Variant report

Variant	rs7674640
Chromosome Location	chr4:103540780-103540781
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	chr4:103421697..103423490-chr4:103540373..103542890,2	MCF-7	breast:
2	chr4:103534263..103536665-chr4:103540346..103543565,3	K562	blood:

Variant related genes	Relation type
ENSG00000260651	Chromatin interaction
ENSG00000109320	Chromatin interaction

Extended variants
information (count: 57 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:54)

rs_ID	r²[population]
rs1054029	0.84[CEU][hapmap];0.85[CHB][hapmap]
rs1054037	0.88[CEU][hapmap];0.85[CHB][hapmap]
rs1077358	0.83[CEU][hapmap];0.85[CHB][hapmap]
rs11724614	0.89[CEU][hapmap];0.86[CHB][hapmap]
rs11727546	0.88[CEU][hapmap];0.85[CHB][hapmap]
rs12498722	0.85[CEU][hapmap];0.86[CHB][hapmap]
rs12644381	0.89[CEU][hapmap];0.86[CHB][hapmap]
rs12648696	0.88[CHB][hapmap]
rs13106304	0.85[CEU][hapmap];0.85[CHB][hapmap]
rs13106325	0.85[CEU][hapmap];0.85[CHB][hapmap]
rs17033015	0.86[JPT][hapmap]
rs179195	0.95[CHB][hapmap];0.82[JPT][hapmap]
rs2125211	0.84[CEU][hapmap];0.85[CHB][hapmap]
rs2272695	0.85[CEU][hapmap];0.82[CHB][hapmap]
rs2272696	0.84[CEU][hapmap];0.86[CHB][hapmap]
rs2272697	0.84[CEU][hapmap];0.85[CHB][hapmap]
rs227276	0.95[CHB][hapmap]
rs227277	0.95[CHB][hapmap]
rs227361	0.95[CHB][hapmap];0.82[JPT][hapmap]
rs228611	0.84[CHB][hapmap]
rs228614	0.95[CHB][hapmap];0.82[JPT][hapmap]
rs228617	0.95[CHB][hapmap];0.82[JPT][hapmap]
rs228618	0.81[CHB][hapmap]
rs228619	0.95[CHB][hapmap];0.83[JPT][hapmap]
rs228623	0.94[CHB][hapmap]
rs2866407	0.84[CEU][hapmap];0.85[CHB][hapmap]
rs2866412	0.84[CEU][hapmap];0.86[CHB][hapmap]
rs2866413	0.84[CEU][hapmap];0.85[CHB][hapmap]
rs2866414	0.84[CEU][hapmap];0.85[CHB][hapmap]
rs2903283	0.87[CEU][hapmap];0.84[CHB][hapmap];0.81[JPT][hapmap]
rs3733202	0.80[CEU][hapmap];0.85[CHB][hapmap]
rs3774968	0.82[JPT][hapmap]
rs4013	0.88[CEU][hapmap];0.85[CHB][hapmap]
rs404574	0.94[CHB][hapmap];0.85[JPT][hapmap]
rs434644	0.95[CHB][hapmap];0.81[JPT][hapmap]
rs4496586	0.86[CHB][hapmap]
rs4547797	0.84[CEU][hapmap];0.85[CHB][hapmap]
rs4586937	0.84[CEU][hapmap]
rs5026472	0.85[CEU][hapmap];0.86[CHB][hapmap]
rs5026473	0.85[CEU][hapmap];0.81[CHB][hapmap]
rs5026474	0.85[CEU][hapmap];0.82[CHB][hapmap]
rs5026476	0.85[CEU][hapmap];0.86[CHB][hapmap]
rs6533020	0.85[CEU][hapmap];0.85[CHB][hapmap]
rs6533021	0.88[CEU][hapmap];0.84[CHB][hapmap]
rs6810869	0.81[CEU][hapmap];0.85[CHB][hapmap]
rs6812747	0.85[CEU][hapmap];0.86[CHB][hapmap]
rs6839064	0.85[CEU][hapmap];0.86[CHB][hapmap]
rs735403	0.84[CEU][hapmap];0.85[CHB][hapmap]
rs735404	0.84[CEU][hapmap];0.85[CHB][hapmap]
rs735405	0.84[CEU][hapmap];0.85[CHB][hapmap]
rs7677509	0.89[CEU][hapmap];0.86[CHB][hapmap]
rs7699231	0.89[CEU][hapmap];0.86[CHB][hapmap]
rs7699678	0.89[CEU][hapmap];0.86[CHB][hapmap]
rs909349	0.84[CEU][hapmap];0.85[CHB][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	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	esv2498239	chr4:103540653-103541980	Weak transcription Enhancers Flanking Active TSS Active TSS	Chromatin interactive region	5 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs7674640	MANBA	cis	multi-tissue	Pritchard

Chromatin state (count:122 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:103483400-103541600	Weak transcription	K562	blood
2	chr4:103513000-103542000	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
3	chr4:103517600-103541600	Weak transcription	Right Atrium	heart
4	chr4:103521400-103554400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
5	chr4:103533000-103541000	Weak transcription	Stomach Mucosa	stomach
6	chr4:103533400-103541800	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
7	chr4:103534000-103540800	Weak transcription	NHDF-Ad	bronchial
8	chr4:103534000-103546200	Weak transcription	Small Intestine	intestine
9	chr4:103534800-103541600	Weak transcription	Psoas Muscle	Psoas
10	chr4:103535400-103541600	Weak transcription	Hela-S3	cervix
11	chr4:103536200-103540800	Weak transcription	A549	lung
12	chr4:103536200-103552800	Weak transcription	Ovary	ovary
13	chr4:103536200-103595400	Weak transcription	Colonic Mucosa	Colon
14	chr4:103536400-103541600	Weak transcription	Brain Angular Gyrus	brain
15	chr4:103536400-103542000	Weak transcription	Fetal Brain Male	brain
16	chr4:103536400-103553400	Weak transcription	Fetal Brain Female	brain
17	chr4:103536600-103540800	Weak transcription	Muscle Satellite Cultured Cells	--
18	chr4:103536600-103541800	Weak transcription	Brain Inferior Temporal Lobe	brain
19	chr4:103536600-103541800	Weak transcription	Pancreatic Islets	Pancreatic Islet
20	chr4:103536600-103542000	Weak transcription	Fetal Kidney	kidney
21	chr4:103536600-103550800	Weak transcription	Thymus	Thymus
22	chr4:103536600-103562600	Weak transcription	Brain Germinal Matrix	brain
23	chr4:103536600-103595800	Weak transcription	Placenta Amnion	Placenta Amnion
24	chr4:103536800-103541600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
25	chr4:103536800-103541800	Weak transcription	Brain Cingulate Gyrus	brain
26	chr4:103536800-103542000	Weak transcription	Brain Hippocampus Middle	brain
27	chr4:103537600-103541600	Weak transcription	Fetal Heart	heart
28	chr4:103537800-103541600	Weak transcription	HUVEC	blood vessel
29	chr4:103537800-103544800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
30	chr4:103537800-103546200	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
31	chr4:103538000-103541000	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
32	chr4:103538000-103541000	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
33	chr4:103538000-103541000	Weak transcription	HMEC	breast
34	chr4:103538000-103541000	Weak transcription	NHLF	lung
35	chr4:103538000-103541200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
36	chr4:103538000-103541600	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
37	chr4:103538000-103544800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
38	chr4:103538000-103545600	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
39	chr4:103538000-103546600	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
40	chr4:103538000-103552800	Weak transcription	Spleen	Spleen
41	chr4:103538200-103540800	Weak transcription	Fetal Intestine Small	intestine
42	chr4:103538200-103540800	Weak transcription	HSMM	muscle
43	chr4:103538200-103541000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
44	chr4:103538200-103541000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
45	chr4:103538200-103541000	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
46	chr4:103538200-103541000	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
47	chr4:103538200-103541600	Weak transcription	iPS-18 Cell Line	embryonic stem cell
48	chr4:103538200-103541600	Weak transcription	iPS-20b Cell Line	embryonic stem cell
49	chr4:103538200-103541600	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
50	chr4:103538200-103541600	Weak transcription	Brain Substantia Nigra	brain

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