Variant report

Variant	rs11916261
Chromosome Location	chr3:50014496-50014497
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	chr3:49976672..49978991-chr3:50012976..50015141,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000004534	Chromatin interaction

Extended variants
information (count: 91 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:87)

rs_ID	r²[population]
rs11130223	0.84[AFR][1000 genomes];1.00[AMR][1000 genomes];0.92[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs11130225	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11130230	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];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11130237	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[YRI][hapmap];0.83[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11130239	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11130240	0.87[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11916999	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[YRI][hapmap];0.88[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs11920034	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[YRI][hapmap];0.88[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs11923132	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11924670	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.81[AFR][1000 genomes];1.00[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs11924711	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.81[AFR][1000 genomes];1.00[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs11925156	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs12486470	0.81[AFR][1000 genomes];1.00[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs12486808	0.88[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12486832	0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12489386	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AMR][1000 genomes];0.92[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs12490944	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[YRI][hapmap];0.88[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12492291	0.82[AFR][1000 genomes];1.00[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs12493565	0.90[AFR][1000 genomes];0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs12494077	0.88[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs12494172	0.88[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs12494916	0.88[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs12495114	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[YRI][hapmap];0.88[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs12495831	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AMR][1000 genomes];0.92[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs12629129	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[YRI][hapmap];0.88[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12629553	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12629677	0.88[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12630917	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs12630959	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs12631248	1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[YRI][hapmap];0.88[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs12631306	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[YRI][hapmap];0.88[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12631309	0.88[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12631608	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12632751	0.81[AFR][1000 genomes];1.00[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs12636045	0.93[AFR][1000 genomes];0.87[AMR][1000 genomes]
rs12636232	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[YRI][hapmap]
rs12636669	0.88[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12637222	0.88[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12637457	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[YRI][hapmap];0.88[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12637681	0.84[AFR][1000 genomes];1.00[AMR][1000 genomes];0.88[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs12638046	0.88[AMR][1000 genomes];0.96[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs1317215	1.00[CEU][hapmap];1.00[JPT][hapmap];0.92[EUR][1000 genomes]
rs13326300	1.00[CEU][hapmap];1.00[JPT][hapmap];0.92[EUR][1000 genomes]
rs2023951	0.81[AFR][1000 genomes];1.00[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs2023952	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[YRI][hapmap];0.88[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs2188151	1.00[JPT][hapmap]
rs2518796	1.00[JPT][hapmap]
rs28478136	0.92[EUR][1000 genomes]
rs35333166	0.93[AFR][1000 genomes];0.87[AMR][1000 genomes]
rs41291716	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs55643042	0.84[AFR][1000 genomes];1.00[AMR][1000 genomes];0.92[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs57009357	0.88[AMR][1000 genomes];0.96[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs57575459	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs58025924	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs58621288	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs58766761	0.85[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs59802870	0.88[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs61263937	0.89[EUR][1000 genomes]
rs61491513	0.88[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61729114	0.88[AMR][1000 genomes];0.96[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs62260717	0.80[EUR][1000 genomes]
rs62260756	0.92[EUR][1000 genomes]
rs62262060	0.92[EUR][1000 genomes]
rs62262095	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs62262096	0.88[AMR][1000 genomes];0.96[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs62262099	0.88[AMR][1000 genomes];0.96[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs62262100	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs62262104	0.88[AMR][1000 genomes];0.98[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs62262105	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs62262116	0.88[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62262117	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62262136	0.93[AFR][1000 genomes];0.81[AMR][1000 genomes];0.80[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs62262138	0.88[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62262144	0.88[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62262145	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62262148	0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62263578	0.88[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62263580	0.88[EUR][1000 genomes]
rs62263584	0.88[EUR][1000 genomes]
rs62263586	0.88[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs62263588	1.00[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs62263590	0.81[AFR][1000 genomes];1.00[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs62263591	0.81[AFR][1000 genomes];0.93[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs62263600	0.87[AMR][1000 genomes]
rs6797500	1.00[CEU][hapmap];1.00[JPT][hapmap];0.92[EUR][1000 genomes]
rs9813644	1.00[CEU][hapmap];1.00[JPT][hapmap];0.86[YRI][hapmap];1.00[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs9859813	1.00[CEU][hapmap];1.00[JPT][hapmap];0.92[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv834688	chr3:49811115-50019299	Weak transcription Active TSS Flanking Active TSS Strong transcription Enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer Genic enhancers Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	60 gene(s)	inside rSNPs	diseases
2	nsv876767	chr3:49918751-50153356	Active TSS Genic enhancers Weak transcription Transcr. at gene 5' and 3' Strong transcription Flanking Active TSS Enhancers Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	54 gene(s)	inside rSNPs	diseases
3	nsv834689	chr3:49962930-50085119	Enhancers Weak transcription Flanking Active TSS Strong transcription Genic enhancers Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	22 gene(s)	inside rSNPs	diseases
4	nsv1012903	chr3:49978765-50071878	Weak transcription Strong transcription Enhancers Genic enhancers Active TSS Flanking Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region	5 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	chr3:49978800-50041000	Weak transcription	H9 Cell Line	embryonic stem cell
2	chr3:49992200-50037000	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
3	chr3:49995400-50033200	Weak transcription	Fetal Brain Male	brain
4	chr3:49998000-50078200	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
5	chr3:49998400-50029600	Weak transcription	Fetal Heart	heart
6	chr3:49998400-50078600	Weak transcription	K562	blood
7	chr3:49998800-50019600	Strong transcription	Primary hematopoietic stem cells short term culture	blood
8	chr3:49999800-50028400	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
9	chr3:50000000-50019600	Strong transcription	Dnd41	blood
10	chr3:50002200-50057000	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
11	chr3:50003000-50033400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
12	chr3:50003800-50014600	Weak transcription	HSMMtube	muscle
13	chr3:50004200-50016000	Strong transcription	Primary T cells fromperipheralblood	blood
14	chr3:50004400-50027600	Weak transcription	NHEK	skin
15	chr3:50004400-50044200	Weak transcription	Pancreatic Islets	Pancreatic Islet
16	chr3:50005000-50017400	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
17	chr3:50005000-50027600	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
18	chr3:50005000-50031400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
19	chr3:50005000-50036800	Weak transcription	Small Intestine	intestine
20	chr3:50005200-50033400	Weak transcription	Esophagus	oesophagus
21	chr3:50005200-50046400	Weak transcription	Psoas Muscle	Psoas
22	chr3:50005200-50050600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
23	chr3:50005400-50022000	Weak transcription	Rectal Smooth Muscle	rectum
24	chr3:50005400-50022200	Weak transcription	Colon Smooth Muscle	Colon
25	chr3:50005400-50036800	Weak transcription	Brain Anterior Caudate	brain
26	chr3:50006000-50064000	Weak transcription	Stomach Mucosa	stomach
27	chr3:50006200-50014600	Weak transcription	Brain Substantia Nigra	brain
28	chr3:50006200-50027800	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
29	chr3:50006200-50028200	Weak transcription	Right Ventricle	heart
30	chr3:50006200-50040800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
31	chr3:50007000-50017600	Strong transcription	Primary T helper naive cells fromperipheralblood	blood
32	chr3:50007600-50020000	Strong transcription	Rectal Mucosa Donor 29	rectum
33	chr3:50008600-50050400	Weak transcription	Placenta Amnion	Placenta Amnion
34	chr3:50008800-50016000	Strong transcription	Primary neutrophils fromperipheralblood	blood
35	chr3:50009000-50022800	Strong transcription	Primary T helper cells fromperipheralblood	blood
36	chr3:50009200-50017800	Strong transcription	Fetal Thymus	thymus
37	chr3:50009200-50018000	Strong transcription	Primary monocytes fromperipheralblood	blood
38	chr3:50009200-50018000	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
39	chr3:50009400-50017600	Strong transcription	Placenta	Placenta
40	chr3:50010400-50015600	Weak transcription	HepG2	liver
41	chr3:50010800-50015200	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
42	chr3:50010800-50021800	Weak transcription	Gastric	stomach
43	chr3:50010800-50087000	Weak transcription	NHLF	lung
44	chr3:50011000-50014600	Weak transcription	HUES6 Cell Line	embryonic stem cell
45	chr3:50011000-50014600	Weak transcription	iPS-20b Cell Line	embryonic stem cell
46	chr3:50011000-50014600	Weak transcription	Primary T cells from cord blood	blood
47	chr3:50011000-50014600	Weak transcription	Sigmoid Colon	Sigmoid Colon
48	chr3:50011000-50014600	Weak transcription	HSMM	muscle
49	chr3:50011000-50014800	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
50	chr3:50011000-50014800	Weak transcription	Fetal Lung	lung

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