Variant report

Variant	rs12992669
Chromosome Location	chr2:183892856-183892857
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	chr2:183891999..183897694-chr2:183897904..183904092,6	MCF-7	breast:

Variant related genes	Relation type
ENSG00000061676	Chromatin interaction

Extended variants
information (count: 91 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:85)

rs_ID	r²[population]
rs10187684	0.90[ASN][1000 genomes]
rs10204853	0.90[ASN][1000 genomes]
rs1022337	1.00[JPT][hapmap]
rs10497617	0.90[ASN][1000 genomes]
rs10931052	1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[ASN][1000 genomes]
rs10931053	1.00[JPT][hapmap];0.81[ASN][1000 genomes]
rs10931055	0.90[ASN][1000 genomes]
rs11889337	0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11899644	1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[ASN][1000 genomes]
rs12470377	0.81[ASN][1000 genomes]
rs12611998	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[YRI][hapmap];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12612383	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];0.86[AMR][1000 genomes];0.92[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs12617567	1.00[JPT][hapmap];0.90[ASN][1000 genomes]
rs12618652	0.93[AMR][1000 genomes];0.87[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs12991342	0.82[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs12992059	0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12994001	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs13000008	0.83[AMR][1000 genomes];0.88[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs13009031	1.00[JPT][hapmap];0.87[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs13010139	0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13409111	0.90[ASN][1000 genomes]
rs1400130	0.81[ASN][1000 genomes]
rs16823896	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];0.86[AMR][1000 genomes];1.00[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs16823906	0.81[ASN][1000 genomes]
rs16823931	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs16823936	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2138486	0.87[CEU][hapmap];1.00[CHB][hapmap];0.82[JPT][hapmap];0.97[EUR][1000 genomes]
rs2368351	1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[ASN][1000 genomes]
rs2675048	0.90[ASN][1000 genomes]
rs2675049	1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[ASN][1000 genomes]
rs2675051	1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[ASN][1000 genomes]
rs2675076	0.90[ASN][1000 genomes]
rs2705741	1.00[JPT][hapmap]
rs2705748	0.90[ASN][1000 genomes]
rs34192739	0.95[AFR][1000 genomes];0.86[AMR][1000 genomes];0.95[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs34254952	0.92[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs34644467	0.87[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs34873881	0.98[AFR][1000 genomes];0.86[AMR][1000 genomes];1.00[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs34930236	0.98[AFR][1000 genomes];0.86[AMR][1000 genomes];1.00[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs35175570	0.84[EUR][1000 genomes]
rs35310711	0.92[EUR][1000 genomes]
rs35318802	0.81[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35368327	0.86[AMR][1000 genomes];0.95[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs35488919	0.83[AFR][1000 genomes];0.86[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35566709	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35628169	0.86[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35720425	0.83[AMR][1000 genomes];0.90[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs35971883	0.97[AFR][1000 genomes];0.86[AMR][1000 genomes];1.00[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs3791246	1.00[CEU][hapmap];1.00[JPT][hapmap];0.91[YRI][hapmap];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs4414644	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs4666604	1.00[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs4666873	0.90[ASN][1000 genomes]
rs4666876	1.00[JPT][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4666881	0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4666882	0.93[AMR][1000 genomes];0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs55739115	0.97[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs60326110	0.90[ASN][1000 genomes]
rs60543070	0.90[ASN][1000 genomes]
rs62190104	0.90[ASN][1000 genomes]
rs6434000	0.90[ASN][1000 genomes]
rs6434001	1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[ASN][1000 genomes]
rs66829551	0.97[AFR][1000 genomes];0.86[AMR][1000 genomes];1.00[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs6714190	0.87[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs6718462	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs6726085	0.87[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs6730114	0.81[ASN][1000 genomes]
rs6730183	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];0.86[AMR][1000 genomes];1.00[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs6732015	1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[ASN][1000 genomes]
rs6735651	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];0.86[AMR][1000 genomes];1.00[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs6745341	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];0.86[AMR][1000 genomes];1.00[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs6761953	1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs67966058	0.81[ASN][1000 genomes]
rs71427864	0.97[AFR][1000 genomes];0.86[AMR][1000 genomes];1.00[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs73042165	0.90[EUR][1000 genomes]
rs73980539	0.95[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7566668	1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[ASN][1000 genomes]
rs7589630	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.86[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7597884	0.90[ASN][1000 genomes]
rs7599002	0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs7599011	0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7605639	0.90[ASN][1000 genomes]
rs7607857	0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9288088	1.00[JPT][hapmap]
rs9333280	1.00[JPT][hapmap];0.81[ASN][1000 genomes]
rs9789450	1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1009882	chr2:183213152-184171519	Weak transcription Strong transcription Flanking Active TSS Enhancers Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	35 gene(s)	inside rSNPs	diseases
2	nsv1005281	chr2:183803173-184093877	Weak transcription Enhancers ZNF genes & repeats Strong transcription Active TSS Bivalent Enhancer Flanking Active TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases
3	nsv875485	chr2:183827018-184195265	Flanking Active TSS Strong transcription Weak transcription Active TSS Enhancers ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	20 gene(s)	inside rSNPs	diseases
4	nsv1010799	chr2:183855680-184244721	Enhancers Strong transcription Weak transcription Active TSS Genic enhancers Flanking Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	20 gene(s)	inside rSNPs	diseases
5	nsv536072	chr2:183855680-184244721	Flanking Active TSS Strong transcription ZNF genes & repeats Enhancers Active TSS Weak transcription Flanking Bivalent TSS/Enh Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	20 gene(s)	inside rSNPs	diseases
6	nsv1003519	chr2:183885544-184015868	Active TSS Flanking Active TSS Enhancers Strong transcription Weak transcription ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:84 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:183814600-183893600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
2	chr2:183846000-183902000	Weak transcription	Lung	lung
3	chr2:183854000-183898800	Weak transcription	Fetal Brain Male	brain
4	chr2:183859600-183899400	Weak transcription	Placenta Amnion	Placenta Amnion
5	chr2:183862400-183894400	Weak transcription	Placenta	Placenta
6	chr2:183875200-183896200	Weak transcription	Brain Cingulate Gyrus	brain
7	chr2:183875200-183896600	Weak transcription	Hela-S3	cervix
8	chr2:183875400-183897000	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
9	chr2:183875400-183899600	Weak transcription	HSMMtube	muscle
10	chr2:183878800-183902000	Weak transcription	Esophagus	oesophagus
11	chr2:183879200-183900200	Weak transcription	Brain Inferior Temporal Lobe	brain
12	chr2:183879600-183897600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
13	chr2:183880200-183900800	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
14	chr2:183881400-183894200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
15	chr2:183881800-183897800	Weak transcription	iPS-15b Cell Line	embryonic stem cell
16	chr2:183882400-183894400	Weak transcription	Brain Angular Gyrus	brain
17	chr2:183882600-183896400	Weak transcription	Fetal Brain Female	brain
18	chr2:183882800-183893200	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
19	chr2:183883400-183896400	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
20	chr2:183886400-183896400	Weak transcription	Cortex derived primary cultured neurospheres	brain
21	chr2:183886600-183894000	Weak transcription	Fetal Muscle Leg	muscle
22	chr2:183886600-183897600	Weak transcription	Fetal Muscle Trunk	muscle
23	chr2:183886600-183898800	Weak transcription	Fetal Intestine Small	intestine
24	chr2:183886600-183899600	Weak transcription	NH-A	brain
25	chr2:183886600-183900600	Weak transcription	Duodenum Mucosa	Duodenum
26	chr2:183886800-183900600	Weak transcription	Fetal Stomach	stomach
27	chr2:183887000-183894800	Weak transcription	HUVEC	blood vessel
28	chr2:183887200-183894200	Weak transcription	HMEC	breast
29	chr2:183887200-183896200	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
30	chr2:183887600-183899200	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
31	chr2:183887800-183897600	Weak transcription	HSMM	muscle
32	chr2:183887800-183898600	Weak transcription	iPS-18 Cell Line	embryonic stem cell
33	chr2:183887800-183899800	Weak transcription	H1 Cell Line	embryonic stem cell
34	chr2:183888000-183896800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
35	chr2:183888600-183899000	Weak transcription	HUES64 Cell Line	embryonic stem cell
36	chr2:183888800-183893800	Weak transcription	K562	blood
37	chr2:183888800-183894200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
38	chr2:183888800-183896400	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
39	chr2:183888800-183897000	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
40	chr2:183888800-183899000	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
41	chr2:183889000-183895600	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
42	chr2:183889200-183897200	Weak transcription	HUES48 Cell Line	embryonic stem cell
43	chr2:183889400-183893600	Weak transcription	Right Atrium	heart
44	chr2:183889400-183894200	Weak transcription	iPS-20b Cell Line	embryonic stem cell
45	chr2:183889600-183894000	Weak transcription	Duodenum Smooth Muscle	Duodenum
46	chr2:183889800-183893200	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
47	chr2:183889800-183893200	Weak transcription	Breast Myoepithelial Primary Cells	Breast
48	chr2:183889800-183893800	Weak transcription	Right Ventricle	heart
49	chr2:183889800-183894000	Weak transcription	Aorta	Aorta
50	chr2:183889800-183894000	Weak transcription	Colon Smooth Muscle	Colon

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