Variant report

Variant	rs17120341
Chromosome Location	chr12:62894636-62894637
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr12:62892704..62894662-chr12:62995139..62997140,2	K562	blood:
2	chr12:62887087..62888673-chr12:62894503..62897008,2	K562	blood:

Variant related genes	Relation type
ENSG00000257354	Chromatin interaction

Extended variants
information (count: 50 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:44)

rs_ID	r²[population]
rs10506442	1.00[CEU][hapmap];0.81[CHB][hapmap];0.93[JPT][hapmap];0.81[AMR][1000 genomes];0.94[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs10506443	0.87[CHB][hapmap];0.93[JPT][hapmap];0.93[ASN][1000 genomes]
rs11614276	0.91[ASN][1000 genomes]
rs12146793	0.89[CHB][hapmap];0.94[JPT][hapmap];0.93[ASN][1000 genomes]
rs12371458	0.91[ASN][1000 genomes]
rs12423344	0.88[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs12424006	1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12427111	1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs13328991	1.00[CEU][hapmap]
rs1532394	1.00[CEU][hapmap]
rs17097966	1.00[CEU][hapmap];0.94[CHB][hapmap];0.93[JPT][hapmap];0.89[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs17098038	1.00[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs17098087	1.00[CEU][hapmap]
rs17098096	1.00[CEU][hapmap]
rs17098098	1.00[CEU][hapmap]
rs1982991	0.89[CHB][hapmap];0.94[JPT][hapmap];0.91[ASN][1000 genomes]
rs4763172	1.00[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4763173	1.00[CEU][hapmap];0.87[CHB][hapmap];0.83[JPT][hapmap];1.00[YRI][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4763176	1.00[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs57715507	0.82[AFR][1000 genomes];0.84[AMR][1000 genomes];0.89[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs59191400	0.82[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs61556144	0.84[AMR][1000 genomes];0.89[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs61919477	0.91[AFR][1000 genomes];0.97[AMR][1000 genomes];0.82[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs61919478	0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs61919479	0.85[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs61919485	0.82[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs61921903	0.81[AMR][1000 genomes]
rs61921904	0.89[AMR][1000 genomes];0.94[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs61921905	0.81[AMR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs61921908	0.89[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs61921909	0.93[ASN][1000 genomes]
rs61921910	0.89[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs61921911	0.88[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs61921913	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61921914	0.83[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7136696	1.00[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.82[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7307786	1.00[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.82[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7309338	1.00[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];0.81[AMR][1000 genomes];1.00[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7316437	0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs73323255	0.95[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs7958721	0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7964791	1.00[CEU][hapmap];0.93[CHB][hapmap];1.00[JPT][hapmap];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7965328	0.85[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7969992	0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv530690	chr12:62678463-62999462	Weak transcription Enhancers Flanking Active TSS Active TSS Strong transcription Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	54 gene(s)	inside rSNPs	diseases
2	nsv899158	chr12:62783967-62937259	Strong transcription Bivalent/Poised TSS Weak transcription Active TSS Flanking Bivalent TSS/Enh Enhancers Genic enhancers Flanking Active TSS Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	10 gene(s)	inside rSNPs	diseases
3	nsv899159	chr12:62783967-62945245	Weak transcription Strong transcription Enhancers Flanking Active TSS Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	11 gene(s)	inside rSNPs	diseases
4	nsv821671	chr12:62794304-63007964	Strong transcription ZNF genes & repeats Active TSS Weak transcription Enhancers Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	53 gene(s)	inside rSNPs	diseases
5	nsv469418	chr12:62893199-62959137	Weak transcription Strong transcription Enhancers Genic enhancers ZNF genes & repeats Active TSS Flanking Active TSS	TF binding region CpG island Chromatin interactive region	8 gene(s)	inside rSNPs	diseases
6	nsv559156	chr12:62893199-62959137	Weak transcription Strong transcription Enhancers Genic enhancers ZNF genes & repeats Active TSS Flanking Active TSS	TF binding region CpG island Chromatin interactive region	8 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:111 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:62861800-62902200	Weak transcription	Fetal Kidney	kidney
2	chr12:62862800-62895400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
3	chr12:62863200-62895200	Weak transcription	Placenta Amnion	Placenta Amnion
4	chr12:62863200-62896800	Weak transcription	HUES64 Cell Line	embryonic stem cell
5	chr12:62863200-62901800	Weak transcription	HUES6 Cell Line	embryonic stem cell
6	chr12:62863200-62937400	Weak transcription	Pancreas	Pancrea
7	chr12:62863400-62895400	Weak transcription	Stomach Smooth Muscle	stomach
8	chr12:62863400-62902000	Weak transcription	HUVEC	blood vessel
9	chr12:62863400-62911000	Weak transcription	Primary T killer memory cells from peripheral blood	blood
10	chr12:62863600-62926400	Weak transcription	Colon Smooth Muscle	Colon
11	chr12:62864000-62899200	Weak transcription	Brain Germinal Matrix	brain
12	chr12:62864000-62901600	Weak transcription	Lung	lung
13	chr12:62864000-62901600	Weak transcription	Rectal Smooth Muscle	rectum
14	chr12:62864000-62906200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
15	chr12:62866000-62895400	Weak transcription	Left Ventricle	heart
16	chr12:62866200-62897000	Weak transcription	K562	blood
17	chr12:62866200-62899200	Weak transcription	Sigmoid Colon	Sigmoid Colon
18	chr12:62866200-62906200	Weak transcription	Aorta	Aorta
19	chr12:62866600-62896000	Weak transcription	Fetal Brain Female	brain
20	chr12:62866600-62906200	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
21	chr12:62866600-62912400	Weak transcription	NHLF	lung
22	chr12:62866600-62953200	Weak transcription	Psoas Muscle	Psoas
23	chr12:62867200-62898600	Weak transcription	Skeletal Muscle Male	skeletal muscle
24	chr12:62869000-62904400	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
25	chr12:62871000-62910800	Weak transcription	Primary T helper naive cells from peripheral blood	blood
26	chr12:62871200-62895200	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
27	chr12:62871800-62895200	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
28	chr12:62871800-62895400	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
29	chr12:62871800-62897200	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
30	chr12:62871800-62926200	Weak transcription	Fetal Brain Male	brain
31	chr12:62872200-62895400	Weak transcription	Rectal Mucosa Donor 29	rectum
32	chr12:62872600-62901600	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
33	chr12:62873400-62895400	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
34	chr12:62874000-62895800	Weak transcription	Breast Myoepithelial Primary Cells	Breast
35	chr12:62874600-62898800	Weak transcription	Fetal Muscle Trunk	muscle
36	chr12:62874600-62917400	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
37	chr12:62874800-62895200	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
38	chr12:62874800-62896000	Weak transcription	HMEC	breast
39	chr12:62875600-62901200	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
40	chr12:62876000-62902000	Weak transcription	Muscle Satellite Cultured Cells	--
41	chr12:62876000-62905800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
42	chr12:62876000-62937400	Weak transcription	Gastric	stomach
43	chr12:62876200-62895600	Weak transcription	HSMM	muscle
44	chr12:62876200-62913000	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
45	chr12:62876400-62902000	Weak transcription	Brain Anterior Caudate	brain
46	chr12:62876800-62897000	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
47	chr12:62877400-62899200	Weak transcription	Ovary	ovary
48	chr12:62877800-62896800	Weak transcription	Brain Hippocampus Middle	brain
49	chr12:62877800-62906200	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
50	chr12:62878600-62897000	Weak transcription	NHEK	skin

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