Variant report

Variant	rs227277
Chromosome Location	chr4:103594938-103594939
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 50 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:49)

rs_ID	r²[population]
rs1054029	0.82[CHB][hapmap]
rs1054037	0.82[CHB][hapmap]
rs1077358	0.81[CHB][hapmap]
rs11724614	0.82[CHB][hapmap]
rs11727546	0.82[CHB][hapmap]
rs12498722	0.82[CHB][hapmap]
rs12644381	0.82[CHB][hapmap]
rs12648696	0.80[CHB][hapmap]
rs13106304	0.82[CHB][hapmap]
rs13106325	0.82[CHB][hapmap]
rs17033015	0.83[CHB][hapmap];0.91[JPT][hapmap]
rs179195	0.96[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap]
rs2125211	0.82[CHB][hapmap]
rs2272696	0.82[CHB][hapmap]
rs2272697	0.82[CHB][hapmap]
rs227276	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs227361	0.85[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap]
rs228611	0.82[CHB][hapmap]
rs228614	0.85[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap]
rs228617	0.96[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap]
rs228618	0.85[CEU][hapmap];0.87[CHB][hapmap];0.82[JPT][hapmap]
rs228619	0.96[CEU][hapmap];1.00[CHB][hapmap];0.96[JPT][hapmap]
rs228623	0.81[CEU][hapmap];1.00[CHB][hapmap];0.91[JPT][hapmap]
rs2866407	0.82[CHB][hapmap]
rs2866412	0.83[CHB][hapmap]
rs2866413	0.82[CHB][hapmap]
rs2866414	0.82[CHB][hapmap]
rs3733202	0.82[CHB][hapmap]
rs3774968	0.87[JPT][hapmap]
rs4013	0.82[CHB][hapmap]
rs404574	0.81[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap]
rs434644	1.00[CHB][hapmap];0.95[JPT][hapmap]
rs4496586	0.82[CHB][hapmap]
rs4547797	0.82[CHB][hapmap]
rs5026472	0.82[CHB][hapmap]
rs5026476	0.82[CHB][hapmap]
rs6533020	0.82[CHB][hapmap]
rs6533021	0.81[CHB][hapmap];0.80[JPT][hapmap]
rs6810869	0.81[CHB][hapmap]
rs6812747	0.82[CHB][hapmap]
rs6839064	0.83[CHB][hapmap]
rs735403	0.82[CHB][hapmap]
rs735404	0.82[CHB][hapmap]
rs735405	0.82[CHB][hapmap]
rs7674640	0.95[CHB][hapmap]
rs7677509	0.83[CHB][hapmap]
rs7699231	0.82[CHB][hapmap]
rs7699678	0.82[CHB][hapmap]
rs909349	0.82[CHB][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:3)

SNP	Gene	Cis/trans	Tissue	Source
rs227277	CISD2	Cis_1M	lymphoblastoid	RTeQTL
rs227277	KRT8P46	cis	lung	GTEx
rs227277	MANBA	cis	multi-tissue	Pritchard

Chromatin state (count:97 , 50 per page) page: 1 2

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	chr4:103542400-103617400	Weak transcription	Rectal Smooth Muscle	rectum
4	chr4:103547000-103658200	Weak transcription	Small Intestine	intestine
5	chr4:103551000-103607600	Strong transcription	Primary monocytes fromperipheralblood	blood
6	chr4:103551000-103607800	Strong transcription	Monocytes-CD14+_RO01746	blood
7	chr4:103553000-103651400	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
8	chr4:103553400-103608200	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
9	chr4:103553400-103651400	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
10	chr4:103556200-103650400	Weak transcription	Pancreas	Pancrea
11	chr4:103557600-103626400	Weak transcription	Lung	lung
12	chr4:103559600-103617200	Weak transcription	Fetal Stomach	stomach
13	chr4:103560000-103595400	Weak transcription	Primary T helper naive cells from peripheral blood	blood
14	chr4:103561000-103614600	Weak transcription	Fetal Muscle Leg	muscle
15	chr4:103563400-103617600	Weak transcription	Brain Cingulate Gyrus	brain
16	chr4:103563600-103609400	Weak transcription	Brain Hippocampus Middle	brain
17	chr4:103568400-103595200	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
18	chr4:103568800-103595400	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
19	chr4:103568800-103595600	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
20	chr4:103570800-103618000	Weak transcription	Brain Inferior Temporal Lobe	brain
21	chr4:103571200-103605800	Weak transcription	NHDF-Ad	bronchial
22	chr4:103571400-103605400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
23	chr4:103571400-103605400	Weak transcription	Brain Substantia Nigra	brain
24	chr4:103571600-103606200	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
25	chr4:103571800-103596600	Weak transcription	Brain Angular Gyrus	brain
26	chr4:103571800-103608600	Weak transcription	Duodenum Mucosa	Duodenum
27	chr4:103571800-103611800	Weak transcription	Brain Anterior Caudate	brain
28	chr4:103571800-103633600	Weak transcription	HepG2	liver
29	chr4:103571800-103655800	Weak transcription	Rectal Mucosa Donor 31	rectum
30	chr4:103572000-103595400	Weak transcription	Fetal Brain Female	brain
31	chr4:103572000-103640800	Weak transcription	Rectal Mucosa Donor 29	rectum
32	chr4:103572800-103612600	Weak transcription	Primary T killer memory cells from peripheral blood	blood
33	chr4:103579400-103615000	Weak transcription	Psoas Muscle	Psoas
34	chr4:103580000-103644000	Weak transcription	Aorta	Aorta
35	chr4:103580400-103640600	Weak transcription	iPS-18 Cell Line	embryonic stem cell
36	chr4:103581200-103603800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
37	chr4:103581200-103609200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
38	chr4:103581200-103627000	Weak transcription	Gastric	stomach
39	chr4:103581400-103598200	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
40	chr4:103581800-103681000	Weak transcription	Spleen	Spleen
41	chr4:103582800-103603400	Weak transcription	Cortex derived primary cultured neurospheres	brain
42	chr4:103584400-103596400	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
43	chr4:103584800-103608400	Strong transcription	Primary neutrophils fromperipheralblood	blood
44	chr4:103585200-103608600	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
45	chr4:103585200-103609200	Strong transcription	Primary hematopoietic stem cells short term culture	blood
46	chr4:103585600-103613800	Weak transcription	Fetal Intestine Large	intestine
47	chr4:103586000-103599200	Weak transcription	GM12878-XiMat	blood
48	chr4:103586000-103607800	Weak transcription	Sigmoid Colon	Sigmoid Colon
49	chr4:103586000-103640600	Weak transcription	Skeletal Muscle Male	skeletal muscle
50	chr4:103587400-103599200	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin

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