Variant report

Variant	rs6440696
Chromosome Location	chr3:150483260-150483261
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:4)
CpG islands
(count:0)
Chromatin interactive
region (count:8)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:4 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr3:150478964-150483373	HepG2	liver:	n/a	n/a
2	HEY1	chr3:150483257-150484555	HepG2	liver:	n/a	n/a
3	POLR2A	chr3:150480701-150484604	GM12891	blood:	n/a	n/a
4	POLR2A	chr3:150476896-150484835	GM12878	blood:	n/a	n/a

No data

(count:8 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr3:150482143..150484358-chr3:150560207..150562152,2	MCF-7	breast:
2	chr3:150482364..150486179-chr3:150581053..150584766,4	MCF-7	breast:
3	chr3:150319354..150323687-chr3:150477863..150484487,11	MCF-7	breast:
4	chr3:150421205..150424923-chr3:150480120..150484463,5	MCF-7	breast:
5	chr3:150261800..150265866-chr3:150477764..150484308,7	MCF-7	breast:
6	chr3:150483248..150484206-chr3:150504302..150505031,2	MCF-7	breast:
7	chr3:150482246..150483991-chr3:150496557..150499454,2	MCF-7	breast:
8	chr3:150433681..150449199-chr3:150473254..150487048,35	MCF-7	breast:

No data

Variant related genes	Relation type
SIAH2	TF binding region
ENSG00000120742	Chromatin interaction
ENSG00000198843	Chromatin interaction
ENSG00000163645	Chromatin interaction
ENSG00000144895	Chromatin interaction
ENSG00000240137	Chromatin interaction
ENSG00000244668	Chromatin interaction

Extended variants
information (count: 51 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:49)

rs_ID	r²[population]
rs1444197	0.81[AMR][1000 genomes];0.81[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs1533711	0.84[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs16862837	0.84[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs16862842	0.81[EUR][1000 genomes]
rs1814463	0.81[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1814464	0.86[AFR][1000 genomes];0.88[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1838337	0.81[AMR][1000 genomes];0.81[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs1879421	0.84[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs1879422	0.81[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs1915365	0.81[AMR][1000 genomes];0.81[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2014279	0.81[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2018246	0.81[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2116685	0.84[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs2166061	0.86[AMR][1000 genomes];0.88[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2869479	0.81[AMR][1000 genomes];0.94[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs34348847	1.00[EUR][1000 genomes]
rs34771595	0.87[EUR][1000 genomes]
rs3851356	0.81[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs41372346	0.81[EUR][1000 genomes]
rs57278175	0.87[EUR][1000 genomes]
rs57869178	1.00[EUR][1000 genomes]
rs58403524	0.81[EUR][1000 genomes]
rs60259684	0.80[AMR][1000 genomes];1.00[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs60523415	0.81[EUR][1000 genomes]
rs6440697	0.88[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs6440698	0.88[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs6769917	0.80[AMR][1000 genomes];1.00[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs6777178	0.80[AMR][1000 genomes];1.00[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs6788895	0.84[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs6795396	0.87[EUR][1000 genomes]
rs6803830	0.81[EUR][1000 genomes]
rs6805481	0.82[AMR][1000 genomes];1.00[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs6806197	0.87[EUR][1000 genomes]
rs71764080	0.81[EUR][1000 genomes]
rs72993403	0.81[EUR][1000 genomes]
rs73003787	0.87[EUR][1000 genomes]
rs73003792	0.82[AMR][1000 genomes];1.00[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs73005814	0.82[EUR][1000 genomes]
rs73010930	0.84[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs73010941	0.86[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs73010947	0.83[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs73010956	0.80[AMR][1000 genomes];1.00[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs73010964	1.00[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs73010965	1.00[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs73010967	0.81[EUR][1000 genomes]
rs73869297	0.87[EUR][1000 genomes]
rs7617507	1.00[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7628481	0.87[EUR][1000 genomes]
rs7628776	0.88[EUR][1000 genomes]

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	nsv532662	chr3:150180747-150633414	Weak transcription Flanking Active TSS Strong transcription Enhancers Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	101 gene(s)	inside rSNPs	diseases
2	esv1820145	chr3:150478018-150487945	Enhancers Active TSS Weak transcription Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	40 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:58 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:150481800-150483600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
2	chr3:150482000-150483400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
3	chr3:150482000-150483600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
4	chr3:150482000-150483800	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
5	chr3:150482000-150483800	Weak transcription	H9 Cell Line	embryonic stem cell
6	chr3:150482000-150483800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
7	chr3:150482000-150488200	Weak transcription	Left Ventricle	heart
8	chr3:150482000-150488200	Weak transcription	Ovary	ovary
9	chr3:150482000-150491600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
10	chr3:150482000-150491800	Weak transcription	Gastric	stomach
11	chr3:150482200-150483400	Weak transcription	NH-A	brain
12	chr3:150482200-150483800	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
13	chr3:150482200-150483800	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
14	chr3:150482200-150483800	Enhancers	Stomach Mucosa	stomach
15	chr3:150482200-150484200	Flanking Active TSS	HepG2	liver
16	chr3:150482200-150484400	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
17	chr3:150482200-150484400	Flanking Active TSS	Primary T helper cells PMA-I stimulated	--
18	chr3:150482200-150485000	Enhancers	Primary B cells from peripheral blood	blood
19	chr3:150482200-150485600	Weak transcription	Right Atrium	heart
20	chr3:150482400-150484400	Enhancers	ES-I3 Cell Line	embryonic stem cell
21	chr3:150482400-150484400	Flanking Active TSS	GM12878-XiMat	blood
22	chr3:150482600-150483600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
23	chr3:150482600-150483600	Enhancers	Primary T helper cells fromperipheralblood	blood
24	chr3:150482600-150483800	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
25	chr3:150482600-150483800	Weak transcription	Fetal Thymus	thymus
26	chr3:150482600-150483800	Weak transcription	HSMM	muscle
27	chr3:150482600-150483800	Weak transcription	NHLF	lung
28	chr3:150482600-150484000	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
29	chr3:150482600-150484000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
30	chr3:150482600-150484000	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
31	chr3:150482600-150484200	Weak transcription	HSMMtube	muscle
32	chr3:150482600-150488000	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
33	chr3:150482600-150488400	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
34	chr3:150482600-150488400	Weak transcription	NHDF-Ad	bronchial
35	chr3:150482600-150488400	Weak transcription	Osteobl	bone
36	chr3:150482800-150483800	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
37	chr3:150482800-150483800	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
38	chr3:150482800-150483800	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
39	chr3:150482800-150483800	Weak transcription	Fetal Intestine Large	intestine
40	chr3:150482800-150483800	Weak transcription	Fetal Intestine Small	intestine
41	chr3:150482800-150483800	Weak transcription	HMEC	breast
42	chr3:150482800-150484400	Enhancers	K562	blood
43	chr3:150482800-150484800	Enhancers	Primary hematopoietic stem cells short term culture	blood
44	chr3:150482800-150488000	Weak transcription	Fetal Heart	heart
45	chr3:150482800-150488200	Weak transcription	Muscle Satellite Cultured Cells	--
46	chr3:150482800-150488400	Weak transcription	Placenta	Placenta
47	chr3:150482800-150488800	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
48	chr3:150482800-150488800	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
49	chr3:150482800-150488800	Weak transcription	Adipose Nuclei	Adipose
50	chr3:150482800-150492600	Weak transcription	Spleen	Spleen

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