Variant report

Variant	rs57354242
Chromosome Location	chr12:124001569-124001570
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 20 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:13)

rs_ID	r²[population]
rs11507746	1.00[EUR][1000 genomes]
rs11507747	1.00[EUR][1000 genomes]
rs28791561	0.82[AFR][1000 genomes];0.92[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs56343236	0.89[AFR][1000 genomes];0.85[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs56399346	0.98[AFR][1000 genomes];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs56798027	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs59188352	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs61509618	0.89[AFR][1000 genomes];0.85[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73412256	1.00[EUR][1000 genomes]
rs73412279	0.88[AFR][1000 genomes];0.85[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73412281	0.90[AFR][1000 genomes];0.85[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs9697674	1.00[EUR][1000 genomes]
rs9778175	1.00[EUR][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	nsv1038841	chr12:123757305-124087671	Weak transcription Enhancers Active TSS Flanking Active TSS Genic enhancers Bivalent/Poised TSS Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	63 gene(s)	inside rSNPs	diseases
2	nsv541622	chr12:123757305-124087671	Enhancers Strong transcription Genic enhancers Active TSS Weak transcription Flanking Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	63 gene(s)	inside rSNPs	diseases
3	esv1822004	chr12:123919287-124013451	Strong transcription Genic enhancers Flanking Active TSS Weak transcription Active TSS Enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases
4	nsv1037260	chr12:123956749-124023069	Enhancers Weak transcription Strong transcription Bivalent/Poised TSS Active TSS Flanking Active TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA	16 gene(s)	inside rSNPs	diseases
5	nsv1050598	chr12:123991646-124214332	Weak transcription Strong transcription Enhancers Genic enhancers Active TSS Flanking Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	45 gene(s)	inside rSNPs	diseases
6	nsv541623	chr12:123991646-124214332	Active TSS Weak transcription Strong transcription Enhancers 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 miRNA target site	45 gene(s)	inside rSNPs	diseases
7	nsv498024	chr12:123994372-124459856	Active TSS Weak transcription Flanking Active TSS Enhancers Bivalent Enhancer Strong transcription Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	63 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	chr12:123944600-124012200	Strong transcription	Fetal Stomach	stomach
2	chr12:123950800-124007600	Weak transcription	Colonic Mucosa	Colon
3	chr12:123957600-124003800	Weak transcription	Rectal Mucosa Donor 31	rectum
4	chr12:123970000-124016400	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
5	chr12:123981800-124004000	Weak transcription	Psoas Muscle	Psoas
6	chr12:123992600-124012800	Weak transcription	Thymus	Thymus
7	chr12:123993600-124011200	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
8	chr12:123994400-124016200	Weak transcription	Primary hematopoietic stem cells	blood
9	chr12:123994600-124003800	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
10	chr12:123994600-124016200	Weak transcription	Primary hematopoietic stem cells short term culture	blood
11	chr12:123994800-124003400	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
12	chr12:123995200-124016400	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
13	chr12:123995400-124009400	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
14	chr12:123995600-124003200	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
15	chr12:123996000-124002200	Weak transcription	Hela-S3	cervix
16	chr12:123996200-124002200	Weak transcription	iPS-18 Cell Line	embryonic stem cell
17	chr12:123997000-124002400	Weak transcription	HUES48 Cell Line	embryonic stem cell
18	chr12:123997200-124003800	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
19	chr12:123997600-124001600	Weak transcription	Pancreas	Pancrea
20	chr12:123997600-124001800	Weak transcription	Duodenum Mucosa	Duodenum
21	chr12:123997600-124002200	Weak transcription	HUES64 Cell Line	embryonic stem cell
22	chr12:123997600-124003000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
23	chr12:123997800-124001600	Weak transcription	Brain Substantia Nigra	brain
24	chr12:123997800-124001600	Weak transcription	NH-A	brain
25	chr12:123997800-124001800	Weak transcription	H1 Cell Line	embryonic stem cell
26	chr12:123997800-124002200	Weak transcription	iPS-20b Cell Line	embryonic stem cell
27	chr12:123997800-124003800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
28	chr12:123997800-124004600	Weak transcription	Fetal Kidney	kidney
29	chr12:123997800-124005600	Weak transcription	Fetal Brain Male	brain
30	chr12:123997800-124007600	Weak transcription	H9 Cell Line	embryonic stem cell
31	chr12:123998000-124002400	Weak transcription	Gastric	stomach
32	chr12:123998000-124004400	Weak transcription	iPS-15b Cell Line	embryonic stem cell
33	chr12:123998000-124006800	Weak transcription	Primary T cells fromperipheralblood	blood
34	chr12:123998600-124001600	Weak transcription	NHLF	lung
35	chr12:123998800-124004000	Weak transcription	Esophagus	oesophagus
36	chr12:123999000-124004400	Weak transcription	Right Atrium	heart
37	chr12:123999200-124015800	Weak transcription	Primary T helper cells PMA-I stimulated	--
38	chr12:123999400-124016400	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
39	chr12:124000000-124002200	Weak transcription	Primary T helper cells fromperipheralblood	blood
40	chr12:124000200-124003400	Strong transcription	Stomach Smooth Muscle	stomach
41	chr12:124000200-124012400	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
42	chr12:124000400-124004000	Strong transcription	Fetal Muscle Trunk	muscle
43	chr12:124000400-124004200	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
44	chr12:124000600-124001800	Genic enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
45	chr12:124000600-124002400	Strong transcription	Aorta	Aorta
46	chr12:124000600-124002800	Strong transcription	Brain Cingulate Gyrus	brain
47	chr12:124000600-124002800	Strong transcription	HSMMtube	muscle
48	chr12:124000600-124002800	Strong transcription	NHEK	skin
49	chr12:124000600-124003000	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
50	chr12:124000600-124003000	Strong transcription	Brain Inferior Temporal Lobe	brain

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