Variant report

Variant	rs6878990
Chromosome Location	chr5:74689249-74689250
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	chr5:74688554..74690802-chr5:74806794..74808772,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000122008	Chromatin interaction
ENSG00000113163	Chromatin interaction

Extended variants
information (count: 40 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:35)

rs_ID	r²[population]
rs10038095	0.82[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs10045497	0.84[CEU][hapmap];0.90[JPT][hapmap];0.80[EUR][1000 genomes]
rs10474433	0.86[GIH][hapmap]
rs11748027	0.83[EUR][1000 genomes]
rs11749783	0.85[CEU][hapmap];0.87[CHB][hapmap];0.91[CHD][hapmap];0.97[GIH][hapmap];0.90[JPT][hapmap];0.83[ASN][1000 genomes]
rs12654264	0.85[CEU][hapmap];0.87[CHB][hapmap];0.91[CHD][hapmap];0.95[GIH][hapmap];0.90[JPT][hapmap];0.82[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs12916	0.81[CEU][hapmap];0.91[CHB][hapmap];0.93[CHD][hapmap];0.90[JPT][hapmap];0.89[ASN][1000 genomes]
rs17244834	0.85[ASN][1000 genomes]
rs2126736	0.85[CEU][hapmap];0.80[CHD][hapmap];0.86[GIH][hapmap]
rs2878417	0.81[CEU][hapmap];0.82[CHB][hapmap];0.90[JPT][hapmap]
rs2878419	0.85[ASN][1000 genomes]
rs3843480	0.80[CEU][hapmap];0.86[CHB][hapmap];0.90[JPT][hapmap];0.81[ASN][1000 genomes]
rs3843481	0.85[CEU][hapmap];0.86[CHB][hapmap];0.90[JPT][hapmap];0.83[ASN][1000 genomes]
rs3846661	0.82[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs3846662	0.89[ASW][hapmap];0.92[CEU][hapmap];0.87[CHB][hapmap];0.93[CHD][hapmap];0.95[GIH][hapmap];0.90[JPT][hapmap];0.85[LWK][hapmap];0.92[MKK][hapmap];0.85[TSI][hapmap];0.87[YRI][hapmap];0.83[AMR][1000 genomes];0.83[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs3846663	0.81[CEU][hapmap];0.87[CHB][hapmap];0.93[CHD][hapmap];0.90[JPT][hapmap];0.82[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs4549504	1.00[ASW][hapmap];0.96[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.85[LWK][hapmap];0.95[MEX][hapmap];0.95[TSI][hapmap];0.87[YRI][hapmap];0.83[AFR][1000 genomes];0.89[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs4604177	1.00[ASW][hapmap];0.96[CEU][hapmap];0.91[CHB][hapmap];0.93[CHD][hapmap];1.00[GIH][hapmap];0.90[JPT][hapmap];0.85[LWK][hapmap];0.95[MEX][hapmap];0.95[MKK][hapmap];0.98[TSI][hapmap];0.87[YRI][hapmap];0.83[AFR][1000 genomes];0.90[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs4704200	0.85[CEU][hapmap];0.88[GIH][hapmap]
rs4704219	0.83[AFR][1000 genomes];0.85[AMR][1000 genomes];0.91[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs4704220	0.83[AFR][1000 genomes];0.88[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs4704221	0.89[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs4704223	0.83[AFR][1000 genomes];0.87[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs4704227	0.86[EUR][1000 genomes]
rs5744552	0.83[AFR][1000 genomes];0.89[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs5744672	0.96[CEU][hapmap];0.86[CHB][hapmap];0.90[JPT][hapmap];0.83[AFR][1000 genomes];0.85[EUR][1000 genomes]
rs5744680	1.00[ASW][hapmap];0.92[CEU][hapmap];0.86[CHB][hapmap];0.93[CHD][hapmap];0.98[GIH][hapmap];0.90[JPT][hapmap];0.85[LWK][hapmap];0.85[MEX][hapmap];0.90[MKK][hapmap];0.91[TSI][hapmap];0.83[EUR][1000 genomes]
rs6453131	0.82[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs6453133	0.87[ASN][1000 genomes]
rs6873472	0.83[AFR][1000 genomes];0.88[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs6882842	0.86[AMR][1000 genomes];0.85[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs6896136	0.83[AFR][1000 genomes];0.87[EUR][1000 genomes]
rs7703051	0.85[CEU][hapmap];0.87[CHB][hapmap];0.91[CHD][hapmap];0.97[GIH][hapmap];0.90[JPT][hapmap];0.81[ASN][1000 genomes]
rs7733436	0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs984976	0.84[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv882192	chr5:74641707-74707762	Strong transcription Weak transcription Genic enhancers Enhancers ZNF genes & repeats Flanking Active TSS Active TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	6 gene(s)	inside rSNPs	diseases
2	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
3	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
4	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
5	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

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs6878990	HMGCR	cis	parietal	SCAN
rs6878990	POC5	cis	parietal	SCAN
rs6878990	HMGCR	cis	cerebellum	SCAN
rs6878990	TNPO1	cis	cerebellum	SCAN

Chromatin state (count:120 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:74656400-74725600	Weak transcription	Placenta Amnion	Placenta Amnion
2	chr5:74656600-74694800	Weak transcription	Brain Angular Gyrus	brain
3	chr5:74656800-74731400	Weak transcription	Rectal Smooth Muscle	rectum
4	chr5:74657800-74708000	Weak transcription	H9 Cell Line	embryonic stem cell
5	chr5:74659800-74720600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
6	chr5:74660000-74722800	Weak transcription	Fetal Heart	heart
7	chr5:74660200-74707800	Weak transcription	Stomach Mucosa	stomach
8	chr5:74665000-74703000	Strong transcription	Primary monocytes fromperipheralblood	blood
9	chr5:74667000-74723200	Strong transcription	Monocytes-CD14+_RO01746	blood
10	chr5:74667200-74693600	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
11	chr5:74668600-74691200	Strong transcription	Liver	Liver
12	chr5:74670800-74709400	Weak transcription	Pancreas	Pancrea
13	chr5:74670800-74720600	Weak transcription	Right Ventricle	heart
14	chr5:74670800-74731400	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
15	chr5:74671000-74722800	Weak transcription	Hela-S3	cervix
16	chr5:74674400-74761400	Weak transcription	Esophagus	oesophagus
17	chr5:74675400-74694800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
18	chr5:74675400-74699600	Weak transcription	Pancreatic Islets	Pancreatic Islet
19	chr5:74675400-74720800	Weak transcription	Small Intestine	intestine
20	chr5:74676200-74695000	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
21	chr5:74676200-74721000	Weak transcription	Brain Hippocampus Middle	brain
22	chr5:74677000-74701000	Weak transcription	A549	lung
23	chr5:74677400-74722800	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
24	chr5:74677600-74693600	Weak transcription	Colon Smooth Muscle	Colon
25	chr5:74677600-74709200	Weak transcription	Gastric	stomach
26	chr5:74677600-74734200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
27	chr5:74677800-74694800	Weak transcription	Fetal Kidney	kidney
28	chr5:74677800-74695200	Weak transcription	Brain Anterior Caudate	brain
29	chr5:74677800-74721000	Weak transcription	NH-A	brain
30	chr5:74677800-74725000	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
31	chr5:74677800-74731400	Weak transcription	Aorta	Aorta
32	chr5:74678000-74708000	Weak transcription	NHLF	lung
33	chr5:74678000-74720600	Weak transcription	Colonic Mucosa	Colon
34	chr5:74678000-74730800	Weak transcription	Psoas Muscle	Psoas
35	chr5:74678200-74691200	Weak transcription	HepG2	liver
36	chr5:74680600-74721000	Weak transcription	HMEC	breast
37	chr5:74680800-74694800	Weak transcription	Stomach Smooth Muscle	stomach
38	chr5:74680800-74722600	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
39	chr5:74681000-74723200	Weak transcription	HUVEC	blood vessel
40	chr5:74681400-74694800	Weak transcription	Placenta	Placenta
41	chr5:74681400-74718400	Weak transcription	Brain Germinal Matrix	brain
42	chr5:74681600-74694800	Weak transcription	Brain Inferior Temporal Lobe	brain
43	chr5:74681600-74695000	Weak transcription	Brain Substantia Nigra	brain
44	chr5:74681800-74720600	Weak transcription	Fetal Brain Male	brain
45	chr5:74682000-74695000	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
46	chr5:74682000-74699000	Weak transcription	Primary T killer memory cells from peripheral blood	blood
47	chr5:74682000-74708000	Weak transcription	H1 Cell Line	embryonic stem cell
48	chr5:74682200-74694200	Weak transcription	iPS-20b Cell Line	embryonic stem cell
49	chr5:74682200-74705000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
50	chr5:74683200-74698600	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin

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