Variant report

Variant	rs12126069
Chromosome Location	chr1:221880851-221880852
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr1:221878250..221880861-chr1:221881070..221882576,2	MCF-7	breast:
2	chr1:221879388..221881826-chr1:221914784..221917945,4	K562	blood:

Variant related genes	Relation type
ENSG00000143507	Chromatin interaction

Extended variants
information (count: 10 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:6)

rs_ID	r²[population]
rs12029722	0.90[ASN][1000 genomes]
rs12749729	0.90[CHB][hapmap];1.00[JPT][hapmap];0.87[ASN][1000 genomes]
rs1519463	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[GIH][hapmap];0.92[MKK][hapmap];1.00[TSI][hapmap];0.87[AFR][1000 genomes];0.80[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs2378455	0.92[CEU][hapmap];0.80[AFR][1000 genomes];0.95[EUR][1000 genomes]
rs7518519	1.00[YRI][hapmap]
rs908857	1.00[ASW][hapmap];0.92[CEU][hapmap];0.95[GIH][hapmap];1.00[TSI][hapmap];0.95[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv469786	chr1:221855871-222040335	Enhancers Weak transcription Active TSS Bivalent Enhancer Flanking Active TSS ZNF genes & repeats Genic enhancers Strong transcription Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	9 gene(s)	inside rSNPs	diseases
2	nsv482867	chr1:221855871-222040335	Enhancers Weak transcription Flanking Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Genic enhancers Active TSS Strong transcription ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	9 gene(s)	inside rSNPs	diseases
3	nsv1002463	chr1:221863355-222095773	Active TSS Enhancers Weak transcription Strong transcription Transcr. at gene 5' and 3' Flanking Active TSS ZNF genes & repeats Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	13 gene(s)	inside rSNPs	diseases
4	nsv535302	chr1:221863355-222095773	Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Active TSS Genic enhancers Transcr. at gene 5' and 3' Strong transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	13 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:108 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:221863800-221888600	Weak transcription	Placenta Amnion	Placenta Amnion
2	chr1:221870000-221885400	Weak transcription	NHEK	skin
3	chr1:221871200-221885800	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
4	chr1:221872200-221882400	Weak transcription	Psoas Muscle	Psoas
5	chr1:221872800-221881200	Strong transcription	HMEC	breast
6	chr1:221873000-221881600	Weak transcription	Rectal Mucosa Donor 31	rectum
7	chr1:221873000-221882600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
8	chr1:221873200-221885200	Weak transcription	NH-A	brain
9	chr1:221873800-221882600	Weak transcription	Rectal Mucosa Donor 29	rectum
10	chr1:221873800-221882600	Weak transcription	Small Intestine	intestine
11	chr1:221873800-221885200	Weak transcription	Hela-S3	cervix
12	chr1:221874200-221881200	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
13	chr1:221874200-221882600	Weak transcription	Fetal Intestine Small	intestine
14	chr1:221874400-221882400	Weak transcription	Gastric	stomach
15	chr1:221875400-221889600	Weak transcription	Fetal Kidney	kidney
16	chr1:221875600-221881000	Strong transcription	Foreskin Fibroblast Primary Cells skin01	Skin
17	chr1:221875600-221881400	Weak transcription	HepG2	liver
18	chr1:221876600-221881600	Weak transcription	Fetal Brain Male	brain
19	chr1:221877200-221881400	Weak transcription	Duodenum Smooth Muscle	Duodenum
20	chr1:221877400-221889200	Weak transcription	Colonic Mucosa	Colon
21	chr1:221877600-221882400	Weak transcription	HUES64 Cell Line	embryonic stem cell
22	chr1:221878000-221885400	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
23	chr1:221878200-221882200	Weak transcription	HUES48 Cell Line	embryonic stem cell
24	chr1:221878600-221882200	Weak transcription	iPS-18 Cell Line	embryonic stem cell
25	chr1:221879200-221881400	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
26	chr1:221879200-221881800	Weak transcription	Pancreatic Islets	Pancreatic Islet
27	chr1:221879400-221881400	Weak transcription	HSMMtube	muscle
28	chr1:221879400-221884600	Enhancers	Brain Inferior Temporal Lobe	brain
29	chr1:221879400-221885000	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
30	chr1:221879600-221881000	Enhancers	Skeletal Muscle Female	skeletal muscle
31	chr1:221879600-221881400	Weak transcription	Primary B cells from peripheral blood	blood
32	chr1:221879600-221881400	Weak transcription	Fetal Lung	lung
33	chr1:221879600-221881400	Weak transcription	Osteobl	bone
34	chr1:221879600-221882000	Enhancers	Primary T killer naive cells fromperipheralblood	blood
35	chr1:221879600-221882400	Weak transcription	iPS-15b Cell Line	embryonic stem cell
36	chr1:221879600-221882600	Weak transcription	Fetal Intestine Large	intestine
37	chr1:221879600-221882800	Enhancers	Primary T cells fromperipheralblood	blood
38	chr1:221879600-221886200	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
39	chr1:221879600-221891000	Enhancers	Primary monocytes fromperipheralblood	blood
40	chr1:221879600-221891800	Enhancers	Fetal Thymus	thymus
41	chr1:221879600-221902400	Enhancers	Brain Substantia Nigra	brain
42	chr1:221879800-221881400	Weak transcription	HUES6 Cell Line	embryonic stem cell
43	chr1:221879800-221881400	Weak transcription	Primary B cells from cord blood	blood
44	chr1:221879800-221881400	Weak transcription	Placenta	Placenta
45	chr1:221879800-221881600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
46	chr1:221879800-221882400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
47	chr1:221879800-221882400	Weak transcription	Left Ventricle	heart
48	chr1:221879800-221882800	Enhancers	Thymus	Thymus
49	chr1:221879800-221885200	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
50	chr1:221879800-221886200	Enhancers	Primary T regulatory cells fromperipheralblood	blood

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