Variant report

Variant	rs1716496
Chromosome Location	chr12:65034439-65034440
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr12:64845007..64847351-chr12:65033223..65035574,2	K562	blood:
2	chr12:65033725..65035733-chr12:65037658..65039391,2	MCF-7	breast:
3	chr12:65024223..65026567-chr12:65034378..65036625,2	K562	blood:
4	chr12:65001510..65003964-chr12:65034333..65037188,2	MCF-7	breast:
5	chr12:65030974..65032522-chr12:65034384..65035894,2	K562	blood:
6	chr12:65030293..65032004-chr12:65033712..65035363,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000256670	Chromatin interaction
ENSG00000183735	Chromatin interaction

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

rSNPs within LD-proxies of this variant (count:55)

rs_ID	r²[population]
rs10784417	0.91[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10784418	0.91[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11175483	0.82[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11175484	0.91[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1147105	0.87[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1147107	0.86[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1244869	0.88[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs1244873	0.83[AFR][1000 genomes];0.87[AMR][1000 genomes];0.91[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs1244878	0.88[AFR][1000 genomes];0.90[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1245168	0.95[AMR][1000 genomes];0.92[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1245169	0.95[AMR][1000 genomes];0.92[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1245179	0.84[AFR][1000 genomes];0.89[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1245180	0.86[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1245181	0.84[AFR][1000 genomes];0.89[AMR][1000 genomes];0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1245183	0.84[AFR][1000 genomes];0.90[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1245184	0.81[AFR][1000 genomes];0.88[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1245185	0.84[AFR][1000 genomes];0.89[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1245186	0.87[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs1245187	0.87[AMR][1000 genomes];0.88[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs1264485	0.83[AFR][1000 genomes];0.89[AMR][1000 genomes];0.90[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs1268914	0.83[AFR][1000 genomes];0.89[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1270437	0.84[AFR][1000 genomes];0.90[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1270836	0.88[AFR][1000 genomes];0.89[AMR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1270837	0.88[AFR][1000 genomes];0.90[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1272547	0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1383117	0.96[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1690259	0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1690272	0.85[AFR][1000 genomes];0.89[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1690273	0.88[AFR][1000 genomes];0.89[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1716490	0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1716506	0.83[AFR][1000 genomes];0.89[AMR][1000 genomes];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1716517	0.91[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1795613	0.97[ASN][1000 genomes]
rs1795618	0.88[AMR][1000 genomes];0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1795621	0.84[AFR][1000 genomes];0.90[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1795622	0.91[AFR][1000 genomes];0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1795624	0.91[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1795625	0.95[AFR][1000 genomes];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1797677	0.83[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs1797678	0.81[AFR][1000 genomes];0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1797679	0.88[AFR][1000 genomes];0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1797684	0.91[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1797688	0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1797689	0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2464347	0.97[ASN][1000 genomes]
rs2620730	0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2682714	0.95[AMR][1000 genomes];0.92[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2682716	0.93[AFR][1000 genomes];0.94[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2682719	0.90[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2682728	0.86[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs2701849	0.95[AMR][1000 genomes];0.92[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2701850	0.95[AMR][1000 genomes];0.92[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7968403	0.95[AMR][1000 genomes];0.92[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7971636	0.97[ASN][1000 genomes]
rs7975455	0.95[AFR][1000 genomes];0.99[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:8 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv832443	chr12:64878856-65057265	Weak transcription Enhancers Active TSS Flanking Active TSS Bivalent Enhancer Genic enhancers ZNF genes & repeats Strong transcription Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	27 gene(s)	inside rSNPs	diseases
2	nsv832444	chr12:64981484-65168472	Active TSS Enhancers Weak transcription ZNF genes & repeats Strong transcription Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	26 gene(s)	inside rSNPs	diseases
3	nsv559203	chr12:65002969-65199922	Genic enhancers Strong transcription Enhancers Weak transcription Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3' Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	29 gene(s)	inside rSNPs	diseases
4	nsv1045216	chr12:65009102-65176894	Flanking Active TSS Enhancers Weak transcription Strong transcription Active TSS Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	15 gene(s)	inside rSNPs	diseases
5	nsv541513	chr12:65009102-65176894	Active TSS Weak transcription Enhancers Strong transcription Genic enhancers ZNF genes & repeats Flanking Active TSS Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	15 gene(s)	inside rSNPs	diseases
6	nsv469457	chr12:65009243-65195977	Enhancers Strong transcription Weak transcription Genic enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Active TSS Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	15 gene(s)	inside rSNPs	diseases
7	nsv559204	chr12:65009243-65195977	Active TSS Flanking Active TSS Enhancers Strong transcription Weak transcription Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	15 gene(s)	inside rSNPs	diseases
8	nsv438218	chr12:65017844-65037483	Enhancers Active TSS Transcr. at gene 5' and 3' Genic enhancers Weak transcription ZNF genes & repeats Flanking Active TSS Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:75 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:65018600-65035000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
2	chr12:65019800-65047400	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
3	chr12:65021400-65043400	Weak transcription	iPS-15b Cell Line	embryonic stem cell
4	chr12:65021800-65037000	Weak transcription	Adipose Nuclei	Adipose
5	chr12:65021800-65038000	Weak transcription	Ovary	ovary
6	chr12:65022400-65039600	Weak transcription	Osteobl	bone
7	chr12:65025000-65059600	Weak transcription	Thymus	Thymus
8	chr12:65025200-65044000	Weak transcription	Fetal Muscle Trunk	muscle
9	chr12:65026400-65043200	Weak transcription	Fetal Stomach	stomach
10	chr12:65027400-65041800	Weak transcription	Spleen	Spleen
11	chr12:65027800-65047600	Weak transcription	Psoas Muscle	Psoas
12	chr12:65028000-65036600	Weak transcription	Lung	lung
13	chr12:65028200-65047400	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
14	chr12:65028400-65037000	Weak transcription	HUVEC	blood vessel
15	chr12:65028400-65038600	Weak transcription	Rectal Smooth Muscle	rectum
16	chr12:65028400-65047400	Weak transcription	NHDF-Ad	bronchial
17	chr12:65028400-65047400	Weak transcription	NHLF	lung
18	chr12:65028600-65056400	Weak transcription	NHEK	skin
19	chr12:65029000-65041800	Weak transcription	Left Ventricle	heart
20	chr12:65029200-65039800	Enhancers	Primary T cells fromperipheralblood	blood
21	chr12:65029200-65041000	Enhancers	Primary T helper naive cells fromperipheralblood	blood
22	chr12:65029200-65041600	Weak transcription	Fetal Muscle Leg	muscle
23	chr12:65029400-65036800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
24	chr12:65029400-65038000	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
25	chr12:65029600-65036600	Weak transcription	Pancreas	Pancrea
26	chr12:65029600-65036800	Weak transcription	GM12878-XiMat	blood
27	chr12:65029600-65037600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
28	chr12:65029600-65038200	Weak transcription	Right Atrium	heart
29	chr12:65029600-65042600	Enhancers	Primary T helper cells fromperipheralblood	blood
30	chr12:65029600-65044000	Weak transcription	Fetal Lung	lung
31	chr12:65030800-65034600	Enhancers	Primary neutrophils fromperipheralblood	blood
32	chr12:65031000-65047600	Weak transcription	Muscle Satellite Cultured Cells	--
33	chr12:65031200-65040000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
34	chr12:65031200-65043400	Weak transcription	HUES48 Cell Line	embryonic stem cell
35	chr12:65031200-65043600	Weak transcription	Duodenum Smooth Muscle	Duodenum
36	chr12:65031200-65043800	Weak transcription	Fetal Intestine Small	intestine
37	chr12:65031400-65042600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
38	chr12:65031400-65043400	Weak transcription	Small Intestine	intestine
39	chr12:65031600-65038200	Weak transcription	Gastric	stomach
40	chr12:65032200-65037200	Enhancers	Primary T helper cells PMA-I stimulated	--
41	chr12:65032200-65040000	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
42	chr12:65032200-65040600	Enhancers	Primary T killer naive cells fromperipheralblood	blood
43	chr12:65032400-65035400	Enhancers	Primary T cells from cord blood	blood
44	chr12:65032600-65034600	Enhancers	Primary T regulatory cells fromperipheralblood	blood
45	chr12:65032600-65041800	Weak transcription	Fetal Heart	heart
46	chr12:65032800-65038000	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
47	chr12:65033000-65035000	Weak transcription	Colon Smooth Muscle	Colon
48	chr12:65033000-65037200	Weak transcription	Stomach Mucosa	stomach
49	chr12:65033000-65041800	Weak transcription	Stomach Smooth Muscle	stomach
50	chr12:65033000-65052600	Weak transcription	Primary hematopoietic stem cells short term culture	blood

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