Variant report

Variant	rs4013
Chromosome Location	chr4:103552813-103552814
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr4:103552180..103554817-chr4:103747906..103750209,3	MCF-7	breast:

Variant related genes	Relation type
ENSG00000246560	Chromatin interaction
ENSG00000109332	Chromatin interaction

Extended variants
information (count: 55 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:53)

rs_ID	r²[population]
rs1054029	1.00[ASW][hapmap];0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.95[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.96[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap]
rs1054037	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.95[MEX][hapmap];0.96[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap]
rs1077358	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap]
rs11724614	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap]
rs11727546	0.96[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.84[YRI][hapmap]
rs12498722	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap]
rs12644381	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap]
rs13106304	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap]
rs13106325	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap]
rs17033015	0.90[JPT][hapmap]
rs179195	0.82[CHB][hapmap];0.82[JPT][hapmap]
rs2125211	0.96[CEU][hapmap];1.00[CHB][hapmap];0.91[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap]
rs2272695	0.96[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap]
rs2272696	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap]
rs2272697	1.00[ASW][hapmap];0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.93[LWK][hapmap];1.00[MEX][hapmap];0.92[MKK][hapmap];1.00[TSI][hapmap];0.96[YRI][hapmap]
rs227276	0.82[CHB][hapmap]
rs227277	0.82[CHB][hapmap]
rs227361	0.82[CHB][hapmap];0.82[JPT][hapmap]
rs228611	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]
rs228614	0.82[CHB][hapmap];0.82[JPT][hapmap]
rs228617	0.82[CHB][hapmap];0.82[JPT][hapmap]
rs228618	0.95[CHB][hapmap];0.82[CHD][hapmap];0.95[JPT][hapmap];0.81[TSI][hapmap]
rs228619	0.82[CHB][hapmap];0.82[JPT][hapmap]
rs228623	0.86[CHB][hapmap];0.82[TSI][hapmap]
rs2866407	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap]
rs2866412	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs2866413	1.00[ASW][hapmap];0.96[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];0.92[MKK][hapmap];1.00[TSI][hapmap];0.96[YRI][hapmap]
rs2866414	1.00[ASW][hapmap];0.96[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];0.92[MKK][hapmap];1.00[TSI][hapmap];0.96[YRI][hapmap]
rs2903283	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs3733202	0.92[CEU][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.82[LWK][hapmap];0.95[MEX][hapmap];1.00[TSI][hapmap]
rs3774968	0.83[JPT][hapmap]
rs404574	0.84[CHB][hapmap];0.83[JPT][hapmap]
rs434644	0.82[CHB][hapmap];0.80[JPT][hapmap]
rs4496586	0.85[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap]
rs4547797	1.00[ASW][hapmap];0.96[CEU][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.91[LWK][hapmap];1.00[MEX][hapmap];0.92[MKK][hapmap];1.00[TSI][hapmap];0.96[YRI][hapmap]
rs4586937	0.96[CEU][hapmap];0.95[CHB][hapmap];0.95[CHD][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];0.86[MKK][hapmap];1.00[TSI][hapmap]
rs5026472	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap]
rs5026473	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap]
rs5026474	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[YRI][hapmap]
rs5026476	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap]
rs6533020	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap]
rs6533021	0.96[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap]
rs6810869	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[YRI][hapmap]
rs6812747	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap]
rs6839064	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap]
rs735403	1.00[ASW][hapmap];0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.95[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap]
rs735404	1.00[ASW][hapmap];0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.96[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap]
rs735405	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap]
rs7674640	0.88[CEU][hapmap];0.85[CHB][hapmap]
rs7677509	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap]
rs7699231	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap]
rs7699678	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap]
rs909349	1.00[ASW][hapmap];0.96[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.86[LWK][hapmap];1.00[MEX][hapmap];0.89[MKK][hapmap];1.00[TSI][hapmap];0.85[YRI][hapmap]

Variant overlapped rSNPs/rCNVs (count:2 , 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

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs4013	MANBA	cis	multi-tissue	Pritchard
rs4013	GSTCD	cis	parietal	SCAN
rs4013	CISD2	cis	parietal	SCAN

Chromatin state (count:117 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:103521400-103554400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
2	chr4:103536200-103595400	Weak transcription	Colonic Mucosa	Colon
3	chr4:103536400-103553400	Weak transcription	Fetal Brain Female	brain
4	chr4:103536600-103562600	Weak transcription	Brain Germinal Matrix	brain
5	chr4:103536600-103595800	Weak transcription	Placenta Amnion	Placenta Amnion
6	chr4:103538200-103555600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
7	chr4:103538200-103555600	Weak transcription	Gastric	stomach
8	chr4:103538200-103555800	Weak transcription	Esophagus	oesophagus
9	chr4:103538800-103555600	Weak transcription	Right Ventricle	heart
10	chr4:103538800-103555800	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
11	chr4:103541800-103562400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
12	chr4:103541800-103571000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
13	chr4:103542200-103555400	Weak transcription	Brain Cingulate Gyrus	brain
14	chr4:103542200-103555400	Weak transcription	Sigmoid Colon	Sigmoid Colon
15	chr4:103542200-103555600	Weak transcription	iPS-15b Cell Line	embryonic stem cell
16	chr4:103542200-103555600	Weak transcription	Brain Anterior Caudate	brain
17	chr4:103542400-103553200	Weak transcription	Brain Inferior Temporal Lobe	brain
18	chr4:103542400-103555400	Weak transcription	Skeletal Muscle Female	skeletal muscle
19	chr4:103542400-103555600	Weak transcription	Skeletal Muscle Male	skeletal muscle
20	chr4:103542400-103557200	Weak transcription	HUES64 Cell Line	embryonic stem cell
21	chr4:103542400-103560800	Weak transcription	Brain Substantia Nigra	brain
22	chr4:103542400-103562200	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
23	chr4:103542400-103578800	Weak transcription	Psoas Muscle	Psoas
24	chr4:103542400-103594400	Weak transcription	K562	blood
25	chr4:103542400-103617400	Weak transcription	Rectal Smooth Muscle	rectum
26	chr4:103542600-103555800	Weak transcription	Brain Hippocampus Middle	brain
27	chr4:103542800-103557200	Weak transcription	Brain Angular Gyrus	brain
28	chr4:103542800-103563800	Weak transcription	Pancreatic Islets	Pancreatic Islet
29	chr4:103544200-103555400	Weak transcription	Pancreas	Pancrea
30	chr4:103545200-103554200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
31	chr4:103545200-103555600	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
32	chr4:103545200-103557200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
33	chr4:103545200-103559800	Weak transcription	Cortex derived primary cultured neurospheres	brain
34	chr4:103545200-103592000	Weak transcription	Fetal Muscle Trunk	muscle
35	chr4:103545800-103555400	Weak transcription	Fetal Stomach	stomach
36	chr4:103547000-103554000	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
37	chr4:103547000-103658200	Weak transcription	Small Intestine	intestine
38	chr4:103548400-103553400	Enhancers	Primary T helper cells fromperipheralblood	blood
39	chr4:103548800-103554000	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
40	chr4:103548800-103554000	Enhancers	Primary T killer naive cells fromperipheralblood	blood
41	chr4:103549000-103570400	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
42	chr4:103549600-103554200	Weak transcription	Liver	Liver
43	chr4:103549600-103555600	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
44	chr4:103549600-103558600	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
45	chr4:103549600-103561600	Weak transcription	NHDF-Ad	bronchial
46	chr4:103549800-103554000	Weak transcription	Fetal Lung	lung
47	chr4:103549800-103554600	Weak transcription	HSMM	muscle
48	chr4:103549800-103561600	Weak transcription	Muscle Satellite Cultured Cells	--
49	chr4:103549800-103561600	Weak transcription	Osteobl	bone
50	chr4:103549800-103572000	Weak transcription	Placenta	Placenta

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