Variant report

Variant	rs12117333
Chromosome Location	chr1:179327958-179327959
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr1:179324764..179330437-chr1:179332106..179336685,6	K562	blood:
2	chr1:179325938..179328666-chr1:179330165..179332477,2	K562	blood:
3	chr1:179317813..179320620-chr1:179325439..179328200,3	MCF-7	breast:
4	chr1:179303201..179305368-chr1:179327214..179329206,2	MCF-7	breast:
5	chr1:179319158..179320695-chr1:179327831..179330357,2	K562	blood:
6	chr1:179315802..179317742-chr1:179327309..179329268,2	K562	blood:

Variant related genes	Relation type
ENSG00000263633	Chromatin interaction
ENSG00000162779	Chromatin interaction

Extended variants
information (count: 36 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:24)

rs_ID	r²[population]
rs10753191	0.88[ASN][1000 genomes]
rs10753192	0.98[EUR][1000 genomes]
rs10798662	0.85[AFR][1000 genomes];0.98[EUR][1000 genomes]
rs10798665	1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10798670	0.83[AFR][1000 genomes];0.96[EUR][1000 genomes]
rs10913731	0.98[EUR][1000 genomes]
rs10913732	0.87[AFR][1000 genomes];0.93[EUR][1000 genomes]
rs10913733	0.91[AFR][1000 genomes];0.98[EUR][1000 genomes]
rs10913734	0.91[ASN][1000 genomes]
rs12047160	0.91[AFR][1000 genomes];0.98[EUR][1000 genomes]
rs12121758	0.94[ASN][1000 genomes]
rs12138619	0.91[AFR][1000 genomes];0.98[EUR][1000 genomes]
rs12141199	0.99[ASN][1000 genomes]
rs12144580	0.85[AFR][1000 genomes];0.98[EUR][1000 genomes]
rs13306728	0.96[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs13306731	0.98[EUR][1000 genomes]
rs3753526	1.00[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs41308413	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs41310929	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs41315575	0.98[EUR][1000 genomes]
rs61824395	0.85[AFR][1000 genomes];0.98[EUR][1000 genomes]
rs6425537	0.98[EUR][1000 genomes]
rs7523799	1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs975025	0.98[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:12 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1005278	chr1:179197645-179371395	Weak transcription Active TSS Enhancers Flanking Active TSS Bivalent Enhancer ZNF genes & repeats Genic enhancers Strong transcription Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region miRNA target site	16 gene(s)	inside rSNPs	diseases
2	esv1804302	chr1:179315357-179333194	Strong transcription Weak transcription Enhancers Flanking Active TSS Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region miRNA target site	4 gene(s)	inside rSNPs	diseases
3	nsv548277	chr1:179319868-179333194	Weak transcription Strong transcription Enhancers Genic enhancers Flanking Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region miRNA target site	3 gene(s)	inside rSNPs	diseases
4	esv1809332	chr1:179320578-179333194	Weak transcription Strong transcription Enhancers Genic enhancers Flanking Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region miRNA target site	3 gene(s)	inside rSNPs	diseases
5	esv2762031	chr1:179323738-179375197	Enhancers Flanking Active TSS Strong transcription Weak transcription Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Genic enhancers	TF binding region CpG island Chromatin interactive region	10 gene(s)	inside rSNPs	diseases
6	nsv548278	chr1:179323919-179333194	Strong transcription Weak transcription Genic enhancers Enhancers	TF binding region CpG island Chromatin interactive region	3 gene(s)	inside rSNPs	diseases
7	nsv518403	chr1:179323919-179371973	Flanking Active TSS Enhancers Weak transcription Active TSS Flanking Bivalent TSS/Enh Strong transcription Bivalent/Poised TSS Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region	10 gene(s)	inside rSNPs	diseases
8	nsv548279	chr1:179323919-179390148	Enhancers Active TSS Weak transcription Strong transcription Transcr. at gene 5' and 3' Flanking Active TSS ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Genic enhancers	TF binding region CpG island Chromatin interactive region	10 gene(s)	inside rSNPs	diseases
9	esv1814621	chr1:179326323-179333194	Strong transcription Weak transcription Enhancers	TF binding region CpG island Chromatin interactive region	3 gene(s)	inside rSNPs	diseases
10	nsv548280	chr1:179326323-179333194	Weak transcription Enhancers Strong transcription	TF binding region CpG island Chromatin interactive region	3 gene(s)	inside rSNPs	diseases
11	esv3453131	chr1:179327629-179332727	Weak transcription Enhancers	TF binding region CpG island Chromatin interactive region	3 gene(s)	inside rSNPs	diseases
12	esv3453132	chr1:179327629-179332727	Weak transcription Enhancers	TF binding region CpG island Chromatin interactive region	3 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:88 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:179264800-179334200	Weak transcription	Colon Smooth Muscle	Colon
2	chr1:179292400-179328000	Weak transcription	Rectal Smooth Muscle	rectum
3	chr1:179300400-179334600	Weak transcription	HUES48 Cell Line	embryonic stem cell
4	chr1:179305600-179334200	Weak transcription	Pancreas	Pancrea
5	chr1:179312600-179334400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
6	chr1:179314800-179334400	Weak transcription	Skeletal Muscle Male	skeletal muscle
7	chr1:179315000-179334400	Weak transcription	Brain Substantia Nigra	brain
8	chr1:179315000-179334400	Weak transcription	Left Ventricle	heart
9	chr1:179315400-179334400	Weak transcription	Fetal Kidney	kidney
10	chr1:179315600-179334400	Weak transcription	Primary neutrophils fromperipheralblood	blood
11	chr1:179315800-179334200	Weak transcription	Fetal Thymus	thymus
12	chr1:179316000-179334000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
13	chr1:179316000-179334200	Weak transcription	Fetal Muscle Trunk	muscle
14	chr1:179316000-179334400	Weak transcription	Fetal Brain Female	brain
15	chr1:179316000-179334400	Weak transcription	Ovary	ovary
16	chr1:179316400-179332800	Weak transcription	Fetal Intestine Small	intestine
17	chr1:179317600-179334400	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
18	chr1:179319200-179334400	Weak transcription	Breast Myoepithelial Primary Cells	Breast
19	chr1:179319800-179334000	Weak transcription	HepG2	liver
20	chr1:179319800-179334200	Weak transcription	Primary T killer memory cells from peripheral blood	blood
21	chr1:179320000-179334600	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
22	chr1:179320800-179334000	Weak transcription	Sigmoid Colon	Sigmoid Colon
23	chr1:179320800-179334200	Weak transcription	Rectal Mucosa Donor 31	rectum
24	chr1:179320800-179334400	Weak transcription	Fetal Lung	lung
25	chr1:179321000-179334200	Weak transcription	Skeletal Muscle Female	skeletal muscle
26	chr1:179321200-179334400	Weak transcription	Fetal Stomach	stomach
27	chr1:179321200-179334400	Weak transcription	Lung	lung
28	chr1:179322400-179334200	Weak transcription	Primary B cells from cord blood	blood
29	chr1:179323000-179330600	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
30	chr1:179323000-179333400	Weak transcription	Placenta	Placenta
31	chr1:179323000-179334200	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
32	chr1:179323000-179334200	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
33	chr1:179323000-179334200	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
34	chr1:179323000-179334400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
35	chr1:179323000-179334400	Weak transcription	Primary hematopoietic stem cells	blood
36	chr1:179323000-179334400	Weak transcription	NH-A	brain
37	chr1:179323000-179334400	Weak transcription	Osteobl	bone
38	chr1:179323200-179330200	Weak transcription	Brain Anterior Caudate	brain
39	chr1:179323200-179330600	Weak transcription	HMEC	breast
40	chr1:179323200-179334200	Weak transcription	Primary hematopoietic stem cells short term culture	blood
41	chr1:179323200-179334200	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
42	chr1:179323200-179334200	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
43	chr1:179323200-179334200	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
44	chr1:179323200-179334200	Weak transcription	A549	lung
45	chr1:179323200-179334400	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
46	chr1:179323200-179334400	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
47	chr1:179323200-179334400	Weak transcription	Brain Cingulate Gyrus	brain
48	chr1:179323200-179334400	Weak transcription	Fetal Heart	heart
49	chr1:179323200-179334400	Weak transcription	Fetal Intestine Large	intestine
50	chr1:179323400-179334000	Weak transcription	Cortex derived primary cultured neurospheres	brain

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