Variant report

Variant	rs538670
Chromosome Location	chr11:77088578-77088579
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr11:77080789..77082811-chr11:77088019..77090076,2	MCF-7	breast:

Extended variants
information (count: 82 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:75)

rs_ID	r²[population]
rs10793248	0.86[AMR][1000 genomes];0.98[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs10899379	0.87[JPT][hapmap]
rs11607378	0.82[EUR][1000 genomes]
rs1225479	0.96[AMR][1000 genomes];0.86[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs1670459	0.91[JPT][hapmap]
rs1793476	0.91[JPT][hapmap]
rs1793483	0.91[JPT][hapmap]
rs1901821	0.83[CEU][hapmap]
rs2007466	0.81[EUR][1000 genomes]
rs2602465	0.81[CHB][hapmap];0.95[JPT][hapmap];0.81[ASN][1000 genomes]
rs2602472	0.83[CHB][hapmap];0.87[JPT][hapmap]
rs2725812	1.00[CEU][hapmap];0.87[CHB][hapmap];0.95[JPT][hapmap];0.80[AMR][1000 genomes];0.91[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2729762	0.95[JPT][hapmap]
rs2844333	0.96[JPT][hapmap];0.81[ASN][1000 genomes]
rs2853097	0.91[AMR][1000 genomes];0.92[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs3015984	0.84[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs3015989	1.00[CEU][hapmap];0.95[CHB][hapmap];0.91[JPT][hapmap];0.89[YRI][hapmap];0.84[AMR][1000 genomes];0.96[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs3015991	0.83[AMR][1000 genomes];0.94[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs3015993	1.00[CEU][hapmap];0.95[CHB][hapmap];0.91[JPT][hapmap];1.00[YRI][hapmap];0.84[AMR][1000 genomes];0.92[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs3019240	0.84[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs3019243	0.82[EUR][1000 genomes]
rs3019258	0.82[AFR][1000 genomes];0.86[AMR][1000 genomes];0.98[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs34420077	0.83[EUR][1000 genomes]
rs4433591	0.84[EUR][1000 genomes]
rs473012	0.88[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs476925	1.00[CEU][hapmap];0.96[CHB][hapmap];1.00[JPT][hapmap];0.83[YRI][hapmap];0.82[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs478134	0.91[AFR][1000 genomes];0.99[AMR][1000 genomes];0.96[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs478475	0.81[AFR][1000 genomes];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs482243	0.95[AMR][1000 genomes];0.93[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs487322	0.81[AFR][1000 genomes];0.99[AMR][1000 genomes];0.96[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs489038	0.81[AFR][1000 genomes];0.99[AMR][1000 genomes];0.95[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs491781	0.95[AMR][1000 genomes];0.88[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs492527	0.88[AFR][1000 genomes];0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4944155	0.82[EUR][1000 genomes]
rs4944158	0.89[AMR][1000 genomes];0.93[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs4945162	0.95[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap];0.82[EUR][1000 genomes]
rs4945166	0.90[CEU][hapmap];0.91[CHB][hapmap];0.95[JPT][hapmap];0.82[EUR][1000 genomes]
rs4945169	0.89[AMR][1000 genomes];0.93[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs495889	1.00[CEU][hapmap];0.95[CHB][hapmap];0.91[JPT][hapmap];1.00[YRI][hapmap];0.82[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs497172	0.97[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs497946	0.91[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs499880	0.91[AMR][1000 genomes];0.93[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs500731	0.82[AFR][1000 genomes];0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs514191	1.00[CEU][hapmap];0.91[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.85[AFR][1000 genomes];0.99[AMR][1000 genomes];0.95[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs517511	0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs539906	0.91[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs556696	0.85[AFR][1000 genomes];0.99[AMR][1000 genomes];0.95[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs561153	0.91[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs562939	0.91[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs568309	0.88[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs57129983	0.82[EUR][1000 genomes]
rs575662	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.91[AFR][1000 genomes];0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs576079	0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs576997	0.85[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs584909	0.91[AFR][1000 genomes];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs599437	0.95[CEU][hapmap];0.96[CHB][hapmap];1.00[JPT][hapmap];0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs605910	0.91[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs614775	0.82[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs618012	0.93[AMR][1000 genomes];0.90[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs61901769	0.82[EUR][1000 genomes]
rs61901802	0.80[AMR][1000 genomes];0.89[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs628325	0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs635291	0.91[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs639857	0.85[AFR][1000 genomes];0.99[AMR][1000 genomes];0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6592715	0.85[EUR][1000 genomes]
rs667331	0.96[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs674652	1.00[CEU][hapmap];0.96[CHB][hapmap];0.91[JPT][hapmap]
rs683497	0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs688212	0.95[CEU][hapmap];0.96[CHB][hapmap];1.00[JPT][hapmap];0.85[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7118869	0.95[CEU][hapmap];0.91[CHB][hapmap];1.00[JPT][hapmap];0.89[EUR][1000 genomes]
rs721382	0.83[EUR][1000 genomes]
rs73496890	0.84[EUR][1000 genomes]
rs7928731	0.82[EUR][1000 genomes]
rs883223	0.87[CEU][hapmap];0.81[JPT][hapmap]
rs98703	0.88[AFR][1000 genomes];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:7 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1048360	chr11:76900813-77387933	Strong transcription Flanking Active TSS Enhancers Weak transcription Active TSS Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	24 gene(s)	inside rSNPs	diseases
2	nsv541089	chr11:76900813-77387933	Active TSS Enhancers Weak transcription Bivalent/Poised TSS Flanking Active TSS Strong transcription ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	24 gene(s)	inside rSNPs	diseases
3	nsv1049603	chr11:76900813-77520411	Strong transcription Weak transcription Active TSS Enhancers Genic enhancers Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	29 gene(s)	inside rSNPs	diseases
4	nsv541090	chr11:76900813-77520411	Weak transcription Enhancers Active TSS Flanking Active TSS Strong transcription ZNF genes & repeats Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	29 gene(s)	inside rSNPs	diseases
5	esv3424135	chr11:76961603-77277087	Strong transcription Active TSS Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent Enhancer Enhancers Weak transcription Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
6	nsv1037724	chr11:77061945-77250391	Flanking Active TSS Enhancers Active TSS Bivalent/Poised TSS Weak transcription Strong transcription ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
7	nsv541091	chr11:77061945-77250391	Weak transcription Active TSS Enhancers Strong transcription Bivalent/Poised TSS Flanking Active TSS Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:112 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:77033400-77090400	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
2	chr11:77046200-77092400	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
3	chr11:77046800-77121600	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
4	chr11:77047200-77096000	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
5	chr11:77047400-77089000	Weak transcription	Primary T cells fromperipheralblood	blood
6	chr11:77047400-77090000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
7	chr11:77055200-77092200	Weak transcription	Small Intestine	intestine
8	chr11:77055200-77117600	Weak transcription	Pancreas	Pancrea
9	chr11:77059800-77088800	Weak transcription	Brain Inferior Temporal Lobe	brain
10	chr11:77064200-77102800	Weak transcription	Brain Substantia Nigra	brain
11	chr11:77066800-77090000	Weak transcription	Brain Angular Gyrus	brain
12	chr11:77067000-77092800	Weak transcription	Rectal Smooth Muscle	rectum
13	chr11:77067000-77093800	Weak transcription	Psoas Muscle	Psoas
14	chr11:77067000-77097000	Weak transcription	Esophagus	oesophagus
15	chr11:77067200-77111800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
16	chr11:77068800-77097000	Weak transcription	Brain Cingulate Gyrus	brain
17	chr11:77069000-77090000	Weak transcription	Fetal Lung	lung
18	chr11:77070000-77102000	Weak transcription	Primary T helper cells PMA-I stimulated	--
19	chr11:77075200-77097200	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
20	chr11:77077000-77090000	Weak transcription	Fetal Thymus	thymus
21	chr11:77077200-77091800	Strong transcription	HUES64 Cell Line	embryonic stem cell
22	chr11:77077600-77092800	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
23	chr11:77078000-77091600	Strong transcription	HUES6 Cell Line	embryonic stem cell
24	chr11:77081000-77093400	Strong transcription	HUES48 Cell Line	embryonic stem cell
25	chr11:77081000-77094600	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
26	chr11:77081200-77091000	Strong transcription	Breast Myoepithelial Primary Cells	Breast
27	chr11:77081200-77091600	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
28	chr11:77081200-77091800	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
29	chr11:77081200-77095600	Strong transcription	GM12878-XiMat	blood
30	chr11:77081200-77096600	Weak transcription	Placenta Amnion	Placenta Amnion
31	chr11:77082000-77095600	Strong transcription	Primary neutrophils fromperipheralblood	blood
32	chr11:77082000-77096200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
33	chr11:77082200-77088800	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
34	chr11:77082200-77091200	Strong transcription	Placenta	Placenta
35	chr11:77082200-77091400	Strong transcription	iPS-18 Cell Line	embryonic stem cell
36	chr11:77082200-77091400	Strong transcription	Primary T cells from cord blood	blood
37	chr11:77082200-77092800	Strong transcription	iPS-20b Cell Line	embryonic stem cell
38	chr11:77082200-77095800	Strong transcription	Primary monocytes fromperipheralblood	blood
39	chr11:77082400-77090600	Weak transcription	Right Ventricle	heart
40	chr11:77082400-77104200	Strong transcription	Monocytes-CD14+_RO01746	blood
41	chr11:77083000-77091000	Strong transcription	Duodenum Mucosa	Duodenum
42	chr11:77083200-77092000	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
43	chr11:77083400-77091000	Strong transcription	Fetal Muscle Leg	muscle
44	chr11:77083400-77091600	Strong transcription	Primary hematopoietic stem cells short term culture	blood
45	chr11:77084000-77089200	Strong transcription	Primary hematopoietic stem cells	blood
46	chr11:77084000-77093200	Weak transcription	Hela-S3	cervix
47	chr11:77084000-77111400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
48	chr11:77084200-77088800	Weak transcription	Skeletal Muscle Female	skeletal muscle
49	chr11:77084200-77107000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
50	chr11:77084400-77088800	Weak transcription	Stomach Smooth Muscle	stomach

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