Variant report

Variant	rs11915398
Chromosome Location	chr3:119212417-119212418
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr3:119200434..119202905-chr3:119211856..119213563,2	MCF-7	breast:
2	chr3:119201366..119207142-chr3:119210949..119217240,7	K562	blood:
3	chr3:119201357..119202998-chr3:119210933..119213323,2	MCF-7	breast:
4	chr3:119181522..119184148-chr3:119211730..119214140,2	K562	blood:
5	chr3:119186615..119189309-chr3:119211919..119214620,2	MCF-7	breast:
6	chr3:119207787..119212909-chr3:119213285..119218402,8	K562	blood:

Variant related genes	Relation type
ENSG00000176142	Chromatin interaction
ENSG00000113845	Chromatin interaction
ENSG00000163389	Chromatin interaction
ENSG00000272662	Chromatin interaction

Extended variants
information (count: 63 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:60)

rs_ID	r²[population]
rs11539377	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[AMR][1000 genomes];0.90[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs11916272	1.00[CEU][hapmap];0.95[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs11916344	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[AMR][1000 genomes];0.90[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs11916488	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11917446	0.95[AMR][1000 genomes];0.90[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs11917642	0.86[EUR][1000 genomes]
rs11918271	0.86[AMR][1000 genomes];0.95[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs11919404	0.86[EUR][1000 genomes]
rs11919541	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11919760	1.00[CEU][hapmap];0.81[YRI][hapmap];0.85[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs11921098	1.00[CEU][hapmap];0.86[EUR][1000 genomes]
rs11922005	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11923882	0.85[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs11925305	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[AMR][1000 genomes];0.90[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs16829840	0.85[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs16829878	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs16829888	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3732414	1.00[CEU][hapmap];0.86[EUR][1000 genomes]
rs503083	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs55696355	0.95[AMR][1000 genomes];0.90[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs55853418	0.95[AMR][1000 genomes];0.90[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs55968892	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs56149432	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs56195264	0.87[AMR][1000 genomes];0.95[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs56413426	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs56710033	0.85[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs57168946	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs57389809	0.85[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs57935532	0.95[EUR][1000 genomes]
rs58398719	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs58639515	0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs58843212	0.95[AMR][1000 genomes];0.90[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs58978800	0.95[AMR][1000 genomes];0.90[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs59482964	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs60006470	0.95[AMR][1000 genomes];0.90[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs6438533	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6762095	0.85[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs6763716	0.95[AMR][1000 genomes];0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6764495	0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6775021	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[AMR][1000 genomes];0.90[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs6776387	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6777140	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6779137	1.00[CEU][hapmap];0.86[EUR][1000 genomes]
rs6783100	1.00[CEU][hapmap];0.86[EUR][1000 genomes]
rs6802790	1.00[CEU][hapmap];0.83[YRI][hapmap];0.85[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs6808654	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[AMR][1000 genomes];0.90[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs6810215	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs716649	1.00[CEU][hapmap];0.86[EUR][1000 genomes]
rs72952928	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72952932	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72952934	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72952950	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72970333	0.85[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs72970352	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73857028	0.90[EUR][1000 genomes]
rs7621149	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7626731	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs7642119	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[AMR][1000 genomes];0.90[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs7642792	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7650975	0.90[EUR][1000 genomes];1.00[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	esv3487859	chr3:118570588-119419623	Weak transcription Active TSS Strong transcription Enhancers Flanking Active TSS ZNF genes & repeats Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	61 gene(s)	inside rSNPs	diseases
2	esv3487860	chr3:118570588-119419623	Strong transcription Enhancers Active TSS Weak transcription ZNF genes & repeats Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	61 gene(s)	inside rSNPs	diseases
3	nsv829695	chr3:119178890-119367996	Active TSS Enhancers Weak transcription Strong transcription Flanking Active TSS Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	44 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	chr3:119188400-119216200	Weak transcription	Placenta Amnion	Placenta Amnion
2	chr3:119188400-119216800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
3	chr3:119188600-119216200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
4	chr3:119188800-119216200	Weak transcription	iPS-15b Cell Line	embryonic stem cell
5	chr3:119189000-119216200	Weak transcription	Stomach Mucosa	stomach
6	chr3:119189000-119216200	Weak transcription	HUVEC	blood vessel
7	chr3:119189000-119216600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
8	chr3:119189800-119216000	Weak transcription	Fetal Heart	heart
9	chr3:119190800-119216400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
10	chr3:119191000-119216400	Weak transcription	Fetal Brain Male	brain
11	chr3:119192400-119216400	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
12	chr3:119196400-119216200	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
13	chr3:119196400-119216600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
14	chr3:119196800-119216800	Weak transcription	Small Intestine	intestine
15	chr3:119197000-119216400	Weak transcription	Colon Smooth Muscle	Colon
16	chr3:119197400-119216600	Weak transcription	Aorta	Aorta
17	chr3:119202400-119213800	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
18	chr3:119204800-119216400	Weak transcription	Rectal Smooth Muscle	rectum
19	chr3:119205000-119216000	Weak transcription	Fetal Kidney	kidney
20	chr3:119205400-119216400	Weak transcription	Primary neutrophils fromperipheralblood	blood
21	chr3:119205600-119216600	Weak transcription	Colonic Mucosa	Colon
22	chr3:119205600-119216600	Weak transcription	Esophagus	oesophagus
23	chr3:119205600-119216600	Weak transcription	Gastric	stomach
24	chr3:119205800-119216000	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
25	chr3:119205800-119216200	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
26	chr3:119205800-119216200	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
27	chr3:119205800-119216200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
28	chr3:119205800-119216600	Weak transcription	Pancreas	Pancrea
29	chr3:119205800-119217000	Weak transcription	Spleen	Spleen
30	chr3:119206000-119216200	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
31	chr3:119206000-119216200	Weak transcription	Fetal Lung	lung
32	chr3:119206000-119216200	Weak transcription	Psoas Muscle	Psoas
33	chr3:119206000-119216600	Weak transcription	Primary T killer memory cells from peripheral blood	blood
34	chr3:119206200-119216000	Weak transcription	NHLF	lung
35	chr3:119206200-119216200	Weak transcription	Skeletal Muscle Male	skeletal muscle
36	chr3:119206200-119216200	Weak transcription	NH-A	brain
37	chr3:119206400-119216200	Weak transcription	Primary hematopoietic stem cells short term culture	blood
38	chr3:119206800-119216200	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
39	chr3:119206800-119216200	Weak transcription	Brain Anterior Caudate	brain
40	chr3:119207000-119216800	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
41	chr3:119207200-119215800	Weak transcription	HepG2	liver
42	chr3:119207200-119216200	Weak transcription	Hela-S3	cervix
43	chr3:119207200-119216600	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
44	chr3:119207400-119216600	Weak transcription	Ovary	ovary
45	chr3:119207600-119216200	Weak transcription	HSMMtube	muscle
46	chr3:119207600-119216400	Weak transcription	Primary T helper naive cells from peripheral blood	blood
47	chr3:119207800-119216600	Weak transcription	H9 Cell Line	embryonic stem cell
48	chr3:119208200-119216200	Weak transcription	Brain Cingulate Gyrus	brain
49	chr3:119208600-119216600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
50	chr3:119208800-119216200	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived

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