Variant report

Variant	rs11920344
Chromosome Location	chr3:78722982-78722983
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr3:78717590..78719118-chr3:78722617..78724436,2	MCF-7	breast:
2	chr3:78715095..78717151-chr3:78722389..78724201,2	MCF-7	breast:

Extended variants
information (count: 85 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:82)

rs_ID	r²[population]
rs10049014	0.94[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs10049102	0.90[CEU][hapmap];0.93[CHB][hapmap];1.00[JPT][hapmap];0.81[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs10428105	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.95[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11914618	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap]
rs11915494	0.85[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11915745	0.85[AMR][1000 genomes];0.90[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11917512	0.89[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11918759	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs11925970	0.91[CEU][hapmap];0.93[CHB][hapmap];1.00[JPT][hapmap];0.85[AMR][1000 genomes];0.90[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11927666	0.92[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11928868	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12106862	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1395784	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1457659	0.90[CEU][hapmap];0.81[CHB][hapmap];0.84[JPT][hapmap]
rs17016453	0.89[AMR][1000 genomes];0.90[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs17016466	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs17303276	0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs17375110	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs17375496	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs17375739	1.00[CEU][hapmap];1.00[CHB][hapmap];0.85[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs1865860	0.85[CEU][hapmap]
rs1865861	0.89[CEU][hapmap]
rs1865863	0.90[CEU][hapmap]
rs2031051	0.85[AMR][1000 genomes];0.90[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2118068	0.86[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2271151	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28494803	0.83[ASN][1000 genomes]
rs3732662	0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs3732663	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs3773220	0.86[CEU][hapmap]
rs3773224	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3773225	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3773226	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3773227	0.91[AMR][1000 genomes];0.91[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs3773231	1.00[CEU][hapmap];0.92[CHB][hapmap];1.00[JPT][hapmap];0.85[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs3773234	1.00[CEU][hapmap];0.93[CHB][hapmap];0.84[JPT][hapmap]
rs3773240	0.95[CEU][hapmap];0.81[CHB][hapmap];0.80[JPT][hapmap]
rs3821601	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs3821602	0.86[CHB][hapmap];0.81[JPT][hapmap]
rs3821603	1.00[CEU][hapmap];0.93[CHB][hapmap];0.84[JPT][hapmap]
rs4263256	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs56372508	0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs58561177	0.85[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs60568341	0.90[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs60749216	0.92[AFR][1000 genomes];0.88[AMR][1000 genomes];0.83[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs61053911	0.85[EUR][1000 genomes]
rs67137735	0.93[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs67347336	0.92[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs67362360	0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs67498832	0.85[AMR][1000 genomes];0.90[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6769933	1.00[CEU][hapmap];0.92[CHB][hapmap];1.00[JPT][hapmap];0.89[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6787349	0.90[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[ASN][1000 genomes]
rs6788434	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[YRI][hapmap];0.84[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6788511	0.90[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[AMR][1000 genomes];0.91[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6806079	0.84[AMR][1000 genomes];0.91[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs73109717	0.89[AMR][1000 genomes];0.90[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs73109772	0.81[ASN][1000 genomes]
rs73850750	0.87[AMR][1000 genomes];0.91[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7610500	0.81[AFR][1000 genomes];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7610686	1.00[CEU][hapmap];0.92[CHB][hapmap];1.00[JPT][hapmap];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7613490	1.00[CEU][hapmap];0.94[JPT][hapmap];0.82[AMR][1000 genomes];0.99[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs7616495	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7622194	1.00[CEU][hapmap];0.93[CHB][hapmap];1.00[JPT][hapmap];0.95[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7624482	0.90[CEU][hapmap];0.93[CHB][hapmap];1.00[JPT][hapmap];0.87[AMR][1000 genomes];0.90[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7653782	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[AMR][1000 genomes];0.91[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs767182	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9309810	0.91[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9309811	0.91[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9309814	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9808950	0.91[CEU][hapmap];0.93[CHB][hapmap];1.00[JPT][hapmap];0.86[AMR][1000 genomes];0.90[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9818170	0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9819398	0.94[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.80[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs9823359	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[AFR][1000 genomes];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9829907	0.81[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9831098	0.90[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9840004	0.82[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs9866912	0.90[CEU][hapmap]
rs9880072	1.00[CEU][hapmap];0.93[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.92[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9880316	0.90[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[AMR][1000 genomes];0.90[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9882811	1.00[CEU][hapmap];0.93[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.90[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9883582	0.91[AMR][1000 genomes];0.89[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs997274	1.00[CEU][hapmap];0.93[CHB][hapmap];1.00[JPT][hapmap]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv529995	chr3:78188643-78739698	Enhancers Weak transcription Strong transcription Active TSS Bivalent/Poised TSS ZNF genes & repeats Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	11 gene(s)	inside rSNPs	diseases
2	nsv1008156	chr3:78444137-78765884	Enhancers Weak transcription ZNF genes & repeats Flanking Active TSS Strong transcription Genic enhancers Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	3 gene(s)	inside rSNPs	diseases
3	esv3426335	chr3:78721862-78723760	Weak transcription ZNF genes & repeats Strong transcription Enhancers	TF binding region Chromatin interactive region	1 gene(s)	inside rSNPs	n/a

No data

Chromatin state (count:44 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:78654200-78746600	Weak transcription	NHDF-Ad	bronchial
2	chr3:78667200-78751200	Weak transcription	Esophagus	oesophagus
3	chr3:78676800-78730600	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
4	chr3:78679200-78733200	Weak transcription	Duodenum Smooth Muscle	Duodenum
5	chr3:78679400-78730600	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
6	chr3:78679400-78736600	Weak transcription	Skeletal Muscle Female	skeletal muscle
7	chr3:78680400-78723600	Weak transcription	Fetal Muscle Leg	muscle
8	chr3:78693400-78730800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
9	chr3:78694200-78730600	Weak transcription	H9 Cell Line	embryonic stem cell
10	chr3:78694400-78733200	Weak transcription	Fetal Kidney	kidney
11	chr3:78702800-78730600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
12	chr3:78703200-78739200	Weak transcription	Fetal Muscle Trunk	muscle
13	chr3:78705400-78723000	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
14	chr3:78706400-78723600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
15	chr3:78706400-78736200	Weak transcription	H1 Cell Line	embryonic stem cell
16	chr3:78706600-78735200	Weak transcription	Primary T cells from cord blood	blood
17	chr3:78706600-78736400	Weak transcription	Stomach Smooth Muscle	stomach
18	chr3:78707000-78735400	Weak transcription	Rectal Smooth Muscle	rectum
19	chr3:78711800-78723600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
20	chr3:78711800-78726800	Weak transcription	Fetal Stomach	stomach
21	chr3:78716000-78724800	Weak transcription	HSMM	muscle
22	chr3:78716000-78739600	Weak transcription	Muscle Satellite Cultured Cells	--
23	chr3:78716600-78733000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
24	chr3:78717600-78723400	Weak transcription	iPS-20b Cell Line	embryonic stem cell
25	chr3:78717600-78724000	Weak transcription	iPS-18 Cell Line	embryonic stem cell
26	chr3:78717600-78733200	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
27	chr3:78717600-78739600	Weak transcription	Osteobl	bone
28	chr3:78717800-78723600	Weak transcription	HUES6 Cell Line	embryonic stem cell
29	chr3:78717800-78736800	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
30	chr3:78717800-78745200	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
31	chr3:78717800-78748400	Weak transcription	Ovary	ovary
32	chr3:78718600-78739200	Weak transcription	HUES48 Cell Line	embryonic stem cell
33	chr3:78719400-78723200	Weak transcription	HUES64 Cell Line	embryonic stem cell
34	chr3:78719400-78730400	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
35	chr3:78719400-78736800	Weak transcription	Breast Myoepithelial Primary Cells	Breast
36	chr3:78719600-78730600	Weak transcription	HepG2	liver
37	chr3:78719600-78753000	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
38	chr3:78720000-78730400	Weak transcription	Fetal Lung	lung
39	chr3:78720000-78737800	Weak transcription	Fetal Brain Female	brain
40	chr3:78720000-78753200	Weak transcription	Brain Hippocampus Middle	brain
41	chr3:78720200-78731600	Weak transcription	Brain Cingulate Gyrus	brain
42	chr3:78721400-78725000	Weak transcription	Fetal Brain Male	brain
43	chr3:78721400-78730400	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
44	chr3:78721400-78730600	Weak transcription	Cortex derived primary cultured neurospheres	brain

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