Variant report

Variant	rs3772979
Chromosome Location	chr3:69127133-69127134
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr3:69097839..69103874-chr3:69126765..69131500,7	K562	blood:
2	chr3:69102756..69104403-chr3:69126707..69129134,2	MCF-7	breast:
3	chr3:69112430..69115275-chr3:69125875..69130297,4	MCF-7	breast:
4	chr3:69060995..69064606-chr3:69126717..69130405,4	K562	blood:
5	chr3:69117327..69121246-chr3:69122493..69127551,4	K562	blood:
6	chr3:69105444..69107005-chr3:69126154..69128272,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000265355	Chromatin interaction
ENSG00000163378	Chromatin interaction
ENSG00000244513	Chromatin interaction
ENSG00000144744	Chromatin interaction
ENSG00000144747	Chromatin interaction

Extended variants
information (count: 39 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:37)

rs_ID	r²[population]
rs10489	0.87[CHB][hapmap];0.81[CHD][hapmap];0.86[JPT][hapmap]
rs1051901	0.81[CHB][hapmap]
rs11128107	0.84[TSI][hapmap]
rs13063094	0.91[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs13090606	0.93[CHB][hapmap];0.81[CHD][hapmap];0.95[GIH][hapmap];0.92[TSI][hapmap];0.82[EUR][1000 genomes]
rs13099820	0.92[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2009602	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.89[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2271118	0.81[CHB][hapmap];0.92[GIH][hapmap];0.86[TSI][hapmap];0.80[EUR][1000 genomes]
rs2271120	0.82[CEU][hapmap];0.81[EUR][1000 genomes]
rs2271122	0.94[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];0.95[JPT][hapmap];0.92[MEX][hapmap];0.86[MKK][hapmap];0.97[TSI][hapmap];0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2279936	0.92[GIH][hapmap];0.89[TSI][hapmap];0.80[EUR][1000 genomes]
rs2292198	0.82[AFR][1000 genomes];0.80[ASN][1000 genomes]
rs2292199	0.83[CEU][hapmap];0.93[CHB][hapmap];0.92[GIH][hapmap];0.92[TSI][hapmap];0.81[ASN][1000 genomes]
rs35718539	0.96[AFR][1000 genomes];0.90[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs3755717	0.96[AFR][1000 genomes];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs3755721	0.86[AFR][1000 genomes];0.80[ASN][1000 genomes]
rs3772980	0.81[CHB][hapmap]
rs3796213	0.81[CHB][hapmap]
rs3821562	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];0.90[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3853157	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.87[MKK][hapmap];0.97[TSI][hapmap];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs56156415	0.96[AFR][1000 genomes];0.87[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs58950441	0.96[AFR][1000 genomes];0.90[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6549165	0.84[TSI][hapmap]
rs6549181	0.93[ASW][hapmap];0.89[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.92[MEX][hapmap];0.93[MKK][hapmap];0.95[TSI][hapmap];0.96[YRI][hapmap];0.96[AFR][1000 genomes];0.84[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6549184	0.87[CHB][hapmap];0.83[CHD][hapmap];0.86[JPT][hapmap]
rs6775065	0.86[AFR][1000 genomes];0.90[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6775256	0.86[CHB][hapmap];0.86[JPT][hapmap];1.00[YRI][hapmap];0.85[AFR][1000 genomes];0.80[ASN][1000 genomes]
rs6777032	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6782474	0.89[CEU][hapmap];0.93[CHB][hapmap];0.88[CHD][hapmap];0.95[GIH][hapmap];0.91[JPT][hapmap];0.86[MKK][hapmap];0.95[TSI][hapmap];0.90[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6787569	0.86[CHB][hapmap];0.83[CHD][hapmap];0.86[JPT][hapmap];0.94[LWK][hapmap];0.98[MKK][hapmap];1.00[YRI][hapmap];0.85[AFR][1000 genomes];0.80[ASN][1000 genomes]
rs6807701	0.85[EUR][1000 genomes]
rs714300	0.89[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7611878	0.84[TSI][hapmap]
rs7615341	0.89[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7625579	0.87[CHB][hapmap];0.85[JPT][hapmap]
rs9813514	0.94[CEU][hapmap];0.93[CHB][hapmap];0.95[JPT][hapmap];0.84[YRI][hapmap];0.92[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs9826616	0.88[EUR][1000 genomes];0.96[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	nsv876933	chr3:69059023-69227379	Enhancers Strong transcription Weak transcription Active TSS Bivalent Enhancer Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	15 gene(s)	inside rSNPs	diseases
2	nsv876934	chr3:69111512-69166895	Enhancers Genic enhancers Strong transcription Flanking Active TSS Active TSS Weak transcription Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region miRNA target site	11 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:124 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:69101800-69128400	Weak transcription	Aorta	Aorta
2	chr3:69102000-69128200	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
3	chr3:69102000-69128400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
4	chr3:69102200-69127200	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
5	chr3:69108400-69128200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
6	chr3:69110600-69127600	Weak transcription	Brain Inferior Temporal Lobe	brain
7	chr3:69110600-69128200	Weak transcription	Right Ventricle	heart
8	chr3:69110600-69128400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
9	chr3:69110600-69128400	Weak transcription	Gastric	stomach
10	chr3:69110600-69128400	Weak transcription	Psoas Muscle	Psoas
11	chr3:69110800-69127600	Weak transcription	Brain Substantia Nigra	brain
12	chr3:69110800-69127800	Weak transcription	Rectal Smooth Muscle	rectum
13	chr3:69110800-69128600	Weak transcription	Esophagus	oesophagus
14	chr3:69110800-69128800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
15	chr3:69110800-69128800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
16	chr3:69111000-69128600	Weak transcription	Lung	lung
17	chr3:69111000-69128800	Weak transcription	Spleen	Spleen
18	chr3:69111200-69128000	Weak transcription	K562	blood
19	chr3:69111200-69128200	Weak transcription	iPS-15b Cell Line	embryonic stem cell
20	chr3:69111200-69128200	Weak transcription	Colonic Mucosa	Colon
21	chr3:69111400-69128400	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
22	chr3:69111600-69128200	Weak transcription	H9 Cell Line	embryonic stem cell
23	chr3:69111800-69128200	Weak transcription	A549	lung
24	chr3:69112200-69128200	Weak transcription	Fetal Kidney	kidney
25	chr3:69112600-69128200	Weak transcription	Fetal Brain Female	brain
26	chr3:69112600-69128200	Weak transcription	Placenta Amnion	Placenta Amnion
27	chr3:69113000-69128200	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
28	chr3:69113400-69127400	Weak transcription	Fetal Lung	lung
29	chr3:69115000-69127800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
30	chr3:69115000-69128400	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
31	chr3:69115800-69128200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
32	chr3:69116400-69127200	Weak transcription	Primary T killer memory cells from peripheral blood	blood
33	chr3:69120400-69127600	Weak transcription	Thymus	Thymus
34	chr3:69120400-69128200	Weak transcription	Ovary	ovary
35	chr3:69120600-69128200	Weak transcription	HSMMtube	muscle
36	chr3:69120800-69128200	Weak transcription	NHLF	lung
37	chr3:69122200-69127200	Weak transcription	NHEK	skin
38	chr3:69122400-69128200	Weak transcription	Sigmoid Colon	Sigmoid Colon
39	chr3:69122600-69127200	Weak transcription	Breast Myoepithelial Primary Cells	Breast
40	chr3:69122600-69127600	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
41	chr3:69122600-69128200	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
42	chr3:69122600-69128200	Weak transcription	Stomach Smooth Muscle	stomach
43	chr3:69122600-69128400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
44	chr3:69122800-69127600	Weak transcription	Rectal Mucosa Donor 29	rectum
45	chr3:69122800-69128200	Weak transcription	Rectal Mucosa Donor 31	rectum
46	chr3:69123000-69128200	Weak transcription	iPS-18 Cell Line	embryonic stem cell
47	chr3:69123000-69128400	Weak transcription	H1 Cell Line	embryonic stem cell
48	chr3:69123800-69127400	Weak transcription	Liver	Liver
49	chr3:69123800-69128200	Weak transcription	iPS-20b Cell Line	embryonic stem cell
50	chr3:69124000-69127200	Weak transcription	Brain Germinal Matrix	brain

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