Variant report

Variant	rs12058100
Chromosome Location	chr1:209950132-209950133
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr1:209940700-209952492	GM12891	blood:	n/a	n/a
2	POLR2A	chr1:209947434-209950183	GM12878	blood:	n/a	n/a
3	POLR2A	chr1:209949657-209951618	GM12878	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr1:209947985..209951764-chr1:209952095..209954768,3	K562	blood:

Variant related genes	Relation type
TRAF3IP3	TF binding region
ENSG00000009790	Chromatin interaction

Extended variants
information (count: 69 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:64)

rs_ID	r²[population]
rs10489343	1.00[AFR][1000 genomes];0.91[AMR][1000 genomes]
rs10779514	1.00[AFR][1000 genomes];0.87[AMR][1000 genomes]
rs10779515	1.00[AFR][1000 genomes];0.91[AMR][1000 genomes]
rs10863789	1.00[AFR][1000 genomes];0.91[AMR][1000 genomes]
rs10863790	1.00[CEU][hapmap];1.00[AFR][1000 genomes];0.91[AMR][1000 genomes]
rs1109430	1.00[AFR][1000 genomes];0.87[AMR][1000 genomes]
rs11119345	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11119346	0.86[EUR][1000 genomes]
rs11119347	1.00[AFR][1000 genomes];0.91[AMR][1000 genomes]
rs11119348	1.00[AFR][1000 genomes];0.91[AMR][1000 genomes]
rs11119360	1.00[AFR][1000 genomes]
rs11585733	1.00[AFR][1000 genomes]
rs11589335	1.00[AFR][1000 genomes]
rs12062600	1.00[AFR][1000 genomes]
rs12063989	1.00[AFR][1000 genomes]
rs12064085	1.00[AFR][1000 genomes]
rs12064211	1.00[AFR][1000 genomes]
rs12064398	1.00[AFR][1000 genomes];0.82[AMR][1000 genomes]
rs12066340	1.00[AFR][1000 genomes]
rs12069187	1.00[AFR][1000 genomes];0.82[AMR][1000 genomes]
rs12075674	1.00[CEU][hapmap];0.87[AMR][1000 genomes]
rs12080691	1.00[CEU][hapmap];0.87[AMR][1000 genomes]
rs12081405	1.00[CEU][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12083685	1.00[CEU][hapmap];0.81[AMR][1000 genomes];0.80[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12405750	1.00[CEU][hapmap];1.00[AFR][1000 genomes];0.91[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs12561766	1.00[AFR][1000 genomes];0.85[EUR][1000 genomes]
rs12563527	1.00[AFR][1000 genomes]
rs12566152	1.00[AFR][1000 genomes];0.91[AMR][1000 genomes]
rs13306422	1.00[AFR][1000 genomes]
rs17015076	0.85[EUR][1000 genomes]
rs17015078	0.85[EUR][1000 genomes]
rs17015217	1.00[CEU][hapmap];1.00[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs17015255	1.00[CEU][hapmap];1.00[AFR][1000 genomes];0.91[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs17015268	1.00[CEU][hapmap];1.00[AFR][1000 genomes];0.91[AMR][1000 genomes]
rs17388240	1.00[AFR][1000 genomes]
rs1856161	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs1883332	1.00[AFR][1000 genomes]
rs2038053	1.00[AFR][1000 genomes];0.85[EUR][1000 genomes]
rs2076149	1.00[AFR][1000 genomes];0.84[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs2076151	1.00[AFR][1000 genomes];0.81[AMR][1000 genomes]
rs2142860	1.00[AFR][1000 genomes];0.84[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs2235370	0.94[AMR][1000 genomes];0.85[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2235371	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs2235377	1.00[CEU][hapmap];1.00[AFR][1000 genomes];0.91[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs2236902	0.85[EUR][1000 genomes]
rs2272866	1.00[AFR][1000 genomes];0.85[EUR][1000 genomes]
rs2282740	1.00[AFR][1000 genomes];0.85[EUR][1000 genomes]
rs2294406	0.84[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs2298930	0.85[EUR][1000 genomes]
rs3753517	1.00[AFR][1000 genomes];0.91[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs41274836	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4140636	1.00[CEU][hapmap];0.93[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4329516	1.00[CEU][hapmap];1.00[AFR][1000 genomes];0.87[AMR][1000 genomes]
rs4545339	0.85[EUR][1000 genomes]
rs4844491	1.00[AFR][1000 genomes];0.81[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs4844494	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs4844496	1.00[CEU][hapmap];1.00[AFR][1000 genomes];0.81[AMR][1000 genomes]
rs4844893	1.00[AFR][1000 genomes];0.85[EUR][1000 genomes]
rs4844894	1.00[AFR][1000 genomes];0.85[EUR][1000 genomes]
rs4844908	1.00[AFR][1000 genomes]
rs57283682	1.00[AFR][1000 genomes];0.85[EUR][1000 genomes]
rs7515014	0.85[EUR][1000 genomes]
rs7517461	0.85[EUR][1000 genomes]
rs7528642	0.85[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv999901	chr1:209600631-210205379	Flanking Active TSS Enhancers Weak transcription Active TSS Bivalent Enhancer Strong transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	76 gene(s)	inside rSNPs	diseases
2	nsv1014034	chr1:209759648-210501731	Enhancers Weak transcription Flanking Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Strong transcription Active TSS Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	45 gene(s)	inside rSNPs	diseases
3	nsv873139	chr1:209828955-210050794	Active TSS Enhancers Weak transcription Bivalent Enhancer Genic enhancers Strong transcription Flanking Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	27 gene(s)	inside rSNPs	diseases
4	nsv1006632	chr1:209886202-209970355	Flanking Active TSS Enhancers Active TSS Weak transcription Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats Strong transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	21 gene(s)	inside rSNPs	diseases
5	nsv4343	chr1:209929932-209974877	Weak transcription Strong transcription Enhancers Transcr. at gene 5' and 3' Genic enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Active TSS ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	18 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:78 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:209942800-209956800	Weak transcription	Small Intestine	intestine
2	chr1:209942800-209957200	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
3	chr1:209943200-209950600	Weak transcription	Psoas Muscle	Psoas
4	chr1:209943400-209952600	Weak transcription	Fetal Intestine Small	intestine
5	chr1:209943600-209951000	Weak transcription	HSMMtube	muscle
6	chr1:209943600-209956600	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
7	chr1:209943800-209950800	Weak transcription	Fetal Muscle Leg	muscle
8	chr1:209943800-209954600	Weak transcription	NHEK	skin
9	chr1:209943800-209956600	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
10	chr1:209943800-209956600	Weak transcription	Brain Hippocampus Middle	brain
11	chr1:209943800-209957000	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
12	chr1:209943800-209957200	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
13	chr1:209944000-209952800	Weak transcription	HMEC	breast
14	chr1:209944000-209956000	Weak transcription	Breast Myoepithelial Primary Cells	Breast
15	chr1:209944000-209956600	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
16	chr1:209944600-209954400	Weak transcription	Fetal Muscle Trunk	muscle
17	chr1:209944800-209951200	Weak transcription	Sigmoid Colon	Sigmoid Colon
18	chr1:209944800-209955200	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
19	chr1:209944800-209956600	Weak transcription	Brain Inferior Temporal Lobe	brain
20	chr1:209944800-209956600	Weak transcription	Right Ventricle	heart
21	chr1:209945000-209950200	Weak transcription	Fetal Intestine Large	intestine
22	chr1:209945000-209953400	Weak transcription	Liver	Liver
23	chr1:209945000-209953600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
24	chr1:209945000-209953800	Weak transcription	Rectal Mucosa Donor 31	rectum
25	chr1:209945000-209956000	Weak transcription	Brain Anterior Caudate	brain
26	chr1:209945000-209956400	Weak transcription	Left Ventricle	heart
27	chr1:209945000-209956600	Weak transcription	Adipose Nuclei	Adipose
28	chr1:209945000-209956600	Weak transcription	Brain Angular Gyrus	brain
29	chr1:209945000-209956600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
30	chr1:209945000-209956600	Weak transcription	Esophagus	oesophagus
31	chr1:209945000-209956600	Weak transcription	Rectal Smooth Muscle	rectum
32	chr1:209945000-209956800	Weak transcription	HUES6 Cell Line	embryonic stem cell
33	chr1:209945000-209956800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
34	chr1:209945200-209954600	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
35	chr1:209945200-209956600	Weak transcription	Colonic Mucosa	Colon
36	chr1:209945200-209956600	Weak transcription	Pancreas	Pancrea
37	chr1:209945200-209957200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
38	chr1:209945400-209954600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
39	chr1:209945400-209956400	Weak transcription	Lung	lung
40	chr1:209945600-209955800	Weak transcription	Duodenum Smooth Muscle	Duodenum
41	chr1:209945600-209956400	Weak transcription	Gastric	stomach
42	chr1:209945600-209956600	Weak transcription	Fetal Lung	lung
43	chr1:209945800-209956600	Strong transcription	Primary neutrophils fromperipheralblood	blood
44	chr1:209946000-209951400	Genic enhancers	Primary T helper naive cells from peripheral blood	blood
45	chr1:209946000-209951800	Genic enhancers	Primary T helper memory cells from peripheral blood 2	blood
46	chr1:209946000-209955800	Weak transcription	K562	blood
47	chr1:209946000-209956000	Weak transcription	Stomach Smooth Muscle	stomach
48	chr1:209946000-209956600	Strong transcription	Primary hematopoietic stem cells short term culture	blood
49	chr1:209946000-209956600	Strong transcription	Fetal Thymus	thymus
50	chr1:209946200-209951200	Genic enhancers	Primary T helper memory cells from peripheral blood 1	blood

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