Variant report

Variant	rs227361
Chromosome Location	chr4:103586977-103586978
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 60 )
Associated
traits (count: 6 )

rSNPs within LD-proxies of this variant (count:59)

rs_ID	r²[population]
rs1054029	0.81[CEU][hapmap];0.82[CHB][hapmap];0.80[MEX][hapmap]
rs1054037	0.82[CHB][hapmap];0.82[JPT][hapmap]
rs1077358	0.80[CHB][hapmap];0.80[JPT][hapmap]
rs11724614	0.82[CHB][hapmap];0.82[JPT][hapmap]
rs11727546	0.84[CEU][hapmap];0.81[CHB][hapmap];0.81[JPT][hapmap]
rs12498722	0.81[CEU][hapmap];0.82[CHB][hapmap];0.82[JPT][hapmap]
rs12644381	0.82[CHB][hapmap];0.82[JPT][hapmap]
rs13106304	0.81[CEU][hapmap];0.82[CHB][hapmap];0.81[JPT][hapmap]
rs13106325	0.81[CEU][hapmap];0.82[CHB][hapmap];0.81[JPT][hapmap]
rs1585214	0.81[JPT][hapmap]
rs1598856	0.81[JPT][hapmap]
rs17033015	0.82[CHB][hapmap];0.95[JPT][hapmap]
rs179195	0.89[CEU][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];0.91[TSI][hapmap]
rs2125211	0.84[CEU][hapmap];0.82[CHB][hapmap];0.82[GIH][hapmap];0.82[JPT][hapmap];0.81[MEX][hapmap]
rs2272695	0.81[CEU][hapmap];0.82[JPT][hapmap]
rs2272696	0.81[CEU][hapmap];0.82[CHB][hapmap];0.82[JPT][hapmap]
rs2272697	0.81[CEU][hapmap];0.82[CHB][hapmap];0.82[JPT][hapmap]
rs227276	0.85[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap]
rs227277	0.85[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap]
rs228611	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	0.94[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.93[LWK][hapmap];1.00[MEX][hapmap];0.96[MKK][hapmap];1.00[TSI][hapmap];0.96[YRI][hapmap]
rs228617	0.88[CEU][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];0.91[TSI][hapmap]
rs228618	1.00[CEU][hapmap];0.87[CHB][hapmap];0.85[CHD][hapmap];0.98[GIH][hapmap];0.87[JPT][hapmap];1.00[MEX][hapmap];0.98[TSI][hapmap]
rs228619	0.88[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap]
rs228623	0.96[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];0.98[GIH][hapmap];0.95[JPT][hapmap];0.98[TSI][hapmap]
rs230510	0.81[JPT][hapmap]
rs230530	0.81[JPT][hapmap]
rs2866407	0.80[CEU][hapmap];0.81[CHB][hapmap];0.81[JPT][hapmap]
rs2866412	0.80[CEU][hapmap];0.82[CHB][hapmap];0.82[JPT][hapmap]
rs2866413	0.81[CEU][hapmap];0.82[CHB][hapmap];0.82[JPT][hapmap]
rs2866414	0.81[CEU][hapmap];0.82[CHB][hapmap];0.82[JPT][hapmap]
rs2903283	0.86[CEU][hapmap];0.83[JPT][hapmap]
rs3733202	0.84[CEU][hapmap];0.82[CHB][hapmap];0.82[JPT][hapmap];0.81[MEX][hapmap]
rs3774932	0.81[JPT][hapmap]
rs3774968	0.91[JPT][hapmap]
rs4013	0.82[CHB][hapmap];0.82[JPT][hapmap]
rs404574	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs434644	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs4496586	0.81[CHB][hapmap];0.81[JPT][hapmap]
rs4547797	0.81[CEU][hapmap];0.82[CHB][hapmap];0.82[JPT][hapmap]
rs4586937	0.81[CEU][hapmap];0.82[JPT][hapmap]
rs5026472	0.81[CEU][hapmap];0.82[CHB][hapmap];0.82[JPT][hapmap]
rs5026473	0.81[CEU][hapmap];0.81[CHB][hapmap];0.82[JPT][hapmap]
rs5026474	0.81[CEU][hapmap];0.82[CHB][hapmap];0.82[JPT][hapmap]
rs5026476	0.81[CEU][hapmap];0.82[CHB][hapmap];0.82[JPT][hapmap]
rs6533020	0.81[CEU][hapmap];0.81[CHB][hapmap];0.82[JPT][hapmap]
rs6533021	0.83[CEU][hapmap];0.80[CHB][hapmap];0.84[JPT][hapmap]
rs6810869	0.80[CHB][hapmap];0.80[JPT][hapmap]
rs6812747	0.81[CEU][hapmap];0.82[CHB][hapmap];0.82[JPT][hapmap]
rs6839064	0.81[CEU][hapmap];0.82[CHB][hapmap];0.82[JPT][hapmap]
rs735403	0.81[CEU][hapmap];0.82[CHB][hapmap];0.82[JPT][hapmap]
rs735404	0.81[CEU][hapmap];0.82[CHB][hapmap];0.82[JPT][hapmap]
rs735405	0.81[CHB][hapmap];0.80[JPT][hapmap]
rs7674640	0.95[CHB][hapmap];0.82[JPT][hapmap]
rs7677509	0.82[CHB][hapmap];0.82[JPT][hapmap]
rs7699231	0.82[CHB][hapmap];0.82[JPT][hapmap]
rs7699678	0.82[CHB][hapmap];0.82[JPT][hapmap]
rs909349	0.81[CEU][hapmap];0.82[CHB][hapmap];0.82[JPT][hapmap]
rs93059	0.81[JPT][hapmap]

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

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	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:6)

SNP	Gene	Cis/trans	Tissue	Source
rs227361	MANBA	cis	parietal	SCAN
rs227361	MANBA	cis	multi-tissue	Pritchard
rs227361	ADH7	cis	cerebellum	SCAN
rs227361	CISD2	cis	parietal	SCAN
rs227361	RG9MTD2	cis	cerebellum	SCAN
rs227361	CISD2	cis	lymphoblastoid	seeQTL

Chromatin state (count:109 , 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	chr4:103542400-103594400	Weak transcription	K562	blood
4	chr4:103542400-103617400	Weak transcription	Rectal Smooth Muscle	rectum
5	chr4:103545200-103592000	Weak transcription	Fetal Muscle Trunk	muscle
6	chr4:103547000-103658200	Weak transcription	Small Intestine	intestine
7	chr4:103551000-103607600	Strong transcription	Primary monocytes fromperipheralblood	blood
8	chr4:103551000-103607800	Strong transcription	Monocytes-CD14+_RO01746	blood
9	chr4:103553000-103651400	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
10	chr4:103553200-103591200	Weak transcription	H9 Cell Line	embryonic stem cell
11	chr4:103553400-103608200	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
12	chr4:103553400-103651400	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
13	chr4:103556000-103593800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
14	chr4:103556200-103588600	Weak transcription	Esophagus	oesophagus
15	chr4:103556200-103650400	Weak transcription	Pancreas	Pancrea
16	chr4:103557600-103626400	Weak transcription	Lung	lung
17	chr4:103559200-103590000	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
18	chr4:103559600-103617200	Weak transcription	Fetal Stomach	stomach
19	chr4:103560000-103595400	Weak transcription	Primary T helper naive cells from peripheral blood	blood
20	chr4:103560800-103587800	Weak transcription	Colon Smooth Muscle	Colon
21	chr4:103561000-103587600	Weak transcription	Fetal Intestine Small	intestine
22	chr4:103561000-103591400	Weak transcription	Thymus	Thymus
23	chr4:103561000-103614600	Weak transcription	Fetal Muscle Leg	muscle
24	chr4:103563400-103617600	Weak transcription	Brain Cingulate Gyrus	brain
25	chr4:103563600-103609400	Weak transcription	Brain Hippocampus Middle	brain
26	chr4:103568400-103595200	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
27	chr4:103568800-103595400	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
28	chr4:103568800-103595600	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
29	chr4:103570800-103618000	Weak transcription	Brain Inferior Temporal Lobe	brain
30	chr4:103571200-103605800	Weak transcription	NHDF-Ad	bronchial
31	chr4:103571400-103605400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
32	chr4:103571400-103605400	Weak transcription	Brain Substantia Nigra	brain
33	chr4:103571600-103606200	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
34	chr4:103571800-103587400	Weak transcription	Duodenum Smooth Muscle	Duodenum
35	chr4:103571800-103587800	Weak transcription	Ovary	ovary
36	chr4:103571800-103596600	Weak transcription	Brain Angular Gyrus	brain
37	chr4:103571800-103608600	Weak transcription	Duodenum Mucosa	Duodenum
38	chr4:103571800-103611800	Weak transcription	Brain Anterior Caudate	brain
39	chr4:103571800-103633600	Weak transcription	HepG2	liver
40	chr4:103571800-103655800	Weak transcription	Rectal Mucosa Donor 31	rectum
41	chr4:103572000-103587400	Weak transcription	Adipose Nuclei	Adipose
42	chr4:103572000-103588000	Weak transcription	Primary T helper cells PMA-I stimulated	--
43	chr4:103572000-103588200	Weak transcription	Fetal Thymus	thymus
44	chr4:103572000-103593600	Weak transcription	H1 Cell Line	embryonic stem cell
45	chr4:103572000-103593600	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
46	chr4:103572000-103593800	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
47	chr4:103572000-103595400	Weak transcription	Fetal Brain Female	brain
48	chr4:103572000-103640800	Weak transcription	Rectal Mucosa Donor 29	rectum
49	chr4:103572800-103612600	Weak transcription	Primary T killer memory cells from peripheral blood	blood
50	chr4:103575200-103590800	Strong transcription	Primary B cells from peripheral blood	blood

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