Variant report

Variant	rs223374
Chromosome Location	chr4:103758301-103758302
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	chr4:103757981..103760210-chr4:103788779..103792058,4	MCF-7	breast:

Variant related genes	Relation type
ENSG00000145354	Chromatin interaction
ENSG00000109332	Chromatin interaction

Extended variants
information (count: 21 )
Associated
traits (count: 5 )

rSNPs within LD-proxies of this variant (count:20)

rs_ID	r²[population]
rs10006474	0.95[CEU][hapmap];0.83[CHB][hapmap];0.85[JPT][hapmap]
rs10516495	0.91[CEU][hapmap];0.84[CHB][hapmap];0.86[JPT][hapmap]
rs10516496	0.91[CEU][hapmap];0.84[CHB][hapmap];0.86[JPT][hapmap]
rs11946020	0.95[CEU][hapmap];0.84[CHB][hapmap];0.86[JPT][hapmap]
rs13150953	0.91[CEU][hapmap];0.84[CHB][hapmap];0.86[JPT][hapmap]
rs223317	1.00[CEU][hapmap]
rs223331	1.00[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap]
rs223361	1.00[CEU][hapmap];0.90[CHB][hapmap];0.95[JPT][hapmap]
rs223366	0.95[CHB][hapmap];0.95[JPT][hapmap]
rs223401	0.87[CEU][hapmap];0.83[JPT][hapmap]
rs223413	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs223471	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs223489	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs223490	0.95[CHB][hapmap];1.00[JPT][hapmap]
rs2866416	0.96[CEU][hapmap]
rs34475639	0.95[CEU][hapmap];0.84[CHB][hapmap];0.86[JPT][hapmap]
rs4699048	0.87[CEU][hapmap];0.88[CHB][hapmap]
rs6816370	0.96[CEU][hapmap];0.85[CHB][hapmap];0.86[JPT][hapmap]
rs6843738	0.95[CEU][hapmap];0.84[CHB][hapmap];0.86[JPT][hapmap]
rs7665026	0.95[CEU][hapmap];0.84[CHB][hapmap];0.86[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	nsv594957	chr4:103728010-103870091	Weak transcription Strong transcription Active TSS Flanking Active TSS Enhancers Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	46 gene(s)	inside rSNPs	diseases

mRNA abundance (count:5)

SNP	Gene	Cis/trans	Tissue	Source
rs223374	MANBA	cis	multi-tissue	Pritchard
rs223374	BDH2	Cis_1M	lymphoblastoid	RTeQTL
rs223374	MANBA	Cis_1M	lymphoblastoid	RTeQTL
rs223374	LRRC37A15P	cis	Thyroid	GTEx
rs223374	KRT8P46	cis	lung	GTEx

Chromatin state (count:35 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:103750000-103763000	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
2	chr4:103750000-103770600	Weak transcription	Fetal Muscle Trunk	muscle
3	chr4:103750600-103760800	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
4	chr4:103750600-103766400	Weak transcription	Stomach Smooth Muscle	stomach
5	chr4:103750600-103767000	Weak transcription	Psoas Muscle	Psoas
6	chr4:103750600-103770400	Weak transcription	Fetal Muscle Leg	muscle
7	chr4:103750600-103771200	Weak transcription	Brain Angular Gyrus	brain
8	chr4:103750800-103762000	Weak transcription	Brain Substantia Nigra	brain
9	chr4:103750800-103764600	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
10	chr4:103750800-103765000	Weak transcription	HSMM	muscle
11	chr4:103750800-103765800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
12	chr4:103750800-103766000	Weak transcription	Skeletal Muscle Female	skeletal muscle
13	chr4:103750800-103766400	Weak transcription	Primary B cells from cord blood	blood
14	chr4:103750800-103766400	Weak transcription	Duodenum Smooth Muscle	Duodenum
15	chr4:103750800-103766600	Weak transcription	Adipose Nuclei	Adipose
16	chr4:103750800-103771400	Weak transcription	Primary hematopoietic stem cells	blood
17	chr4:103750800-103788000	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
18	chr4:103751000-103764600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
19	chr4:103751000-103766400	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
20	chr4:103751200-103762800	Weak transcription	Fetal Intestine Small	intestine
21	chr4:103751400-103762600	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
22	chr4:103751400-103766600	Weak transcription	Brain Hippocampus Middle	brain
23	chr4:103751600-103780200	Weak transcription	Dnd41	blood
24	chr4:103753200-103760400	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
25	chr4:103753600-103776000	Weak transcription	Primary hematopoietic stem cells short term culture	blood
26	chr4:103753800-103769600	Weak transcription	iPS-18 Cell Line	embryonic stem cell
27	chr4:103754000-103766000	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
28	chr4:103754000-103770800	Weak transcription	K562	blood
29	chr4:103754200-103765000	Weak transcription	Left Ventricle	heart
30	chr4:103754200-103768800	Weak transcription	Fetal Thymus	thymus
31	chr4:103754400-103759200	Weak transcription	Primary T cells from cord blood	blood
32	chr4:103755000-103767200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
33	chr4:103755400-103769200	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
34	chr4:103755800-103764600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
35	chr4:103758200-103771200	Weak transcription	A549	lung

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