Variant report

Variant	rs11811805
Chromosome Location	chr1:78438903-78438904
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr1:78435772..78437977-chr1:78438825..78441558,2	MCF-7	breast:
2	chr1:78436988..78440391-chr1:78442144..78445660,4	MCF-7	breast:
3	chr1:78432055..78439376-chr1:78440995..78447364,11	MCF-7	breast:

Variant related genes	Relation type
ENSG00000162613	Chromatin interaction
ENSG00000137960	Chromatin interaction
ENSG00000162616	Chromatin interaction

Extended variants
information (count: 51 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:48)

rs_ID	r²[population]
rs1039863	1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[ASN][1000 genomes]
rs10735751	1.00[CHB][hapmap];0.91[JPT][hapmap]
rs10873961	0.98[AFR][1000 genomes];0.89[AMR][1000 genomes];0.91[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs10873962	0.86[AFR][1000 genomes]
rs10873963	1.00[CHB][hapmap];0.90[JPT][hapmap];0.89[YRI][hapmap];0.84[AFR][1000 genomes]
rs11162401	0.99[ASN][1000 genomes]
rs1166696	0.92[AFR][1000 genomes];0.96[AMR][1000 genomes];0.92[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1166699	0.92[ASN][1000 genomes]
rs1166700	1.00[CEU][hapmap];0.94[CHB][hapmap];0.90[JPT][hapmap];0.91[AFR][1000 genomes];0.97[AMR][1000 genomes];0.91[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs11805942	0.99[ASN][1000 genomes]
rs11806130	0.97[ASN][1000 genomes]
rs1510244	0.96[AFR][1000 genomes];0.87[AMR][1000 genomes];0.91[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs17101101	0.99[ASN][1000 genomes]
rs1749911	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];0.90[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1749913	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[AFR][1000 genomes];0.97[AMR][1000 genomes];0.92[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1780044	1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[ASN][1000 genomes]
rs1780045	1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[ASN][1000 genomes]
rs1780047	1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[ASN][1000 genomes]
rs1780048	0.86[AFR][1000 genomes];0.97[AMR][1000 genomes];0.89[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1780052	0.82[AFR][1000 genomes];0.92[AMR][1000 genomes];0.81[ASN][1000 genomes]
rs2296452	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2296454	1.00[CHB][hapmap];1.00[JPT][hapmap];0.99[ASN][1000 genomes]
rs3736909	1.00[CHB][hapmap];1.00[JPT][hapmap];0.99[ASN][1000 genomes]
rs3767024	1.00[CHB][hapmap];1.00[JPT][hapmap];0.99[ASN][1000 genomes]
rs3767025	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[YRI][hapmap];0.94[AFR][1000 genomes];0.97[AMR][1000 genomes];0.94[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs3790586	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs4083559	0.89[ASN][1000 genomes]
rs4107671	0.95[AFR][1000 genomes];0.89[AMR][1000 genomes];0.91[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs4483454	0.92[ASN][1000 genomes]
rs4543852	0.94[AFR][1000 genomes];0.89[AMR][1000 genomes];0.91[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs4631748	1.00[CHB][hapmap];0.91[JPT][hapmap];0.90[YRI][hapmap]
rs4949823	0.83[CHB][hapmap]
rs6424648	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[AFR][1000 genomes];0.89[AMR][1000 genomes];0.91[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs6424653	1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[ASN][1000 genomes]
rs6604878	0.82[CHB][hapmap]
rs6675105	1.00[CHB][hapmap];0.90[JPT][hapmap]
rs6680447	0.85[ASN][1000 genomes]
rs6702465	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[AMR][1000 genomes];0.90[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs72685363	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs72685364	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs72685368	0.94[AFR][1000 genomes];0.97[AMR][1000 genomes];0.92[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7520255	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[AFR][1000 genomes];0.90[AMR][1000 genomes];0.93[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7523874	0.89[AFR][1000 genomes];0.89[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs7524504	0.95[AFR][1000 genomes];0.89[AMR][1000 genomes];0.91[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs7547599	0.83[CHB][hapmap];0.82[JPT][hapmap]
rs9661687	0.85[AFR][1000 genomes];1.00[AMR][1000 genomes];0.90[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs9662129	0.93[CHB][hapmap];1.00[JPT][hapmap];0.92[ASN][1000 genomes]
rs9729146	0.85[CEU][hapmap];0.93[CHB][hapmap];1.00[JPT][hapmap];0.92[AFR][1000 genomes];0.97[AMR][1000 genomes];0.92[EUR][1000 genomes];0.92[ASN][1000 genomes]

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	esv1794082	chr1:78102426-78492221	Weak transcription Flanking Active TSS Active TSS Enhancers Genic enhancers Strong transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	108 gene(s)	inside rSNPs	diseases
2	esv3434340	chr1:78153780-78607103	Weak transcription Enhancers Strong transcription Flanking Active TSS Genic enhancers Active TSS Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	98 gene(s)	inside rSNPs	diseases
3	nsv518855	chr1:78416669-78456355	Genic enhancers Strong transcription Weak transcription Enhancers Transcr. at gene 5' and 3' Flanking Active TSS Active TSS ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	30 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:126 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:78405800-78442200	Strong transcription	Fetal Thymus	thymus
2	chr1:78406600-78440600	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
3	chr1:78408400-78439600	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
4	chr1:78415800-78440200	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
5	chr1:78418400-78440800	Strong transcription	Primary hematopoietic stem cells short term culture	blood
6	chr1:78424600-78440600	Weak transcription	Stomach Mucosa	stomach
7	chr1:78426400-78439600	Weak transcription	Spleen	Spleen
8	chr1:78429600-78441800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
9	chr1:78430800-78440800	Weak transcription	Psoas Muscle	Psoas
10	chr1:78432200-78441400	Weak transcription	Thymus	Thymus
11	chr1:78432200-78442400	Weak transcription	Esophagus	oesophagus
12	chr1:78432400-78439000	Weak transcription	Fetal Stomach	stomach
13	chr1:78432400-78440600	Weak transcription	Brain Hippocampus Middle	brain
14	chr1:78432400-78440800	Weak transcription	Brain Germinal Matrix	brain
15	chr1:78432400-78441200	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
16	chr1:78432400-78441200	Weak transcription	Aorta	Aorta
17	chr1:78432400-78442200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
18	chr1:78432400-78442400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
19	chr1:78432400-78442400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
20	chr1:78432600-78440000	Weak transcription	Skeletal Muscle Male	skeletal muscle
21	chr1:78432600-78443400	Weak transcription	Placenta Amnion	Placenta Amnion
22	chr1:78432800-78441400	Genic enhancers	Primary T helper cells fromperipheralblood	blood
23	chr1:78433000-78440600	Weak transcription	Fetal Heart	heart
24	chr1:78433000-78440600	Weak transcription	Rectal Smooth Muscle	rectum
25	chr1:78433200-78440600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
26	chr1:78433800-78440800	Weak transcription	Brain Substantia Nigra	brain
27	chr1:78433800-78441600	Weak transcription	Colonic Mucosa	Colon
28	chr1:78433800-78443600	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
29	chr1:78434800-78439400	Weak transcription	Fetal Muscle Trunk	muscle
30	chr1:78434800-78440000	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
31	chr1:78434800-78440200	Weak transcription	NHLF	lung
32	chr1:78434800-78440600	Weak transcription	Brain Angular Gyrus	brain
33	chr1:78434800-78440600	Weak transcription	Brain Anterior Caudate	brain
34	chr1:78434800-78440600	Weak transcription	Fetal Brain Female	brain
35	chr1:78434800-78440800	Weak transcription	Fetal Lung	lung
36	chr1:78434800-78441400	Weak transcription	Cortex derived primary cultured neurospheres	brain
37	chr1:78434800-78442200	Weak transcription	H9 Cell Line	embryonic stem cell
38	chr1:78435200-78440400	Weak transcription	Stomach Smooth Muscle	stomach
39	chr1:78435200-78440800	Weak transcription	HSMMtube	muscle
40	chr1:78435200-78441200	Weak transcription	Fetal Kidney	kidney
41	chr1:78435200-78441400	Weak transcription	Primary hematopoietic stem cells	blood
42	chr1:78435400-78439200	Weak transcription	HUVEC	blood vessel
43	chr1:78435400-78440200	Weak transcription	Adipose Nuclei	Adipose
44	chr1:78435400-78440400	Weak transcription	Skeletal Muscle Female	skeletal muscle
45	chr1:78435400-78440800	Genic enhancers	Primary T regulatory cells fromperipheralblood	blood
46	chr1:78435400-78441200	Weak transcription	Primary neutrophils fromperipheralblood	blood
47	chr1:78435400-78441200	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
48	chr1:78435600-78439600	Enhancers	Primary T helper naive cells fromperipheralblood	blood
49	chr1:78436000-78440200	Weak transcription	Osteobl	bone
50	chr1:78436200-78440400	Weak transcription	Pancreatic Islets	Pancreatic Islet

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