Variant report

Variant	rs12129512
Chromosome Location	chr1:10572967-10572968
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr1:10570510..10573214-chr1:10855273..10856908,2	MCF-7	breast:
2	chr1:10566900..10569422-chr1:10571271..10572995,2	K562	blood:
3	chr1:10570193..10573088-chr1:10575798..10579645,3	MCF-7	breast:
4	chr1:10569482..10571483-chr1:10572910..10575292,2	MCF-7	breast:
5	chr1:10570481..10573299-chr1:10599222..10600978,2	K562	blood:
6	chr1:10571375..10572978-chr1:10573706..10575534,2	K562	blood:
7	chr1:10552985..10554515-chr1:10570159..10573130,2	K562	blood:

Variant related genes	Relation type
ENSG00000130940	Chromatin interaction

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

rSNPs within LD-proxies of this variant (count:12)

rs_ID	r²[population]
rs11121587	1.00[YRI][hapmap]
rs12065251	0.84[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs12124486	0.81[AMR][1000 genomes];0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12402967	0.81[AMR][1000 genomes];0.86[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12725704	0.81[AMR][1000 genomes];0.86[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12729844	0.86[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs17035305	1.00[YRI][hapmap]
rs2027087	0.86[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2483677	1.00[YRI][hapmap];0.92[AFR][1000 genomes]
rs34132699	1.00[ASN][1000 genomes]
rs34372628	0.83[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs6667629	0.93[CEU][hapmap];0.86[EUR][1000 genomes];0.93[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:8 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv2757722	chr1:10238070-10582554	Weak transcription Enhancers Genic enhancers Active TSS Strong transcription Flanking Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	39 gene(s)	inside rSNPs	diseases
2	esv2758920	chr1:10238070-10582554	Strong transcription Weak transcription Flanking Active TSS Enhancers ZNF genes & repeats Active TSS Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	39 gene(s)	inside rSNPs	diseases
3	nsv817370	chr1:10305470-10697150	Weak transcription Flanking Active TSS Enhancers Strong transcription Transcr. at gene 5' and 3' Active TSS Genic enhancers ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	33 gene(s)	inside rSNPs	diseases
4	nsv1008021	chr1:10363794-10802633	Strong transcription Enhancers Weak transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Flanking Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Active TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	36 gene(s)	inside rSNPs	diseases
5	esv2764192	chr1:10383734-10594186	Strong transcription Weak transcription Enhancers Bivalent Enhancer Flanking Active TSS Active TSS Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	26 gene(s)	inside rSNPs	diseases
6	nsv1003498	chr1:10445928-10607351	Weak transcription Enhancers Flanking Active TSS Genic enhancers Strong transcription Active TSS Bivalent Enhancer ZNF genes & repeats 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	26 gene(s)	inside rSNPs	diseases
7	nsv998731	chr1:10464176-10607351	Weak transcription Active TSS Strong transcription Enhancers Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	21 gene(s)	inside rSNPs	diseases
8	nsv2521	chr1:10553530-10598171	Weak transcription Active TSS Genic enhancers Enhancers Flanking Active TSS Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	9 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:118 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:10566400-10577800	Enhancers	Fetal Thymus	thymus
2	chr1:10566800-10579800	Enhancers	Liver	Liver
3	chr1:10568800-10573800	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
4	chr1:10568800-10576600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
5	chr1:10569000-10573600	Weak transcription	iPS-18 Cell Line	embryonic stem cell
6	chr1:10569000-10578800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
7	chr1:10569600-10577800	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
8	chr1:10569800-10573600	Weak transcription	iPS-15b Cell Line	embryonic stem cell
9	chr1:10569800-10575000	Weak transcription	Fetal Muscle Trunk	muscle
10	chr1:10570000-10573800	Enhancers	Fetal Intestine Large	intestine
11	chr1:10570200-10574400	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
12	chr1:10570800-10574400	Weak transcription	iPS-20b Cell Line	embryonic stem cell
13	chr1:10570800-10574400	Weak transcription	Fetal Heart	heart
14	chr1:10570800-10579800	Weak transcription	Aorta	Aorta
15	chr1:10570800-10595600	Weak transcription	Primary B cells from cord blood	blood
16	chr1:10571000-10573400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
17	chr1:10571000-10573400	Weak transcription	Fetal Stomach	stomach
18	chr1:10571000-10573600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
19	chr1:10571000-10574400	Weak transcription	H1 Cell Line	embryonic stem cell
20	chr1:10571000-10574400	Weak transcription	Breast Myoepithelial Primary Cells	Breast
21	chr1:10571000-10574800	Weak transcription	HUES64 Cell Line	embryonic stem cell
22	chr1:10571000-10574800	Weak transcription	Brain Germinal Matrix	brain
23	chr1:10571000-10576000	Weak transcription	Brain Hippocampus Middle	brain
24	chr1:10571000-10576600	Weak transcription	Placenta	Placenta
25	chr1:10571000-10577000	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
26	chr1:10571000-10577000	Weak transcription	H9 Cell Line	embryonic stem cell
27	chr1:10571200-10573200	Weak transcription	HUES48 Cell Line	embryonic stem cell
28	chr1:10571200-10573400	Weak transcription	Brain Inferior Temporal Lobe	brain
29	chr1:10571200-10573600	Weak transcription	Brain Cingulate Gyrus	brain
30	chr1:10571200-10573600	Weak transcription	Duodenum Smooth Muscle	Duodenum
31	chr1:10571200-10573800	Weak transcription	HUES6 Cell Line	embryonic stem cell
32	chr1:10571200-10574400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
33	chr1:10571200-10574800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
34	chr1:10571200-10575800	Weak transcription	Pancreas	Pancrea
35	chr1:10571200-10576400	Weak transcription	Gastric	stomach
36	chr1:10571400-10574400	Weak transcription	Fetal Kidney	kidney
37	chr1:10571400-10574600	Genic enhancers	K562	blood
38	chr1:10571400-10579400	Weak transcription	Pancreatic Islets	Pancreatic Islet
39	chr1:10571600-10574200	Weak transcription	Fetal Lung	lung
40	chr1:10571600-10575800	Weak transcription	Stomach Mucosa	stomach
41	chr1:10571600-10576400	Enhancers	Primary hematopoietic stem cells	blood
42	chr1:10571600-10576800	Weak transcription	Small Intestine	intestine
43	chr1:10571600-10578000	Enhancers	Primary T killer naive cells fromperipheralblood	blood
44	chr1:10571600-10579200	Weak transcription	Rectal Mucosa Donor 29	rectum
45	chr1:10571800-10573000	Weak transcription	Stomach Smooth Muscle	stomach
46	chr1:10571800-10573400	Weak transcription	Cortex derived primary cultured neurospheres	brain
47	chr1:10571800-10573600	Weak transcription	Rectal Smooth Muscle	rectum
48	chr1:10571800-10574000	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
49	chr1:10571800-10574400	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
50	chr1:10571800-10574400	Weak transcription	Left Ventricle	heart

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