Variant report

Variant	rs3733907
Chromosome Location	chr5:74665860-74665861
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr5:74663956-74666439	HepG2	liver:	n/a	n/a
2	POLR2A	chr5:74663925-74666110	K562	blood:	n/a	n/a

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-ANKRD31-2	chr5:74664312-74667666	NONHSAT102205

Variant related genes	Relation type
ENSG00000242198	TF binding region

Extended variants
information (count: 15 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:12)

rs_ID	r²[population]
rs10515197	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.93[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.83[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12659791	0.88[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs17648288	0.90[LWK][hapmap];1.00[YRI][hapmap];0.82[AFR][1000 genomes]
rs2303151	1.00[ASW][hapmap];0.93[CHD][hapmap]
rs3756558	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]
rs3761739	1.00[CEU][hapmap];0.94[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.93[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.88[AMR][1000 genomes];0.95[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs4704215	0.84[ASN][1000 genomes]
rs55727654	0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs55926501	0.93[AFR][1000 genomes];0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs5744625	1.00[CEU][hapmap];0.92[CHB][hapmap];0.93[JPT][hapmap];0.84[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs5744662	0.86[AFR][1000 genomes];0.82[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs7726771	0.82[ASN][1000 genomes]

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	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

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs3733907	COL4A3BP	cis	parietal	SCAN
rs3733907	HMGCR	cis	parietal	SCAN
rs3733907	HMGCR	cis	cerebellum	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:74656400-74669800	Weak transcription	Ovary	ovary
2	chr5:74656400-74670400	Weak transcription	Right Ventricle	heart
3	chr5:74656400-74673600	Weak transcription	Psoas Muscle	Psoas
4	chr5:74656400-74673600	Weak transcription	Small Intestine	intestine
5	chr5:74656400-74673600	Weak transcription	Spleen	Spleen
6	chr5:74656400-74674000	Weak transcription	Brain Germinal Matrix	brain
7	chr5:74656400-74674800	Weak transcription	Primary T helper naive cells from peripheral blood	blood
8	chr5:74656400-74674800	Weak transcription	Brain Substantia Nigra	brain
9	chr5:74656400-74676800	Weak transcription	Fetal Brain Male	brain
10	chr5:74656400-74687200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
11	chr5:74656400-74725600	Weak transcription	Placenta Amnion	Placenta Amnion
12	chr5:74656600-74668400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
13	chr5:74656600-74670600	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
14	chr5:74656600-74675600	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
15	chr5:74656600-74675800	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
16	chr5:74656600-74675800	Weak transcription	Brain Cingulate Gyrus	brain
17	chr5:74656600-74676800	Weak transcription	Primary T killer memory cells from peripheral blood	blood
18	chr5:74656600-74677200	Weak transcription	Aorta	Aorta
19	chr5:74656600-74694800	Weak transcription	Brain Angular Gyrus	brain
20	chr5:74656800-74669600	Weak transcription	Hela-S3	cervix
21	chr5:74656800-74670200	Weak transcription	HepG2	liver
22	chr5:74656800-74670400	Weak transcription	Brain Inferior Temporal Lobe	brain
23	chr5:74656800-74676200	Weak transcription	Colonic Mucosa	Colon
24	chr5:74656800-74731400	Weak transcription	Rectal Smooth Muscle	rectum
25	chr5:74657400-74674800	Weak transcription	A549	lung
26	chr5:74657600-74673600	Weak transcription	Lung	lung
27	chr5:74657800-74668600	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
28	chr5:74657800-74668800	Weak transcription	Primary B cells from peripheral blood	blood
29	chr5:74657800-74669400	Weak transcription	Duodenum Smooth Muscle	Duodenum
30	chr5:74657800-74708000	Weak transcription	H9 Cell Line	embryonic stem cell
31	chr5:74658000-74674800	Weak transcription	H1 Cell Line	embryonic stem cell
32	chr5:74658400-74668600	Weak transcription	Adipose Nuclei	Adipose
33	chr5:74658400-74673200	Weak transcription	iPS-18 Cell Line	embryonic stem cell
34	chr5:74658600-74669600	Weak transcription	Brain Anterior Caudate	brain
35	chr5:74658600-74673200	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
36	chr5:74658600-74674800	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
37	chr5:74658600-74674800	Weak transcription	Fetal Kidney	kidney
38	chr5:74658800-74667200	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
39	chr5:74658800-74668200	Weak transcription	Primary T helper cells PMA-I stimulated	--
40	chr5:74658800-74669400	Weak transcription	HSMMtube	muscle
41	chr5:74659000-74668600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
42	chr5:74659000-74668600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
43	chr5:74659000-74668600	Weak transcription	Sigmoid Colon	Sigmoid Colon
44	chr5:74659000-74668800	Weak transcription	Primary T cells fromperipheralblood	blood
45	chr5:74659000-74669200	Weak transcription	Fetal Brain Female	brain
46	chr5:74659000-74674600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
47	chr5:74659200-74667400	Weak transcription	Fetal Intestine Large	intestine
48	chr5:74659200-74668400	Weak transcription	iPS-20b Cell Line	embryonic stem cell
49	chr5:74659200-74668600	Weak transcription	Primary T helper cells fromperipheralblood	blood
50	chr5:74659200-74668600	Weak transcription	Dnd41	blood

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