Variant report

Variant	rs12989726
Chromosome Location	chr2:153312628-153312629
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 29 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:23)

rs_ID	r²[population]
rs10931146	0.88[JPT][hapmap];0.80[ASN][1000 genomes]
rs11897348	0.81[EUR][1000 genomes]
rs12105467	1.00[CEU][hapmap];1.00[JPT][hapmap];0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12992900	1.00[CEU][hapmap];0.89[CHB][hapmap];1.00[JPT][hapmap];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs13033468	1.00[CEU][hapmap];0.88[JPT][hapmap];0.88[YRI][hapmap];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs16831135	0.92[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs16831229	1.00[CEU][hapmap];0.88[JPT][hapmap];0.88[AMR][1000 genomes];0.95[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs16831246	1.00[CEU][hapmap];0.89[CHB][hapmap];1.00[JPT][hapmap];0.81[YRI][hapmap];0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs16831247	1.00[CEU][hapmap];0.89[CHB][hapmap];1.00[JPT][hapmap];0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs16831263	0.85[EUR][1000 genomes]
rs2881338	1.00[CEU][hapmap];1.00[JPT][hapmap];0.86[AMR][1000 genomes];0.95[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs34027587	0.88[EUR][1000 genomes]
rs34520795	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs35455499	0.93[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs4664108	0.89[CHB][hapmap];0.86[JPT][hapmap];0.88[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs4664111	1.00[CEU][hapmap];1.00[JPT][hapmap];0.85[AMR][1000 genomes];0.95[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs4664584	1.00[CEU][hapmap];0.88[CHB][hapmap];1.00[JPT][hapmap];0.83[AMR][1000 genomes];0.95[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs4664588	0.86[AMR][1000 genomes];0.95[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs60280470	0.85[EUR][1000 genomes]
rs67374211	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6739557	1.00[CEU][hapmap]
rs71417228	0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7582905	0.83[AMR][1000 genomes];0.98[EUR][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	nsv834419	chr2:153179420-153381476	Weak transcription Strong transcription Enhancers Flanking Active TSS Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	3 gene(s)	inside rSNPs	diseases
2	esv3693436	chr2:153219836-153479857	Weak transcription Active TSS Enhancers Flanking Active TSS Strong transcription Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
3	nsv875291	chr2:153251742-153339823	Enhancers Weak transcription Flanking Active TSS Genic enhancers Active TSS Strong transcription Bivalent Enhancer Transcr. at gene 5' and 3'	Chromatin interactive region	2 gene(s)	inside rSNPs	diseases
4	nsv1013777	chr2:153273637-153538546	Weak transcription Strong transcription Genic enhancers Enhancers Flanking Active TSS ZNF genes & repeats Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	9 gene(s)	inside rSNPs	diseases
5	esv2754362	chr2:153297577-153366129	Enhancers Flanking Active TSS Weak transcription ZNF genes & repeats Active TSS Genic enhancers Strong transcription Transcr. at gene 5' and 3' Bivalent Enhancer	Chromatin interactive region	2 gene(s)	inside rSNPs	diseases
6	nsv875292	chr2:153308471-153357383	Enhancers Weak transcription Flanking Active TSS Active TSS Transcr. at gene 5' and 3' Genic enhancers Strong transcription ZNF genes & repeats Bivalent Enhancer	Chromatin interactive region	2 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:51 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:153301000-153314200	Weak transcription	Placenta	Placenta
2	chr2:153301800-153321000	Weak transcription	Right Atrium	heart
3	chr2:153302400-153321600	Weak transcription	Left Ventricle	heart
4	chr2:153302800-153314800	Weak transcription	Aorta	Aorta
5	chr2:153303400-153322600	Weak transcription	NHLF	lung
6	chr2:153304400-153321800	Weak transcription	Muscle Satellite Cultured Cells	--
7	chr2:153305600-153321800	Weak transcription	Fetal Intestine Small	intestine
8	chr2:153306200-153319800	Weak transcription	Psoas Muscle	Psoas
9	chr2:153306200-153320200	Weak transcription	Duodenum Smooth Muscle	Duodenum
10	chr2:153307600-153313200	Enhancers	HepG2	liver
11	chr2:153309400-153321600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
12	chr2:153309400-153323600	Enhancers	Brain Angular Gyrus	brain
13	chr2:153309600-153313200	Enhancers	Brain Inferior Temporal Lobe	brain
14	chr2:153310400-153312800	Weak transcription	NH-A	brain
15	chr2:153310400-153313200	Enhancers	Brain Hippocampus Middle	brain
16	chr2:153310400-153313400	Enhancers	Brain Cingulate Gyrus	brain
17	chr2:153310400-153314000	Weak transcription	Adipose Nuclei	Adipose
18	chr2:153310400-153317000	Enhancers	Brain Substantia Nigra	brain
19	chr2:153310400-153318400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
20	chr2:153310600-153313000	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
21	chr2:153311400-153312800	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
22	chr2:153311400-153313800	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
23	chr2:153311600-153318600	Weak transcription	Skeletal Muscle Female	skeletal muscle
24	chr2:153311800-153312800	Weak transcription	H1 Cell Line	embryonic stem cell
25	chr2:153311800-153312800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
26	chr2:153311800-153312800	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
27	chr2:153311800-153321600	Weak transcription	Lung	lung
28	chr2:153312000-153313200	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
29	chr2:153312000-153315600	Weak transcription	HUES48 Cell Line	embryonic stem cell
30	chr2:153312000-153315600	Weak transcription	iPS-20b Cell Line	embryonic stem cell
31	chr2:153312000-153317000	Weak transcription	Ovary	ovary
32	chr2:153312000-153318800	Weak transcription	Cortex derived primary cultured neurospheres	brain
33	chr2:153312000-153320400	Weak transcription	Fetal Brain Male	brain
34	chr2:153312000-153321400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
35	chr2:153312200-153313200	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
36	chr2:153312400-153312800	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
37	chr2:153312400-153312800	Weak transcription	iPS-15b Cell Line	embryonic stem cell
38	chr2:153312400-153313000	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
39	chr2:153312400-153313000	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
40	chr2:153312400-153313000	Enhancers	HMEC	breast
41	chr2:153312400-153313800	Enhancers	NHEK	skin
42	chr2:153312600-153312800	Enhancers	iPS-18 Cell Line	embryonic stem cell
43	chr2:153312600-153313000	Enhancers	Hela-S3	cervix
44	chr2:153312600-153313000	Enhancers	Osteobl	bone
45	chr2:153312600-153313200	Enhancers	ES-WA7 Cell Line	embryonic stem cell
46	chr2:153312600-153313200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
47	chr2:153312600-153313200	Enhancers	HUES6 Cell Line	embryonic stem cell
48	chr2:153312600-153313200	Enhancers	HUES64 Cell Line	embryonic stem cell
49	chr2:153312600-153313200	Enhancers	A549	lung
50	chr2:153312600-153314200	Weak transcription	Brain Anterior Caudate	brain

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