Variant report

Variant	rs3935470
Chromosome Location	chr5:74352180-74352181
allele	C/T
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	chr5:74351191-74352391	H1-hESC	embryonic stem cell:	n/a	n/a
2	JUN	chr5:74351437-74352298	H1-hESC	embryonic stem cell:	n/a	chr5:74351967-74351980
3	SRF	chr5:74351390-74352243	H1-hESC	embryonic stem cell:	n/a	chr5:74351600-74351617
4	POLR2A	chr5:74352057-74352335	H1-hESC	embryonic stem cell:	n/a	n/a
5	JUND	chr5:74351557-74352497	H1-hESC	embryonic stem cell:	n/a	n/a
6	TBP	chr5:74351406-74352398	H1-hESC	embryonic stem cell:	n/a	n/a
7	SRF	chr5:74351391-74352309	ECC-1	luminal epithelium:	n/a	chr5:74351600-74351617
8	TAF7	chr5:74351286-74352444	H1-hESC	embryonic stem cell:	n/a	n/a
9	POLR2A	chr5:74351999-74352351	H1-hESC	embryonic stem cell:	n/a	n/a
10	POLR2A	chr5:74351350-74352380	H1-hESC	embryonic stem cell:	n/a	n/a
11	CREB1	chr5:74351429-74352200	H1-hESC	embryonic stem cell:	n/a	n/a
12	POLR2A	chr5:74340910-74352626	H1-hESC	embryonic stem cell:	n/a	n/a
13	ATF2	chr5:74351364-74352195	H1-hESC	embryonic stem cell:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr5:74346800..74348616-chr5:74350730..74353345,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000250889	TF binding region
ENSG00000250889	Chromatin interaction

Extended variants
information (count: 29 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:27)

rs_ID	r²[population]
rs10462354	1.00[ASW][hapmap];0.80[CEU][hapmap]
rs10942729	1.00[ASW][hapmap];0.80[CEU][hapmap]
rs12656177	0.83[EUR][1000 genomes]
rs1345704	0.80[CEU][hapmap]
rs1363577	1.00[ASW][hapmap];0.80[CEU][hapmap]
rs1363579	0.83[CEU][hapmap]
rs1422697	0.80[CEU][hapmap]
rs1422698	1.00[ASW][hapmap];0.80[CEU][hapmap]
rs1422701	0.80[CEU][hapmap]
rs1477937	1.00[ASW][hapmap]
rs2216638	1.00[ASW][hapmap];0.80[CEU][hapmap]
rs4627970	0.80[CEU][hapmap]
rs4703657	1.00[ASW][hapmap];0.80[CEU][hapmap]
rs6864324	1.00[ASW][hapmap];0.80[CEU][hapmap]
rs6864485	0.80[CEU][hapmap]
rs6866661	1.00[ASW][hapmap]
rs6879894	1.00[ASW][hapmap];0.80[CEU][hapmap]
rs6896474	1.00[ASW][hapmap];0.80[CEU][hapmap]
rs6898116	1.00[ASW][hapmap]
rs7356697	0.83[EUR][1000 genomes]
rs7704104	0.80[CEU][hapmap]
rs7707246	0.82[EUR][1000 genomes]
rs7735057	0.80[CEU][hapmap]
rs9293650	1.00[ASW][hapmap];0.80[CEU][hapmap]
rs9654426	0.80[CEU][hapmap]
rs9654428	0.80[CEU][hapmap]
rs9654429	0.80[CEU][hapmap]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1018865	chr5:74246293-74494552	Weak transcription Active TSS Flanking Active TSS Enhancers Bivalent Enhancer Genic enhancers Strong transcription Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
2	esv1835096	chr5:74336883-74356857	Enhancers Weak transcription Strong transcription Flanking Active TSS Bivalent Enhancer Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	n/a

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs3935470	HMGCR	cis	cerebellum	SCAN

Chromatin state (count:45 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:74350200-74357200	Enhancers	Primary hematopoietic stem cells short term culture	blood
2	chr5:74350400-74352200	Enhancers	Placenta Amnion	Placenta Amnion
3	chr5:74350400-74352400	Enhancers	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
4	chr5:74350400-74352400	Enhancers	Placenta	Placenta
5	chr5:74350400-74352800	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
6	chr5:74350400-74355000	Enhancers	Primary T killer naive cells fromperipheralblood	blood
7	chr5:74350400-74355800	Enhancers	Primary T cells effector/memory enriched fromperipheralblood	blood
8	chr5:74350400-74360000	Enhancers	Fetal Thymus	thymus
9	chr5:74350600-74352400	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
10	chr5:74350600-74352400	Weak transcription	Primary hematopoietic stem cells	blood
11	chr5:74350600-74352400	Enhancers	NHDF-Ad	bronchial
12	chr5:74350600-74353000	Enhancers	Primary T helper naive cells fromperipheralblood	blood
13	chr5:74350600-74356400	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
14	chr5:74350600-74357400	Enhancers	Primary T cells fromperipheralblood	blood
15	chr5:74350800-74352400	Enhancers	iPS DF 6.9 Cell Line	embryonic stem cell
16	chr5:74350800-74352600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
17	chr5:74350800-74352800	Enhancers	H1 Cell Line	embryonic stem cell
18	chr5:74350800-74353000	Enhancers	Thymus	Thymus
19	chr5:74350800-74353200	Enhancers	Primary T helper naive cells from peripheral blood	blood
20	chr5:74350800-74357200	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
21	chr5:74350800-74357400	Enhancers	Primary T helper cells fromperipheralblood	blood
22	chr5:74350800-74359600	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
23	chr5:74350800-74367600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
24	chr5:74351000-74352400	Enhancers	Stomach Smooth Muscle	stomach
25	chr5:74351000-74352600	Enhancers	iPS-18 Cell Line	embryonic stem cell
26	chr5:74351000-74353000	Enhancers	Primary T cells from cord blood	blood
27	chr5:74351000-74353400	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
28	chr5:74351000-74355000	Enhancers	Primary T killer memory cells from peripheral blood	blood
29	chr5:74351000-74357000	Enhancers	Primary T regulatory cells fromperipheralblood	blood
30	chr5:74351200-74354800	Enhancers	Primary T helper cells PMA-I stimulated	--
31	chr5:74351400-74352400	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
32	chr5:74351400-74353600	Enhancers	iPS-20b Cell Line	embryonic stem cell
33	chr5:74351400-74353800	Enhancers	Hela-S3	cervix
34	chr5:74351600-74352400	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
35	chr5:74351600-74352400	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
36	chr5:74351600-74353200	Enhancers	HUES64 Cell Line	embryonic stem cell
37	chr5:74351600-74355600	Weak transcription	Pancreas	Pancrea
38	chr5:74351800-74352400	Enhancers	NH-A	brain
39	chr5:74351800-74353200	Enhancers	HUES6 Cell Line	embryonic stem cell
40	chr5:74351800-74353400	Enhancers	ES-I3 Cell Line	embryonic stem cell
41	chr5:74352000-74352200	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
42	chr5:74352000-74352400	Flanking Active TSS	HUES48 Cell Line	embryonic stem cell
43	chr5:74352000-74352600	Enhancers	H9 Cell Line	embryonic stem cell
44	chr5:74352000-74352600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
45	chr5:74352000-74356000	Enhancers	Primary T helper 17 cells PMA-I stimulated	--

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