Variant report

Variant	rs755082
Chromosome Location	chr3:42542992-42542993
allele	A/C
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	CTCF	chr3:42542940-42543090	GM12874	blood:	n/a	n/a
2	CTCF	chr3:42542984-42543044	Pancreas_OC	pancreas:	n/a	n/a
3	E2F6	chr3:42542766-42544628	H1-hESC	embryonic stem cell:	n/a	chr3:42543156-42543166 chr3:42544079-42544088 chr3:42542968-42542978 chr3:42544023-42544032
4	CTCF	chr3:42542960-42543110	GM12801	blood:	n/a	n/a
5	E2F6	chr3:42542720-42544609	H1-hESC	embryonic stem cell:	n/a	chr3:42543156-42543166 chr3:42544079-42544088 chr3:42542968-42542978 chr3:42544023-42544032
6	CTBP2	chr3:42542581-42544333	H1-hESC	embryonic stem cell:	n/a	n/a
7	MAX	chr3:42542801-42544630	H1-hESC	embryonic stem cell:	n/a	chr3:42544354-42544364
8	SIN3A	chr3:42542545-42544245	H1-hESC	embryonic stem cell:	n/a	chr3:42543175-42543189 chr3:42544122-42544131 chr3:42543460-42543471 chr3:42543617-42543626
9	MAX	chr3:42542424-42544191	H1-hESC	embryonic stem cell:	n/a	n/a
10	CTCF	chr3:42542953-42544353	SK-N-SH	brain:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr3:42529189..42533440-chr3:42542111..42547805,7	MCF-7	breast:
2	chr3:42542597..42545270-chr3:42568668..42571142,2	K562	blood:

Variant related genes	Relation type
VIPR1	TF binding region
ENSG00000114812	Chromatin interaction

Extended variants
information (count: 10 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:5)

rs_ID	r²[population]
rs1876504	0.96[YRI][hapmap];0.87[AFR][1000 genomes];0.93[AMR][1000 genomes]
rs1876506	0.85[ASW][hapmap];0.83[LWK][hapmap];1.00[MEX][hapmap];0.96[YRI][hapmap];0.88[AFR][1000 genomes];0.93[AMR][1000 genomes]
rs7615762	0.96[YRI][hapmap];1.00[AFR][1000 genomes];0.93[AMR][1000 genomes]
rs7628235	1.00[MEX][hapmap];0.89[YRI][hapmap]
rs7651400	0.91[AFR][1000 genomes];0.93[AMR][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	nsv529987	chr3:41921995-42591771	Bivalent Enhancer Weak transcription Flanking Active TSS Strong transcription Enhancers Flanking Bivalent TSS/Enh Active TSS 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	32 gene(s)	inside rSNPs	diseases
2	nsv1005533	chr3:41953873-42596375	Enhancers Flanking Bivalent TSS/Enh Genic enhancers Weak transcription Flanking Active TSS Strong transcription Bivalent/Poised TSS Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	31 gene(s)	inside rSNPs	diseases
3	esv1804804	chr3:42515186-42582403	Flanking Active TSS Enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Weak transcription Transcr. at gene 5' and 3' Strong transcription Genic enhancers Bivalent/Poised TSS Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
4	nsv527430	chr3:42534042-42557199	Weak transcription Enhancers Genic enhancers Active TSS Bivalent Enhancer Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Strong transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
5	esv1814102	chr3:42539966-42582403	Flanking Active TSS Weak transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Enhancers Active TSS Genic enhancers Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:87 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:42535000-42543000	Weak transcription	Left Ventricle	heart
2	chr3:42535600-42543000	Weak transcription	Lung	lung
3	chr3:42538400-42543000	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
4	chr3:42542000-42544800	Bivalent/Poised TSS	ES-I3 Cell Line	embryonic stem cell
5	chr3:42542200-42545200	Bivalent/Poised TSS	HUES6 Cell Line	embryonic stem cell
6	chr3:42542400-42543000	Bivalent Enhancer	Cortex derived primary cultured neurospheres	brain
7	chr3:42542400-42543000	Bivalent Enhancer	Foreskin Keratinocyte Primary Cells skin02	Skin
8	chr3:42542400-42543200	Bivalent/Poised TSS	iPS DF 6.9 Cell Line	embryonic stem cell
9	chr3:42542400-42543400	Bivalent/Poised TSS	H1 Cell Line	embryonic stem cell
10	chr3:42542400-42543400	Bivalent/Poised TSS	H9 Cell Line	embryonic stem cell
11	chr3:42542400-42544600	Bivalent/Poised TSS	HUES64 Cell Line	embryonic stem cell
12	chr3:42542600-42543000	Flanking Bivalent TSS/Enh	ES-UCSF4 Cell Line	embryonic stem cell
13	chr3:42542600-42543000	Bivalent Enhancer	Primary B cells from peripheral blood	blood
14	chr3:42542600-42543000	Bivalent Enhancer	Primary T cells from cord blood	blood
15	chr3:42542600-42543000	Bivalent Enhancer	Primary T cells fromperipheralblood	blood
16	chr3:42542600-42543000	Bivalent Enhancer	Primary hematopoietic stem cells short term culture	blood
17	chr3:42542600-42543000	Bivalent Enhancer	Foreskin Melanocyte Primary Cells skin01	Skin
18	chr3:42542600-42543000	Bivalent Enhancer	Fetal Adrenal Gland	Adrenal Gland
19	chr3:42542600-42543000	Bivalent Enhancer	Fetal Brain Female	brain
20	chr3:42542600-42543000	Bivalent Enhancer	Fetal Muscle Trunk	muscle
21	chr3:42542600-42543000	Bivalent Enhancer	Placenta	Placenta
22	chr3:42542600-42543000	Bivalent Enhancer	Fetal Stomach	stomach
23	chr3:42542600-42543200	Bivalent/Poised TSS	iPS-18 Cell Line	embryonic stem cell
24	chr3:42542600-42543200	Enhancers	Fetal Heart	heart
25	chr3:42542600-42543600	Bivalent Enhancer	Placenta Amnion	Placenta Amnion
26	chr3:42542600-42544000	Flanking Active TSS	Breast Myoepithelial Primary Cells	Breast
27	chr3:42542600-42544200	Flanking Bivalent TSS/Enh	Adipose Nuclei	Adipose
28	chr3:42542600-42544200	Flanking Bivalent TSS/Enh	Colonic Mucosa	Colon
29	chr3:42542600-42544400	Flanking Bivalent TSS/Enh	Ganglion Eminence derived primary cultured neurospheres	brain
30	chr3:42542600-42544800	Bivalent/Poised TSS	ES-WA7 Cell Line	embryonic stem cell
31	chr3:42542600-42545000	Bivalent/Poised TSS	iPS-15b Cell Line	embryonic stem cell
32	chr3:42542600-42545200	Bivalent/Poised TSS	HUES48 Cell Line	embryonic stem cell
33	chr3:42542600-42545200	Bivalent/Poised TSS	iPS-20b Cell Line	embryonic stem cell
34	chr3:42542800-42543000	Bivalent Enhancer	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
35	chr3:42542800-42543000	Bivalent/Poised TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
36	chr3:42542800-42543000	Bivalent Enhancer	Primary B cells from cord blood	blood
37	chr3:42542800-42543000	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
38	chr3:42542800-42543000	Enhancers	Primary T helper naive cells from peripheral blood	blood
39	chr3:42542800-42543000	Bivalent Enhancer	Primary T helper naive cells fromperipheralblood	blood
40	chr3:42542800-42543000	Bivalent Enhancer	Primary T helper cells PMA-I stimulated	--
41	chr3:42542800-42543000	Bivalent/Poised TSS	Primary T regulatory cells fromperipheralblood	blood
42	chr3:42542800-42543000	Enhancers	Primary T cells effector/memory enriched fromperipheralblood	blood
43	chr3:42542800-42543000	Enhancers	Primary T killer naive cells fromperipheralblood	blood
44	chr3:42542800-42543000	Bivalent/Poised TSS	Foreskin Fibroblast Primary Cells skin01	Skin
45	chr3:42542800-42543000	Bivalent Enhancer	Foreskin Melanocyte Primary Cells skin03	Skin
46	chr3:42542800-42543000	Bivalent Enhancer	Primary mononuclear cells fromperipheralblood	Blood
47	chr3:42542800-42543000	Flanking Active TSS	Liver	Liver
48	chr3:42542800-42543000	Enhancers	Brain Anterior Caudate	brain
49	chr3:42542800-42543000	Active TSS	Brain Cingulate Gyrus	brain
50	chr3:42542800-42543000	Bivalent Enhancer	Brain Dorsolateral Prefrontal Cortex	brain

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