Variant report

Variant	rs1244873
Chromosome Location	chr12:65072628-65072629
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:0)
CpG islands
(count:0)
Chromatin interactive
region (count:11)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:11 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr12:65015837..65020171-chr12:65071764..65075735,5	MCF-7	breast:
2	chr12:65071996..65072673-chr12:65090056..65090690,2	MCF-7	breast:
3	chr12:64798134..64800228-chr12:65072624..65075360,2	MCF-7	breast:
4	chr12:65002929..65006277-chr12:65071938..65074275,3	K562	blood:
5	chr12:65071734..65074838-chr12:65083895..65087734,4	MCF-7	breast:
6	chr12:65054544..65056091-chr12:65072277..65074215,2	MCF-7	breast:
7	chr12:65002605..65004429-chr12:65071938..65074362,2	K562	blood:
8	chr12:65001203..65007582-chr12:65070748..65075652,10	MCF-7	breast:
9	chr12:65001640..65007196-chr12:65068991..65073992,9	MCF-7	breast:
10	chr12:65065436..65068310-chr12:65070713..65073194,2	K562	blood:
11	chr12:65018029..65021346-chr12:65072247..65076410,6	MCF-7	breast:

No data

Variant related genes	Relation type
ENSG00000268028	Chromatin interaction
ENSG00000184575	Chromatin interaction
ENSG00000153179	Chromatin interaction
ENSG00000256670	Chromatin interaction
ENSG00000207546	Chromatin interaction

Extended variants
information (count: 64 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:57)

rs_ID	r²[population]
rs10784417	0.81[AFR][1000 genomes];0.86[AMR][1000 genomes];0.91[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs10784418	1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[YRI][hapmap];0.91[AFR][1000 genomes];0.86[AMR][1000 genomes];0.93[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs11175483	0.86[AMR][1000 genomes];0.91[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs11175484	0.81[AFR][1000 genomes];0.86[AMR][1000 genomes];0.91[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs1147105	1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs1147107	1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs1244869	1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1244878	0.86[YRI][hapmap];0.95[AFR][1000 genomes];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs1245168	1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[AMR][1000 genomes];0.86[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs1245169	0.83[AMR][1000 genomes];0.85[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs1245179	0.98[AFR][1000 genomes];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs1245180	1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs1245181	0.88[CHB][hapmap];0.86[JPT][hapmap];0.98[AFR][1000 genomes];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs1245183	0.98[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs1245184	0.95[AFR][1000 genomes];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs1245185	0.98[AFR][1000 genomes];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs1245186	0.85[AMR][1000 genomes];0.90[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs1245187	0.87[AFR][1000 genomes];0.95[AMR][1000 genomes];0.92[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1261880	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs1264485	1.00[CHB][hapmap];0.91[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1268914	1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs1270437	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs1270836	0.95[AFR][1000 genomes];0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs1270837	1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[YRI][hapmap];0.95[AFR][1000 genomes];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs1272547	0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs1383117	1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[YRI][hapmap];0.86[AFR][1000 genomes];0.86[AMR][1000 genomes];0.91[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs1690259	1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[YRI][hapmap];0.82[AFR][1000 genomes];0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs1690272	0.81[CHB][hapmap];0.93[YRI][hapmap];0.91[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs1690273	1.00[CHB][hapmap];0.89[JPT][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs1716490	0.84[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs1716496	0.83[AFR][1000 genomes];0.87[AMR][1000 genomes];0.91[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs1716506	1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[YRI][hapmap];1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs1716517	0.85[AFR][1000 genomes];0.86[AMR][1000 genomes];0.91[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs1795613	0.80[ASN][1000 genomes]
rs1795618	0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs1795621	1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[YRI][hapmap];0.98[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs1795622	1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[YRI][hapmap];0.91[AFR][1000 genomes];0.85[AMR][1000 genomes];0.95[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs1795624	0.91[AFR][1000 genomes];0.86[AMR][1000 genomes];0.93[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs1795625	0.88[AFR][1000 genomes];0.85[AMR][1000 genomes];0.91[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs1797677	0.86[CHB][hapmap];0.84[JPT][hapmap];0.95[AMR][1000 genomes];0.93[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs1797678	0.87[AFR][1000 genomes];0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs1797679	1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[YRI][hapmap];0.95[AFR][1000 genomes];0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs1797684	1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[YRI][hapmap];0.91[AFR][1000 genomes];0.86[AMR][1000 genomes];0.92[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs1797688	1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[AMR][1000 genomes];0.93[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs1797689	1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[AMR][1000 genomes];0.93[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2464347	0.80[ASN][1000 genomes]
rs2620730	1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[AMR][1000 genomes];0.95[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2682714	1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[AMR][1000 genomes];0.86[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs2682716	0.86[AFR][1000 genomes];0.82[AMR][1000 genomes];0.90[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2682719	0.90[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2682728	1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2701849	0.90[CHB][hapmap];1.00[JPT][hapmap];0.81[YRI][hapmap];0.83[AMR][1000 genomes];0.86[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs2701850	0.83[AMR][1000 genomes];0.86[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs7313765	1.00[CHB][hapmap];0.90[JPT][hapmap]
rs7968403	0.83[AMR][1000 genomes];0.86[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs7971636	0.80[ASN][1000 genomes]
rs7975455	0.88[AFR][1000 genomes];0.86[AMR][1000 genomes];0.89[EUR][1000 genomes];0.83[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	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
2	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
3	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
4	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
5	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
6	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
7	nsv899209	chr12:65068686-65184236	Weak transcription Enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Active TSS Strong transcription Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	13 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:116 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:65060000-65073400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
2	chr12:65063600-65073400	Enhancers	Rectal Mucosa Donor 31	rectum
3	chr12:65064000-65073400	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
4	chr12:65064000-65073400	Weak transcription	Fetal Brain Male	brain
5	chr12:65064000-65076000	Enhancers	Fetal Thymus	thymus
6	chr12:65064000-65078200	Enhancers	Primary B cells from peripheral blood	blood
7	chr12:65066000-65078600	Enhancers	Spleen	Spleen
8	chr12:65066800-65073200	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
9	chr12:65066800-65073600	Weak transcription	Esophagus	oesophagus
10	chr12:65067000-65073200	Enhancers	Primary neutrophils fromperipheralblood	blood
11	chr12:65067000-65073200	Weak transcription	HSMM	muscle
12	chr12:65067000-65075000	Weak transcription	Ovary	ovary
13	chr12:65067200-65073600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
14	chr12:65067400-65073800	Enhancers	Primary T helper cells fromperipheralblood	blood
15	chr12:65067400-65076800	Weak transcription	Brain Angular Gyrus	brain
16	chr12:65067800-65073200	Weak transcription	Fetal Muscle Trunk	muscle
17	chr12:65067800-65073400	Weak transcription	Brain Anterior Caudate	brain
18	chr12:65068000-65073400	Weak transcription	Brain Hippocampus Middle	brain
19	chr12:65068000-65074800	Weak transcription	H9 Cell Line	embryonic stem cell
20	chr12:65068000-65075800	Weak transcription	iPS-18 Cell Line	embryonic stem cell
21	chr12:65068000-65076800	Weak transcription	Brain Germinal Matrix	brain
22	chr12:65068400-65087200	Weak transcription	Liver	Liver
23	chr12:65068600-65073200	Weak transcription	Fetal Lung	lung
24	chr12:65068600-65074800	Weak transcription	HUES64 Cell Line	embryonic stem cell
25	chr12:65068600-65075200	Weak transcription	Gastric	stomach
26	chr12:65068600-65076600	Weak transcription	Fetal Kidney	kidney
27	chr12:65068600-65076800	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
28	chr12:65068600-65078000	Weak transcription	Dnd41	blood
29	chr12:65068600-65079400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
30	chr12:65068800-65073200	Enhancers	Primary T cells fromperipheralblood	blood
31	chr12:65069200-65073200	Enhancers	Primary T regulatory cells fromperipheralblood	blood
32	chr12:65069400-65077000	Weak transcription	Psoas Muscle	Psoas
33	chr12:65069600-65073200	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
34	chr12:65069600-65073400	Weak transcription	Fetal Stomach	stomach
35	chr12:65069600-65073600	Weak transcription	Pancreas	Pancrea
36	chr12:65069600-65073800	Weak transcription	Small Intestine	intestine
37	chr12:65069800-65073000	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
38	chr12:65069800-65073200	Weak transcription	Fetal Intestine Small	intestine
39	chr12:65069800-65073400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
40	chr12:65069800-65073400	Weak transcription	Right Ventricle	heart
41	chr12:65069800-65073400	Weak transcription	Skeletal Muscle Male	skeletal muscle
42	chr12:65069800-65073600	Weak transcription	Cortex derived primary cultured neurospheres	brain
43	chr12:65069800-65074800	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
44	chr12:65070000-65072800	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
45	chr12:65070000-65072800	Weak transcription	Osteobl	bone
46	chr12:65070000-65073000	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
47	chr12:65070000-65073200	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
48	chr12:65070000-65073200	Weak transcription	Placenta	Placenta
49	chr12:65070000-65073200	Weak transcription	HSMMtube	muscle
50	chr12:65070000-65073200	Weak transcription	NH-A	brain

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