Placenta	Placenta
15	chr4:103550200-103582800	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
16	chr4:103550400-103573000	Weak transcription	Fetal Kidney	kidney
17	chr4:103551000-103562600	Strong transcription	Primary neutrophils fromperipheralblood	blood
18	chr4:103551000-103563000	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
19	chr4:103551000-103565000	Strong transcription	Primary B cells from cord blood	blood
20	chr4:103551000-103607600	Strong transcription	Primary monocytes fromperipheralblood	blood
21	chr4:103551000-103607800	Strong transcription	Monocytes-CD14+_RO01746	blood
22	chr4:103551600-103564000	Strong transcription	Primary hematopoietic stem cells short term culture	blood
23	chr4:103551800-103563200	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
24	chr4:103552000-103562800	Strong transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
25	chr4:103552000-103563400	Strong transcription	Primary B cells from peripheral blood	blood
26	chr4:103552400-103579600	Weak transcription	Fetal Heart	heart
27	chr4:103552800-103561800	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
28	chr4:103553000-103651400	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
29	chr4:103553200-103591200	Weak transcription	H9 Cell Line	embryonic stem cell
30	chr4:103553400-103567800	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
31	chr4:103553400-103568000	Weak transcription	Primary T killer memory cells from peripheral blood	blood
32	chr4:103553400-103568800	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
33	chr4:103553400-103608200	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
34	chr4:103553400-103651400	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
35	chr4:103554600-103567800	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
36	chr4:103556000-103570400	Weak transcription	Fetal Brain Female	brain
37	chr4:103556000-103593800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
38	chr4:103556200-103561800	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
39	chr4:103556200-103562000	Weak transcription	Brain Cingulate Gyrus	brain
40	chr4:103556200-103562600	Weak transcription	Spleen	Spleen
41	chr4:103556200-103571200	Weak transcription	iPS-18 Cell Line	embryonic stem cell
42	chr4:103556200-103572800	Weak transcription	Right Ventricle	heart
43	chr4:103556200-103581000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
44	chr4:103556200-103581000	Weak transcription	Gastric	stomach
45	chr4:103556200-103582200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
46	chr4:103556200-103588600	Weak transcription	Esophagus	oesophagus
47	chr4:103556200-103650400	Weak transcription	Pancreas	Pancrea
48	chr4:103556600-103569400	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
49	chr4:103557200-103573600	Weak transcription	A549	lung
50	chr4:103557600-103562200	Weak transcription	Brain Angular Gyrus	brain

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