Variant report

Variant	rs3796172
Chromosome Location	chr3:156528631-156528632
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:2)
CpG islands
(count:0)
Chromatin interactive
region (count:5)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:2 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr3:156528353-156528688	MCF-7	breast:	n/a	n/a
2	POLR2A	chr3:156528424-156528675	MCF-7	breast:	n/a	n/a

No data

(count:5 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr3:156467361..156469859-chr3:156528012..156530054,3	MCF-7	breast:
2	chr3:156527949..156530289-chr3:156543460..156546861,3	K562	blood:
3	chr3:156388866..156397270-chr3:156524172..156537549,71	MCF-7	breast:
4	chr3:156392305..156394108-chr3:156527817..156529889,2	MCF-7	breast:
5	chr3:156527592..156531932-chr3:156540848..156546879,8	MCF-7	breast:

No data

Variant related genes	Relation type
PA2G4P4	TF binding region
ENSG00000163659	Chromatin interaction
ENSG00000243926	Chromatin interaction
ENSG00000240875	Chromatin interaction
ENSG00000197980	Chromatin interaction

Extended variants
information (count: 69 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:65)

rs_ID	r²[population]
rs11710516	1.00[JPT][hapmap];0.89[ASN][1000 genomes]
rs11717138	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[YRI][hapmap];0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11927500	1.00[JPT][hapmap]
rs13321802	1.00[JPT][hapmap]
rs1430412	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs16826858	1.00[JPT][hapmap]
rs16826864	1.00[JPT][hapmap];0.84[ASN][1000 genomes]
rs16826899	1.00[JPT][hapmap]
rs16826906	1.00[JPT][hapmap]
rs16826948	1.00[JPT][hapmap]
rs171077	0.89[ASN][1000 genomes]
rs171080	1.00[JPT][hapmap];0.84[ASN][1000 genomes]
rs180746	0.89[ASN][1000 genomes]
rs182936	1.00[JPT][hapmap];0.89[ASN][1000 genomes]
rs2163296	0.94[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs237246	1.00[JPT][hapmap];0.89[ASN][1000 genomes]
rs2633815	1.00[JPT][hapmap]
rs28661978	0.84[ASN][1000 genomes]
rs2874490	1.00[JPT][hapmap]
rs2874491	1.00[JPT][hapmap]
rs343992	1.00[JPT][hapmap];0.95[ASN][1000 genomes]
rs344023	0.89[ASN][1000 genomes]
rs344032	0.84[ASN][1000 genomes]
rs344047	0.89[ASN][1000 genomes]
rs344048	0.89[ASN][1000 genomes]
rs344049	0.89[ASN][1000 genomes]
rs344050	0.89[ASN][1000 genomes]
rs344063	1.00[JPT][hapmap]
rs344076	1.00[JPT][hapmap];0.84[ASN][1000 genomes]
rs344077	0.84[ASN][1000 genomes]
rs344078	1.00[JPT][hapmap];0.84[ASN][1000 genomes]
rs344081	1.00[JPT][hapmap];0.84[ASN][1000 genomes]
rs344083	1.00[JPT][hapmap];0.84[ASN][1000 genomes]
rs344085	0.84[ASN][1000 genomes]
rs344086	1.00[JPT][hapmap];0.84[ASN][1000 genomes]
rs344088	1.00[JPT][hapmap];0.84[ASN][1000 genomes]
rs344090	1.00[JPT][hapmap];0.84[ASN][1000 genomes]
rs344091	1.00[JPT][hapmap];0.84[ASN][1000 genomes]
rs344092	1.00[JPT][hapmap]
rs414683	1.00[JPT][hapmap]
rs4680304	0.81[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs491423	1.00[JPT][hapmap]
rs59244547	0.84[ASN][1000 genomes]
rs6441099	1.00[JPT][hapmap]
rs6441100	1.00[JPT][hapmap]
rs6441104	1.00[JPT][hapmap]
rs6763233	1.00[JPT][hapmap]
rs6763644	1.00[JPT][hapmap]
rs6786167	1.00[JPT][hapmap]
rs6787535	1.00[JPT][hapmap]
rs6787952	1.00[JPT][hapmap]
rs6792917	1.00[JPT][hapmap]
rs6795327	1.00[JPT][hapmap]
rs6795516	1.00[JPT][hapmap]
rs6802042	1.00[JPT][hapmap]
rs6802511	1.00[JPT][hapmap]
rs7609851	1.00[JPT][hapmap]
rs7618306	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7630909	1.00[JPT][hapmap]
rs7634472	0.92[EUR][1000 genomes]
rs7635521	1.00[JPT][hapmap]
rs7650127	1.00[JPT][hapmap]
rs9847692	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9861359	1.00[JPT][hapmap]
rs9878709	1.00[JPT][hapmap]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv428745	chr3:156405054-156577840	Enhancers Strong transcription Weak transcription Genic enhancers Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	49 gene(s)	inside rSNPs	diseases
2	nsv877685	chr3:156444383-156611676	Enhancers Active TSS Weak transcription Flanking Active TSS Strong transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	48 gene(s)	inside rSNPs	diseases
3	nsv877686	chr3:156489509-156557697	Weak transcription Flanking Active TSS Enhancers Active TSS Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats Strong transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	42 gene(s)	inside rSNPs	diseases
4	nsv967081	chr3:156527290-156529310	Weak transcription Enhancers ZNF genes & repeats Genic enhancers Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:48 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:156502800-156529000	Weak transcription	Liver	Liver
2	chr3:156511200-156529000	Weak transcription	Primary T cells from cord blood	blood
3	chr3:156511400-156530400	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
4	chr3:156517400-156529000	Weak transcription	A549	lung
5	chr3:156518000-156529800	Weak transcription	Pancreatic Islets	Pancreatic Islet
6	chr3:156520200-156530400	Weak transcription	Right Ventricle	heart
7	chr3:156522200-156530400	Weak transcription	Gastric	stomach
8	chr3:156522400-156529000	Weak transcription	Primary hematopoietic stem cells short term culture	blood
9	chr3:156525000-156529000	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
10	chr3:156526200-156529000	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
11	chr3:156526200-156529000	Weak transcription	K562	blood
12	chr3:156526200-156530600	Weak transcription	HUES48 Cell Line	embryonic stem cell
13	chr3:156526400-156529000	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
14	chr3:156526400-156529000	Weak transcription	NH-A	brain
15	chr3:156526400-156530600	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
16	chr3:156526600-156529000	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
17	chr3:156526800-156528800	Weak transcription	Muscle Satellite Cultured Cells	--
18	chr3:156527000-156529000	Weak transcription	Skeletal Muscle Female	skeletal muscle
19	chr3:156527000-156529000	Weak transcription	Osteobl	bone
20	chr3:156527000-156529200	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
21	chr3:156527000-156530400	Weak transcription	Primary T helper cells fromperipheralblood	blood
22	chr3:156527200-156528800	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
23	chr3:156527200-156533200	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
24	chr3:156527400-156531600	Enhancers	Fetal Intestine Small	intestine
25	chr3:156527400-156533800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
26	chr3:156527800-156529000	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
27	chr3:156527800-156533000	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
28	chr3:156527800-156533800	Enhancers	HMEC	breast
29	chr3:156528200-156528800	Genic enhancers	NHEK	skin
30	chr3:156528200-156530000	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
31	chr3:156528200-156533600	Weak transcription	Stomach Smooth Muscle	stomach
32	chr3:156528400-156528800	Enhancers	Esophagus	oesophagus
33	chr3:156528400-156528800	ZNF genes & repeats	Lung	lung
34	chr3:156528400-156529000	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
35	chr3:156528400-156529400	Enhancers	Duodenum Mucosa	Duodenum
36	chr3:156528400-156530800	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
37	chr3:156528400-156531000	Enhancers	Rectal Mucosa Donor 31	rectum
38	chr3:156528400-156531200	Enhancers	Fetal Intestine Large	intestine
39	chr3:156528400-156531200	Enhancers	HUVEC	blood vessel
40	chr3:156528400-156531200	Enhancers	NHDF-Ad	bronchial
41	chr3:156528400-156532800	Enhancers	Breast Myoepithelial Primary Cells	Breast
42	chr3:156528600-156528800	Enhancers	Right Atrium	heart
43	chr3:156528600-156528800	Enhancers	Small Intestine	intestine
44	chr3:156528600-156529400	Enhancers	Sigmoid Colon	Sigmoid Colon
45	chr3:156528600-156529400	Genic enhancers	GM12878-XiMat	blood
46	chr3:156528600-156530000	Enhancers	HSMMtube	muscle
47	chr3:156528600-156531200	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
48	chr3:156528600-156531200	Enhancers	HepG2	liver

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