Variant report

Variant	rs3796376
Chromosome Location	chr3:46009491-46009492
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr3:45994933..45997538-chr3:46007570..46009630,2	K562	blood:
2	chr3:46000938..46003324-chr3:46007900..46010295,2	K562	blood:
3	chr3:46009297..46011383-chr3:46015916..46019063,3	K562	blood:
4	chr3:46002701..46006681-chr3:46007479..46011297,4	K562	blood:
5	chr3:46008363..46011066-chr3:46026720..46029201,2	MCF-7	breast:

Extended variants
information (count: 44 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:40)

rs_ID	r²[population]
rs12054287	1.00[CEU][hapmap]
rs12630101	0.84[CHB][hapmap];0.84[CHD][hapmap]
rs12635494	0.83[ASN][1000 genomes]
rs12639598	0.82[CHD][hapmap]
rs1491960	0.89[CEU][hapmap]
rs17078449	0.89[CEU][hapmap];0.81[CHB][hapmap];0.85[CHD][hapmap];0.85[JPT][hapmap];0.84[MEX][hapmap];0.91[TSI][hapmap];0.86[AMR][1000 genomes];0.86[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs17078454	0.86[AMR][1000 genomes];0.86[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs1994490	0.85[CHB][hapmap];0.88[CHD][hapmap];0.83[ASN][1000 genomes]
rs2234351	0.86[AMR][1000 genomes];0.86[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs35537559	0.82[EUR][1000 genomes]
rs3733100	0.90[CHB][hapmap];0.83[ASN][1000 genomes]
rs3774638	0.88[CEU][hapmap];0.85[CHB][hapmap];0.85[JPT][hapmap];0.86[AMR][1000 genomes];0.86[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs3774640	0.86[AMR][1000 genomes];0.86[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs3796375	0.85[CHB][hapmap];0.86[CHD][hapmap];0.81[ASN][1000 genomes]
rs3821883	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs3821884	0.85[CHB][hapmap];0.88[CHD][hapmap]
rs4490402	0.89[CEU][hapmap]
rs57204020	0.86[AMR][1000 genomes];0.86[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs59226168	0.80[EUR][1000 genomes]
rs59767267	0.96[AMR][1000 genomes];0.94[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs60237998	0.85[EUR][1000 genomes]
rs60779624	0.86[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs62242787	0.86[AMR][1000 genomes];0.86[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs62242788	0.93[AMR][1000 genomes];0.91[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs62242796	0.82[EUR][1000 genomes]
rs62245106	0.93[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs62245108	0.86[EUR][1000 genomes]
rs6778225	0.86[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs6778324	0.86[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs6781121	0.84[JPT][hapmap]
rs6781668	1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6800954	0.89[CEU][hapmap];0.80[CHD][hapmap];0.91[TSI][hapmap];0.85[EUR][1000 genomes]
rs737452	0.82[CHD][hapmap]
rs751552	0.85[CHB][hapmap];0.86[CHD][hapmap]
rs751553	0.85[CHB][hapmap];0.86[CHD][hapmap]
rs7623476	0.85[CEU][hapmap]
rs7629999	0.89[AMR][1000 genomes];0.80[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs7631809	0.86[EUR][1000 genomes]
rs7643426	0.94[CEU][hapmap];0.83[CHD][hapmap];1.00[JPT][hapmap];0.91[TSI][hapmap];0.88[AMR][1000 genomes];0.83[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs936939	0.89[CEU][hapmap];0.85[CHB][hapmap];0.85[CHD][hapmap];0.85[JPT][hapmap];0.91[TSI][hapmap];0.86[AMR][1000 genomes];0.86[EUR][1000 genomes];0.86[ASN][1000 genomes]

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	nsv876734	chr3:45725031-46468467	Weak transcription Enhancers Active TSS Flanking Active TSS Genic enhancers Bivalent/Poised TSS Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	42 gene(s)	inside rSNPs	diseases
2	nsv498008	chr3:45733423-46319401	Strong transcription Active TSS Genic enhancers Enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Weak transcription Flanking 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	29 gene(s)	inside rSNPs	diseases
3	nsv834678	chr3:45804294-46010256	Enhancers Flanking Bivalent TSS/Enh Strong transcription Weak transcription Bivalent Enhancer Flanking Active TSS Genic enhancers Active TSS ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	11 gene(s)	inside rSNPs	diseases
4	nsv876736	chr3:45900621-46027410	Strong transcription Enhancers Transcr. at gene 5' and 3' Weak transcription Genic enhancers Bivalent Enhancer Flanking Active TSS ZNF genes & repeats Active TSS Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	8 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:126 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:45959400-46009800	Weak transcription	Placenta Amnion	Placenta Amnion
2	chr3:45980800-46013400	Strong transcription	Primary hematopoietic stem cells short term culture	blood
3	chr3:45981600-46025000	Strong transcription	Fetal Intestine Large	intestine
4	chr3:45983200-46012400	Strong transcription	Monocytes-CD14+_RO01746	blood
5	chr3:45986400-46012200	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
6	chr3:45986400-46026600	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
7	chr3:45986600-46012000	Strong transcription	Primary monocytes fromperipheralblood	blood
8	chr3:45986600-46026800	Strong transcription	HUES48 Cell Line	embryonic stem cell
9	chr3:45986800-46012200	Strong transcription	Primary B cells from peripheral blood	blood
10	chr3:45987200-46013600	Strong transcription	Primary hematopoietic stem cells	blood
11	chr3:45987200-46027200	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
12	chr3:45987400-46026600	Strong transcription	HUES6 Cell Line	embryonic stem cell
13	chr3:45987800-46012200	Strong transcription	HepG2	liver
14	chr3:45987800-46026400	Strong transcription	iPS-20b Cell Line	embryonic stem cell
15	chr3:45987800-46026800	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
16	chr3:45987800-46027200	Strong transcription	HUES64 Cell Line	embryonic stem cell
17	chr3:45988000-46012000	Strong transcription	H1 Cell Line	embryonic stem cell
18	chr3:45988000-46026600	Strong transcription	iPS-18 Cell Line	embryonic stem cell
19	chr3:45988200-46009800	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
20	chr3:45988200-46012000	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
21	chr3:45988800-46011800	Strong transcription	Lung	lung
22	chr3:45989400-46013800	Strong transcription	Dnd41	blood
23	chr3:45990600-46017200	Strong transcription	Rectal Mucosa Donor 29	rectum
24	chr3:45991200-46012000	Strong transcription	Sigmoid Colon	Sigmoid Colon
25	chr3:45991200-46017400	Strong transcription	Rectal Mucosa Donor 31	rectum
26	chr3:45991400-46009800	Strong transcription	Aorta	Aorta
27	chr3:45991400-46009800	Strong transcription	NHLF	lung
28	chr3:45992600-46013200	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
29	chr3:45992600-46013600	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
30	chr3:45993000-46013600	Strong transcription	Thymus	Thymus
31	chr3:45996200-46025400	Strong transcription	Liver	Liver
32	chr3:45998400-46009600	Strong transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
33	chr3:45999200-46010600	Strong transcription	iPS-15b Cell Line	embryonic stem cell
34	chr3:45999200-46011600	Strong transcription	iPS DF 6.9 Cell Line	embryonic stem cell
35	chr3:45999200-46011800	Strong transcription	H9 Cell Line	embryonic stem cell
36	chr3:45999200-46011800	Strong transcription	Pancreas	Pancrea
37	chr3:45999200-46012200	Genic enhancers	Primary T cells fromperipheralblood	blood
38	chr3:45999400-46012000	Strong transcription	Ovary	ovary
39	chr3:45999400-46018200	Strong transcription	Fetal Lung	lung
40	chr3:46000000-46029600	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
41	chr3:46000400-46010200	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
42	chr3:46000800-46009800	Strong transcription	NHDF-Ad	bronchial
43	chr3:46000800-46010000	Strong transcription	Osteobl	bone
44	chr3:46001000-46012200	Strong transcription	Foreskin Melanocyte Primary Cells skin01	Skin
45	chr3:46002000-46011400	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
46	chr3:46002000-46014200	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
47	chr3:46002200-46011800	Strong transcription	Spleen	Spleen
48	chr3:46002200-46018600	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
49	chr3:46002400-46010200	Strong transcription	NHEK	skin
50	chr3:46002400-46012800	Strong transcription	Cortex derived primary cultured neurospheres	brain

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