Variant report

Variant	rs2871960
Chromosome Location	chr3:141121814-141121815
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr3:141103343..141105459-chr3:141119625..141122357,2	MCF-7	breast:
2	chr3:141085384..141087888-chr3:141119776..141122327,3	MCF-7	breast:
3	chr3:141106008..141109150-chr3:141119369..141122507,3	MCF-7	breast:
4	chr3:141084785..141090037-chr3:141119214..141123075,16	MCF-7	breast:
5	chr3:141120069..141122089-chr3:141143062..141145117,2	MCF-7	breast:
6	chr3:141086056..141088881-chr3:141120759..141122855,2	K562	blood:

Variant related genes	Relation type
ENSG00000249417	Chromatin interaction
ENSG00000177311	Chromatin interaction

Extended variants
information (count: 32 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:30)

rs_ID	r²[population]
rs13068733	0.84[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13077048	0.90[EUR][1000 genomes]
rs1344672	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1344674	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1346408	0.81[CEU][hapmap]
rs1582874	1.00[CEU][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];0.92[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs1863868	0.81[CEU][hapmap];0.81[JPT][hapmap]
rs1991431	1.00[CEU][hapmap];0.84[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs4683605	0.84[AFR][1000 genomes];0.96[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs4683606	0.95[AFR][1000 genomes];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs57345461	1.00[ASN][1000 genomes]
rs58473751	1.00[ASN][1000 genomes]
rs6440003	1.00[ASW][hapmap];1.00[CEU][hapmap];0.90[CHB][hapmap];1.00[CHD][hapmap];0.85[GIH][hapmap];1.00[JPT][hapmap];0.81[LWK][hapmap];1.00[MEX][hapmap];0.97[MKK][hapmap];0.97[TSI][hapmap];0.84[AFR][1000 genomes];0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6440006	0.96[CEU][hapmap];0.90[CHB][hapmap];1.00[JPT][hapmap];0.86[AMR][1000 genomes];0.91[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6762826	0.90[JPT][hapmap]
rs6763927	1.00[CEU][hapmap];0.93[CHB][hapmap];1.00[JPT][hapmap];0.87[AMR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6763931	1.00[ASW][hapmap];1.00[CEU][hapmap];0.90[CHB][hapmap];0.97[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.88[MKK][hapmap];1.00[TSI][hapmap];0.84[AFR][1000 genomes];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6764769	1.00[ASW][hapmap];1.00[CEU][hapmap];0.90[CHB][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.81[LWK][hapmap];1.00[MEX][hapmap];0.97[MKK][hapmap];0.97[TSI][hapmap];0.84[AFR][1000 genomes];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6785012	0.95[AFR][1000 genomes];0.88[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs6802753	0.84[JPT][hapmap]
rs6808936	1.00[CEU][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];0.88[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs724016	0.91[ASW][hapmap];1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7613516	0.81[CEU][hapmap]
rs7624084	0.89[CEU][hapmap];0.89[CHB][hapmap];1.00[JPT][hapmap];0.82[AMR][1000 genomes];0.86[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7625643	0.88[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs7632381	0.90[ASW][hapmap];1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];0.88[MKK][hapmap];0.97[TSI][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7650602	0.81[AMR][1000 genomes];0.88[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs9846396	1.00[CEU][hapmap];0.97[GIH][hapmap];0.96[MEX][hapmap];0.80[MKK][hapmap];0.81[TSI][hapmap];0.82[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs9853018	0.84[AFR][1000 genomes];0.90[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs9856584	0.90[CHB][hapmap];1.00[JPT][hapmap];0.91[ASN][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	nsv829744	chr3:141016749-141189168	Genic enhancers Strong transcription Transcr. at gene 5' and 3' Weak transcription Enhancers Active TSS Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	14 gene(s)	inside rSNPs	diseases
2	esv3397896	chr3:141120287-141122835	Weak transcription Active TSS Flanking Bivalent TSS/Enh Flanking Active TSS Enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Strong transcription Genic enhancers Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs2871960	ZBTB38	cis	cerebellum	SCAN
rs2871960	RASA2	cis	cerebellum	SCAN
rs2871960	SPSB4	cis	parietal	SCAN

Chromatin state (count:125 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:141116800-141122600	Weak transcription	K562	blood
2	chr3:141120400-141122400	Active TSS	Breast Myoepithelial Primary Cells	Breast
3	chr3:141120400-141122400	Active TSS	Psoas Muscle	Psoas
4	chr3:141120400-141122400	Active TSS	GM12878-XiMat	blood
5	chr3:141120400-141122600	Active TSS	Right Atrium	heart
6	chr3:141120600-141122000	Active TSS	H9 Cell Line	embryonic stem cell
7	chr3:141120600-141122000	Active TSS	iPS DF 6.9 Cell Line	embryonic stem cell
8	chr3:141120600-141122000	Active TSS	iPS DF 19.11 Cell Line	embryonic stem cell
9	chr3:141120600-141122000	Active TSS	Primary T cells effector/memory enriched fromperipheralblood	blood
10	chr3:141120600-141122000	Active TSS	Esophagus	oesophagus
11	chr3:141120600-141122200	Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
12	chr3:141120600-141122200	Active TSS	Fetal Brain Female	brain
13	chr3:141120600-141122400	Active TSS	Pancreatic Islets	Pancreatic Islet
14	chr3:141120600-141122400	Active TSS	Ovary	ovary
15	chr3:141120600-141122400	Active TSS	Pancreas	Pancrea
16	chr3:141120600-141122600	Active TSS	Aorta	Aorta
17	chr3:141120600-141122800	Active TSS	Duodenum Smooth Muscle	Duodenum
18	chr3:141120600-141122800	Active TSS	Left Ventricle	heart
19	chr3:141120600-141123000	Active TSS	Right Ventricle	heart
20	chr3:141120800-141122000	Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
21	chr3:141120800-141122000	Active TSS	Placenta Amnion	Placenta Amnion
22	chr3:141120800-141122000	Active TSS	Sigmoid Colon	Sigmoid Colon
23	chr3:141120800-141122000	Active TSS	Small Intestine	intestine
24	chr3:141120800-141122000	Active TSS	A549	lung
25	chr3:141120800-141122200	Flanking Active TSS	Primary mononuclear cells fromperipheralblood	Blood
26	chr3:141120800-141122200	Active TSS	Rectal Mucosa Donor 29	rectum
27	chr3:141120800-141122200	Active TSS	HSMMtube	muscle
28	chr3:141120800-141122200	Flanking Active TSS	NH-A	brain
29	chr3:141120800-141122400	Active TSS	Primary T helper naive cells from peripheral blood	blood
30	chr3:141120800-141122400	Active TSS	Primary T killer memory cells from peripheral blood	blood
31	chr3:141120800-141122400	Active TSS	Skeletal Muscle Female	skeletal muscle
32	chr3:141120800-141122600	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
33	chr3:141120800-141122600	Active TSS	Brain Angular Gyrus	brain
34	chr3:141120800-141122600	Active TSS	Brain Hippocampus Middle	brain
35	chr3:141121000-141122000	Active TSS	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
36	chr3:141121000-141122000	Active TSS	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
37	chr3:141121000-141122000	Active TSS	H1 Derived Mesenchymal Stem Cells	ES cell derived
38	chr3:141121000-141122000	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
39	chr3:141121000-141122000	Bivalent/Poised TSS	iPS-15b Cell Line	embryonic stem cell
40	chr3:141121000-141122000	Active TSS	iPS-18 Cell Line	embryonic stem cell
41	chr3:141121000-141122000	Active TSS	ES-UCSF4 Cell Line	embryonic stem cell
42	chr3:141121000-141122000	Active TSS	Primary T helper memory cells from peripheral blood 2	blood
43	chr3:141121000-141122000	Active TSS	Primary T helper naive cells fromperipheralblood	blood
44	chr3:141121000-141122000	Active TSS	Primary T helper memory cells from peripheral blood 1	blood
45	chr3:141121000-141122000	Active TSS	Primary T helper cells PMA-I stimulated	--
46	chr3:141121000-141122000	Active TSS	Primary T killer naive cells fromperipheralblood	blood
47	chr3:141121000-141122000	Active TSS	Fetal Intestine Large	intestine
48	chr3:141121000-141122000	Active TSS	Rectal Smooth Muscle	rectum
49	chr3:141121000-141122000	Active TSS	Hela-S3	cervix
50	chr3:141121000-141122200	Active TSS	H9 Derived Neuron Cultured Cells	ES cell derived

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