Variant report

Variant	rs6788895
Chromosome Location	chr3:150467808-150467809
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 55 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:54)

rs_ID	r²[population]
rs10513377	0.82[CHB][hapmap]
rs1148368	0.83[ASN][1000 genomes]
rs12695960	0.85[ASN][1000 genomes]
rs1444197	1.00[CEU][hapmap]
rs1533711	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[MEX][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs16862837	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.85[LWK][hapmap];1.00[MEX][hapmap];0.86[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs16862842	1.00[CEU][hapmap];0.89[JPT][hapmap]
rs1814463	0.82[EUR][1000 genomes]
rs1814464	0.82[EUR][1000 genomes]
rs1879420	1.00[CEU][hapmap];0.86[CHB][hapmap];0.91[CHD][hapmap];1.00[JPT][hapmap];0.82[ASN][1000 genomes]
rs1879421	0.89[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.92[MKK][hapmap];1.00[TSI][hapmap];0.90[YRI][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1879422	0.98[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1991781	0.86[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2014279	1.00[CEU][hapmap];0.82[EUR][1000 genomes]
rs2018246	1.00[CEU][hapmap];0.82[CHB][hapmap];0.89[JPT][hapmap];1.00[TSI][hapmap];0.82[AMR][1000 genomes];0.82[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2116684	1.00[CEU][hapmap];0.86[CHB][hapmap];1.00[JPT][hapmap]
rs2116685	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2166061	0.87[AFR][1000 genomes];0.98[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs34348847	1.00[CEU][hapmap];0.84[JPT][hapmap];1.00[TSI][hapmap];0.82[EUR][1000 genomes]
rs3851356	1.00[CEU][hapmap];1.00[TSI][hapmap];0.82[EUR][1000 genomes]
rs41372346	1.00[CEU][hapmap];0.84[JPT][hapmap]
rs41454348	1.00[CEU][hapmap]
rs481236	0.95[CHB][hapmap];0.93[CHD][hapmap];0.89[JPT][hapmap];0.96[ASN][1000 genomes]
rs502941	0.91[CHB][hapmap];0.91[CHD][hapmap];0.81[GIH][hapmap];0.89[JPT][hapmap];0.96[ASN][1000 genomes]
rs55899470	0.86[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs57275328	0.86[AMR][1000 genomes];0.83[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs57824095	0.86[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs57869178	0.82[EUR][1000 genomes]
rs594926	0.91[CHB][hapmap];0.91[CHD][hapmap];0.89[JPT][hapmap];0.96[ASN][1000 genomes]
rs60259684	0.82[EUR][1000 genomes]
rs6440696	0.84[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs6440697	1.00[CEU][hapmap];0.82[MEX][hapmap];1.00[TSI][hapmap];0.84[AMR][1000 genomes]
rs6769917	0.82[EUR][1000 genomes]
rs6777178	0.82[EUR][1000 genomes]
rs6789306	1.00[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap];0.82[AMR][1000 genomes];0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6805481	1.00[CEU][hapmap];0.82[MEX][hapmap];1.00[TSI][hapmap];0.80[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs73003792	0.80[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs73006998	0.82[AMR][1000 genomes];0.81[ASN][1000 genomes]
rs73006999	0.86[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73008903	0.86[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73008905	0.86[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73008907	0.82[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73010930	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73010941	0.90[AFR][1000 genomes];0.98[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs73010956	0.82[EUR][1000 genomes]
rs73010964	0.82[EUR][1000 genomes]
rs73010965	0.82[EUR][1000 genomes]
rs7615125	1.00[CEU][hapmap];0.82[CHB][hapmap];0.95[JPT][hapmap];0.82[AMR][1000 genomes];0.80[ASN][1000 genomes]
rs7615292	1.00[CEU][hapmap];0.82[CHB][hapmap];0.84[CHD][hapmap];0.84[GIH][hapmap];0.95[JPT][hapmap];0.82[AMR][1000 genomes];0.80[ASN][1000 genomes]
rs7617507	0.88[ASW][hapmap];1.00[CEU][hapmap];0.82[MEX][hapmap];1.00[TSI][hapmap];0.82[EUR][1000 genomes]
rs7628481	1.00[CEU][hapmap]
rs7628776	1.00[CEU][hapmap]
rs7636866	1.00[CEU][hapmap];0.94[CHB][hapmap];0.95[JPT][hapmap];0.88[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs939476	0.82[CHB][hapmap]

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

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv532662	chr3:150180747-150633414	Weak transcription Flanking Active TSS Strong transcription Enhancers Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	101 gene(s)	inside rSNPs	diseases

Variant related diseases (count:1)

Disease	PMID	Source
Breast cancer	22951594	GWAS catalog

Chromatin state (count:118 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:150453800-150478000	Weak transcription	Brain Germinal Matrix	brain
2	chr3:150454600-150469800	Weak transcription	iPS-15b Cell Line	embryonic stem cell
3	chr3:150454600-150477200	Weak transcription	H9 Cell Line	embryonic stem cell
4	chr3:150456400-150477600	Weak transcription	H1 Cell Line	embryonic stem cell
5	chr3:150456600-150477600	Weak transcription	Fetal Brain Male	brain
6	chr3:150456800-150477400	Weak transcription	iPS-20b Cell Line	embryonic stem cell
7	chr3:150457000-150478800	Weak transcription	HUES64 Cell Line	embryonic stem cell
8	chr3:150457600-150477600	Weak transcription	HUVEC	blood vessel
9	chr3:150458200-150469600	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
10	chr3:150458400-150471600	Genic enhancers	HepG2	liver
11	chr3:150458800-150469400	Weak transcription	Primary T killer memory cells from peripheral blood	blood
12	chr3:150459000-150477600	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
13	chr3:150459400-150468400	Genic enhancers	Primary T helper cells PMA-I stimulated	--
14	chr3:150460200-150477600	Weak transcription	HUES48 Cell Line	embryonic stem cell
15	chr3:150460400-150468800	Weak transcription	Colonic Mucosa	Colon
16	chr3:150460400-150469000	Weak transcription	Fetal Thymus	thymus
17	chr3:150460400-150469600	Weak transcription	HUES6 Cell Line	embryonic stem cell
18	chr3:150460400-150475200	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
19	chr3:150460400-150477600	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
20	chr3:150460600-150469600	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
21	chr3:150460600-150469800	Weak transcription	Fetal Stomach	stomach
22	chr3:150460600-150470600	Weak transcription	Breast Myoepithelial Primary Cells	Breast
23	chr3:150460600-150470800	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
24	chr3:150461200-150471800	Enhancers	Stomach Mucosa	stomach
25	chr3:150461200-150474000	Weak transcription	Dnd41	blood
26	chr3:150461600-150468200	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
27	chr3:150461600-150469000	Weak transcription	Placenta Amnion	Placenta Amnion
28	chr3:150461600-150469200	Weak transcription	Primary T cells from cord blood	blood
29	chr3:150461800-150468600	Genic enhancers	Primary T helper 17 cells PMA-I stimulated	--
30	chr3:150461800-150469600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
31	chr3:150461800-150472000	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
32	chr3:150462800-150477000	Weak transcription	Brain Angular Gyrus	brain
33	chr3:150463000-150475400	Weak transcription	Cortex derived primary cultured neurospheres	brain
34	chr3:150463000-150477800	Weak transcription	NH-A	brain
35	chr3:150463000-150478400	Weak transcription	HSMM	muscle
36	chr3:150463200-150468400	Weak transcription	Fetal Lung	lung
37	chr3:150463200-150469600	Weak transcription	Fetal Muscle Leg	muscle
38	chr3:150463200-150469600	Weak transcription	Rectal Smooth Muscle	rectum
39	chr3:150463200-150469600	Weak transcription	HMEC	breast
40	chr3:150463200-150470600	Weak transcription	NHLF	lung
41	chr3:150463200-150475600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
42	chr3:150463200-150477600	Weak transcription	Brain Cingulate Gyrus	brain
43	chr3:150463400-150468400	Enhancers	Fetal Adrenal Gland	Adrenal Gland
44	chr3:150463800-150469000	Enhancers	Ovary	ovary
45	chr3:150464200-150469800	Enhancers	Rectal Mucosa Donor 31	rectum
46	chr3:150464800-150468400	Weak transcription	Thymus	Thymus
47	chr3:150464800-150468800	Weak transcription	Primary T cells fromperipheralblood	blood
48	chr3:150464800-150469600	Weak transcription	Brain Anterior Caudate	brain
49	chr3:150464800-150470600	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
50	chr3:150464800-150470600	Weak transcription	Fetal Muscle Trunk	muscle

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