Variant report

Variant	rs12136558
Chromosome Location	chr1:224029996-224029997
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr1:224011037..224013548-chr1:224029939..224032384,3	MCF-7	breast:
2	chr1:223997873..223999794-chr1:224029438..224032178,2	MCF-7	breast:
3	chr1:224000966..224003720-chr1:224029904..224032182,2	MCF-7	breast:
4	chr1:224010151..224012081-chr1:224029415..224031184,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000143514	Chromatin interaction

Extended variants
information (count: 12 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:5)

rs_ID	r²[population]
rs12073545	0.85[EUR][1000 genomes]
rs4653676	0.88[AMR][1000 genomes];0.86[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6604725	1.00[CEU][hapmap];0.92[CHB][hapmap];0.86[JPT][hapmap];1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];0.84[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6663152	0.90[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs7517765	1.00[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];1.00[AFR][1000 genomes];0.94[AMR][1000 genomes];0.82[EUR][1000 genomes];0.88[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	esv3361888	chr1:223725597-224114846	Enhancers Strong transcription Weak transcription Active TSS Flanking Active TSS Transcr. at gene 5' and 3' Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	34 gene(s)	inside rSNPs	diseases
2	nsv1007380	chr1:223834380-224042190	Strong transcription Weak transcription Enhancers Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS Active TSS Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	31 gene(s)	inside rSNPs	diseases
3	nsv535310	chr1:223834380-224042190	ZNF genes & repeats Enhancers Weak transcription Strong transcription Active TSS Flanking Active TSS Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	31 gene(s)	inside rSNPs	diseases
4	esv34082	chr1:223851018-224144509	Enhancers Genic enhancers Active TSS Weak transcription Flanking Active TSS Strong transcription Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	33 gene(s)	inside rSNPs	diseases
5	nsv1008800	chr1:223904653-224061032	Weak transcription Enhancers Strong transcription Flanking Active TSS Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	13 gene(s)	inside rSNPs	diseases
6	esv2757772	chr1:223935220-224363163	Genic enhancers ZNF genes & repeats Weak transcription Flanking Active TSS Active TSS Strong transcription Enhancers Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	36 gene(s)	inside rSNPs	diseases
7	esv2759000	chr1:223935220-224363163	Enhancers Weak transcription Genic enhancers Strong transcription Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	36 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:120 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:224020600-224032400	Weak transcription	Placenta Amnion	Placenta Amnion
2	chr1:224020800-224031600	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
3	chr1:224023000-224030600	Weak transcription	Fetal Kidney	kidney
4	chr1:224023200-224031600	Weak transcription	Hela-S3	cervix
5	chr1:224024000-224031800	Weak transcription	Brain Inferior Temporal Lobe	brain
6	chr1:224024000-224031800	Weak transcription	Thymus	Thymus
7	chr1:224024200-224031600	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
8	chr1:224024200-224031600	Weak transcription	Rectal Mucosa Donor 29	rectum
9	chr1:224024200-224031600	Weak transcription	Rectal Mucosa Donor 31	rectum
10	chr1:224024200-224031800	Weak transcription	Adipose Nuclei	Adipose
11	chr1:224024400-224031800	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
12	chr1:224024600-224030800	Weak transcription	Primary B cells from cord blood	blood
13	chr1:224024600-224031600	Weak transcription	Primary B cells from peripheral blood	blood
14	chr1:224024600-224031800	Weak transcription	Breast Myoepithelial Primary Cells	Breast
15	chr1:224024600-224031800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
16	chr1:224024600-224031800	Weak transcription	Brain Cingulate Gyrus	brain
17	chr1:224024600-224031800	Weak transcription	Esophagus	oesophagus
18	chr1:224025200-224030000	Weak transcription	H9 Cell Line	embryonic stem cell
19	chr1:224025200-224030600	Weak transcription	NHEK	skin
20	chr1:224025200-224031800	Weak transcription	Rectal Smooth Muscle	rectum
21	chr1:224025600-224032200	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
22	chr1:224026000-224030000	Weak transcription	Duodenum Mucosa	Duodenum
23	chr1:224026000-224031600	Weak transcription	Fetal Intestine Small	intestine
24	chr1:224026200-224030000	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
25	chr1:224026200-224031800	Weak transcription	Colon Smooth Muscle	Colon
26	chr1:224026400-224030000	Weak transcription	Primary monocytes fromperipheralblood	blood
27	chr1:224026400-224030000	Weak transcription	Primary T cells fromperipheralblood	blood
28	chr1:224026400-224030000	Enhancers	Primary T helper cells PMA-I stimulated	--
29	chr1:224026400-224030000	Weak transcription	Small Intestine	intestine
30	chr1:224026400-224030400	Weak transcription	Primary T cells from cord blood	blood
31	chr1:224026400-224030600	Weak transcription	HepG2	liver
32	chr1:224026400-224030600	Weak transcription	HUVEC	blood vessel
33	chr1:224026400-224031600	Weak transcription	Primary neutrophils fromperipheralblood	blood
34	chr1:224026400-224031600	Weak transcription	Primary hematopoietic stem cells short term culture	blood
35	chr1:224026400-224031600	Weak transcription	Fetal Intestine Large	intestine
36	chr1:224026400-224031600	Weak transcription	Right Atrium	heart
37	chr1:224026400-224031600	Weak transcription	Stomach Mucosa	stomach
38	chr1:224026400-224031800	Weak transcription	H1 Cell Line	embryonic stem cell
39	chr1:224026400-224031800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
40	chr1:224026400-224031800	Weak transcription	Brain Hippocampus Middle	brain
41	chr1:224026400-224031800	Weak transcription	Fetal Thymus	thymus
42	chr1:224026400-224031800	Weak transcription	Gastric	stomach
43	chr1:224026400-224031800	Weak transcription	Stomach Smooth Muscle	stomach
44	chr1:224026400-224032400	Weak transcription	Lung	lung
45	chr1:224026400-224032600	Weak transcription	Spleen	Spleen
46	chr1:224026600-224030200	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
47	chr1:224026600-224030400	Weak transcription	Dnd41	blood
48	chr1:224026600-224030400	Weak transcription	Monocytes-CD14+_RO01746	blood
49	chr1:224026600-224030600	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
50	chr1:224026600-224030600	Weak transcription	Brain Germinal Matrix	brain

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