Variant report

Variant	rs3756558
Chromosome Location	chr5:74863041-74863042
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	chr5:74805960..74807609-chr5:74862131..74863821,2	K562	blood:

Variant related genes	Relation type
ENSG00000122008	Chromatin interaction
ENSG00000113163	Chromatin interaction

Extended variants
information (count: 22 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:11)

rs_ID	r²[population]
rs10515197	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.92[MKK][hapmap];0.88[TSI][hapmap];0.85[EUR][1000 genomes]
rs12659791	0.91[EUR][1000 genomes]
rs17562686	0.85[LWK][hapmap];1.00[YRI][hapmap]
rs3733907	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.93[JPT][hapmap];1.00[MEX][hapmap];0.92[MKK][hapmap];0.88[TSI][hapmap];0.84[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs55727654	0.83[EUR][1000 genomes]
rs55926501	0.83[EUR][1000 genomes]
rs5744625	1.00[CEU][hapmap];0.92[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs5744662	0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs5744707	0.85[LWK][hapmap];1.00[YRI][hapmap]
rs5744724	0.93[CHD][hapmap]
rs7717355	0.80[MEX][hapmap]

Variant overlapped rSNPs/rCNVs (count:11 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv882193	chr5:74656175-74917862	ZNF genes & repeats Weak transcription Enhancers Strong transcription Active TSS Flanking Active TSS Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	15 gene(s)	inside rSNPs	diseases
2	nsv882194	chr5:74656175-74946455	Strong transcription Genic enhancers Weak transcription Enhancers Active TSS Flanking Active TSS ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	15 gene(s)	inside rSNPs	diseases
3	nsv882195	chr5:74678937-74896798	Weak transcription Enhancers ZNF genes & repeats Active TSS Strong transcription Genic enhancers Flanking Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	12 gene(s)	inside rSNPs	diseases
4	nsv882196	chr5:74678937-74917862	Weak transcription Enhancers Strong transcription Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent Enhancer Active TSS ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	13 gene(s)	inside rSNPs	diseases
5	nsv882197	chr5:74692776-74946455	Enhancers Weak transcription ZNF genes & repeats Strong transcription Genic enhancers Active TSS Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	13 gene(s)	inside rSNPs	diseases
6	nsv882198	chr5:74736065-74896798	Strong transcription Enhancers ZNF genes & repeats Active TSS Weak transcription Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	12 gene(s)	inside rSNPs	diseases
7	nsv882199	chr5:74757758-74946455	Weak transcription Enhancers Active TSS Flanking Active TSS Genic enhancers Strong transcription ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	13 gene(s)	inside rSNPs	diseases
8	nsv1027368	chr5:74759999-75663712	Active TSS Strong transcription Flanking Active TSS Enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Weak transcription Bivalent Enhancer ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	39 gene(s)	inside rSNPs	diseases
9	nsv882201	chr5:74787310-74890618	Weak transcription Flanking Active TSS Genic enhancers Strong transcription Enhancers ZNF genes & repeats Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region miRNA target site	11 gene(s)	inside rSNPs	diseases
10	nsv882202	chr5:74808417-74946455	Strong transcription Enhancers ZNF genes & repeats Weak transcription Flanking Active TSS Genic enhancers Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	8 gene(s)	inside rSNPs	diseases
11	nsv518475	chr5:74863041-75411804	Strong transcription Active TSS Flanking Active TSS Weak transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Enhancers Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	26 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs3756558	COL4A3BP	cis	parietal	SCAN
rs3756558	HMGCR	cis	cerebellum	SCAN
rs3756558	HMGCR	cis	parietal	SCAN

Chromatin state (count:118 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:74818200-74897400	Weak transcription	Thymus	Thymus
2	chr5:74822800-74896000	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
3	chr5:74831200-74877200	Weak transcription	Fetal Kidney	kidney
4	chr5:74833400-74906800	Weak transcription	Brain Substantia Nigra	brain
5	chr5:74837600-74874400	Weak transcription	Fetal Brain Male	brain
6	chr5:74839400-74897400	Weak transcription	Sigmoid Colon	Sigmoid Colon
7	chr5:74841200-74899400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
8	chr5:74846200-74865400	Weak transcription	Colonic Mucosa	Colon
9	chr5:74850000-74878000	Weak transcription	HepG2	liver
10	chr5:74850200-74896200	Weak transcription	Primary T killer memory cells from peripheral blood	blood
11	chr5:74850800-74865200	Weak transcription	Fetal Thymus	thymus
12	chr5:74851200-74872600	Weak transcription	Rectal Mucosa Donor 31	rectum
13	chr5:74853400-74867200	Weak transcription	Brain Hippocampus Middle	brain
14	chr5:74853600-74865400	Weak transcription	Rectal Mucosa Donor 29	rectum
15	chr5:74853800-74869400	Weak transcription	Liver	Liver
16	chr5:74854000-74863600	Weak transcription	Dnd41	blood
17	chr5:74854000-74865400	Weak transcription	Fetal Intestine Large	intestine
18	chr5:74854000-74883400	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
19	chr5:74855600-74865400	Weak transcription	Aorta	Aorta
20	chr5:74855600-74872600	Weak transcription	Primary neutrophils fromperipheralblood	blood
21	chr5:74859600-74871000	Weak transcription	Brain Angular Gyrus	brain
22	chr5:74860400-74863600	Weak transcription	Primary T cells from cord blood	blood
23	chr5:74860800-74870400	Weak transcription	Brain Anterior Caudate	brain
24	chr5:74861000-74864000	Enhancers	Primary T helper cells PMA-I stimulated	--
25	chr5:74861000-74871000	Weak transcription	Brain Cingulate Gyrus	brain
26	chr5:74861200-74864400	Enhancers	Primary monocytes fromperipheralblood	blood
27	chr5:74861400-74864200	Enhancers	Stomach Mucosa	stomach
28	chr5:74861600-74864000	Enhancers	HUES6 Cell Line	embryonic stem cell
29	chr5:74861600-74864200	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
30	chr5:74861600-74864400	Enhancers	Left Ventricle	heart
31	chr5:74861600-74864400	Flanking Active TSS	GM12878-XiMat	blood
32	chr5:74861800-74863200	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
33	chr5:74861800-74864000	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
34	chr5:74861800-74864200	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
35	chr5:74861800-74864400	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
36	chr5:74862000-74863200	Enhancers	Primary T cells effector/memory enriched fromperipheralblood	blood
37	chr5:74862000-74863800	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
38	chr5:74862000-74864000	Enhancers	Primary B cells from peripheral blood	blood
39	chr5:74862000-74864000	Enhancers	NHEK	skin
40	chr5:74862200-74863400	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
41	chr5:74862200-74863600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
42	chr5:74862200-74864000	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
43	chr5:74862200-74864400	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
44	chr5:74862200-74864400	Enhancers	Fetal Adrenal Gland	Adrenal Gland
45	chr5:74862200-74864400	Enhancers	NHLF	lung
46	chr5:74862200-74865400	Weak transcription	Breast Myoepithelial Primary Cells	Breast
47	chr5:74862200-74873400	Weak transcription	Fetal Brain Female	brain
48	chr5:74862200-74897800	Weak transcription	Brain Germinal Matrix	brain
49	chr5:74862400-74863200	Flanking Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
50	chr5:74862400-74863600	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived

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