Variant report

Variant	rs12749977
Chromosome Location	chr1:224363930-224363931
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr1:224363055..224364051-chr8:102217454..102218022,3	MCF-7	breast:
2	chr1:224363073..224364083-chr8:102217577..102218188,4	MCF-7	breast:

Variant related genes	Relation type
ENSG00000120963	Chromatin interaction

Extended variants
information (count: 28 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:26)

rs_ID	r²[population]
rs10916370	0.84[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11576702	0.84[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs11582248	0.85[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11582460	0.85[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12410321	0.84[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs12722938	0.96[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12736412	0.80[AMR][1000 genomes];0.90[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12737029	0.80[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs12739782	0.81[AMR][1000 genomes];0.84[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs16844823	0.82[AFR][1000 genomes];0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs16856443	0.83[ASN][1000 genomes]
rs2008340	0.80[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs2087795	0.85[ASN][1000 genomes]
rs35177633	0.96[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs35243286	0.83[ASN][1000 genomes]
rs35540939	0.81[AMR][1000 genomes];0.84[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs61826374	0.84[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs61826409	0.82[AFR][1000 genomes];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs61827700	0.80[EUR][1000 genomes]
rs6656849	0.84[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6657195	0.81[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs6687643	0.84[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs71644775	0.86[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs71644776	0.85[ASN][1000 genomes]
rs71644777	0.96[AFR][1000 genomes];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9662363	0.82[EUR][1000 genomes];0.90[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv832692	chr1:224206536-224407717	Strong transcription Enhancers Flanking Active TSS Weak transcription Genic enhancers Transcr. at gene 5' and 3' Active TSS Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	34 gene(s)	inside rSNPs	diseases
2	nsv8857	chr1:224359943-224383023	Strong transcription Flanking Active TSS Active TSS Enhancers Weak transcription Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	18 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:37 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:224346400-224370000	Weak transcription	Esophagus	oesophagus
2	chr1:224359000-224369200	Weak transcription	Primary T helper naive cells from peripheral blood	blood
3	chr1:224359000-224369200	Weak transcription	Primary T helper cells PMA-I stimulated	--
4	chr1:224359000-224370200	Weak transcription	Small Intestine	intestine
5	chr1:224362800-224369600	Weak transcription	Fetal Intestine Small	intestine
6	chr1:224363200-224364000	Active TSS	ES-I3 Cell Line	embryonic stem cell
7	chr1:224363200-224364600	Enhancers	Placenta	Placenta
8	chr1:224363200-224365800	Enhancers	Primary neutrophils fromperipheralblood	blood
9	chr1:224363400-224369600	Weak transcription	Fetal Intestine Large	intestine
10	chr1:224363400-224370000	Weak transcription	HUES48 Cell Line	embryonic stem cell
11	chr1:224363600-224364000	Active TSS	ES-WA7 Cell Line	embryonic stem cell
12	chr1:224363600-224370000	Weak transcription	HMEC	breast
13	chr1:224363800-224364000	Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
14	chr1:224363800-224364200	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
15	chr1:224363800-224364400	Weak transcription	Osteobl	bone
16	chr1:224363800-224364600	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
17	chr1:224363800-224367200	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
18	chr1:224363800-224368000	Weak transcription	Fetal Thymus	thymus
19	chr1:224363800-224368400	Weak transcription	Breast Myoepithelial Primary Cells	Breast
20	chr1:224363800-224368600	Weak transcription	NHEK	skin
21	chr1:224363800-224368800	Weak transcription	Primary B cells from cord blood	blood
22	chr1:224363800-224369000	Weak transcription	Primary B cells from peripheral blood	blood
23	chr1:224363800-224369600	Weak transcription	Thymus	Thymus
24	chr1:224363800-224369800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
25	chr1:224363800-224369800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
26	chr1:224363800-224369800	Weak transcription	Duodenum Smooth Muscle	Duodenum
27	chr1:224363800-224369800	Weak transcription	Stomach Smooth Muscle	stomach
28	chr1:224363800-224369800	Weak transcription	Monocytes-CD14+_RO01746	blood
29	chr1:224363800-224370000	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
30	chr1:224363800-224370000	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
31	chr1:224363800-224370000	Weak transcription	Brain Anterior Caudate	brain
32	chr1:224363800-224370200	Weak transcription	H1 Cell Line	embryonic stem cell
33	chr1:224363800-224370200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
34	chr1:224363800-224370200	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
35	chr1:224363800-224370200	Weak transcription	Brain Hippocampus Middle	brain
36	chr1:224363800-224370200	Weak transcription	Brain Substantia Nigra	brain
37	chr1:224363800-224370400	Weak transcription	Lung	lung

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