Variant report

Variant	rs10497090
Chromosome Location	chr2:152804330-152804331
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	chr2:152803348..152805157-chr2:152810668..152812299,2	K562	blood:
2	chr2:152683277..152685736-chr2:152803172..152805723,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000162980	Chromatin interaction

Extended variants
information (count: 42 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:35)

rs_ID	r²[population]
rs10178110	1.00[JPT][hapmap]
rs10184416	1.00[JPT][hapmap]
rs10200299	0.90[EUR][1000 genomes]
rs10497091	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10930839	1.00[CEU][hapmap];0.90[CHB][hapmap];1.00[JPT][hapmap];0.92[YRI][hapmap];0.90[AFR][1000 genomes];0.89[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs11895837	1.00[CEU][hapmap];0.90[CHB][hapmap];1.00[JPT][hapmap];0.92[YRI][hapmap];0.90[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs12693174	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs13000853	1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[YRI][hapmap];0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs13391908	0.90[EUR][1000 genomes]
rs13394320	0.81[JPT][hapmap]
rs13413766	1.00[JPT][hapmap]
rs13421962	1.00[JPT][hapmap]
rs13423176	0.90[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs13432920	0.90[EUR][1000 genomes]
rs1519714	1.00[CEU][hapmap];1.00[JPT][hapmap];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs1554365	1.00[JPT][hapmap];0.81[ASN][1000 genomes]
rs17270290	1.00[JPT][hapmap]
rs17270346	1.00[JPT][hapmap];0.81[AMR][1000 genomes];0.94[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs28438674	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs34880899	0.81[AMR][1000 genomes];0.94[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs4664070	0.83[CEU][hapmap];1.00[JPT][hapmap];0.93[EUR][1000 genomes]
rs4664073	0.81[JPT][hapmap]
rs4664510	1.00[JPT][hapmap]
rs4664512	1.00[JPT][hapmap]
rs4664515	0.83[EUR][1000 genomes]
rs6725537	0.86[JPT][hapmap];0.81[ASN][1000 genomes]
rs6742375	1.00[JPT][hapmap]
rs6743872	1.00[EUR][1000 genomes]
rs6756645	0.80[CEU][hapmap];1.00[JPT][hapmap]
rs71350311	0.90[EUR][1000 genomes]
rs7571637	0.81[CEU][hapmap]
rs7591461	0.81[JPT][hapmap]
rs867437	0.94[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs908937	0.80[CEU][hapmap];1.00[JPT][hapmap]
rs952338	0.94[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:7 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1005746	chr2:152361972-153059840	Strong transcription Weak transcription Bivalent/Poised TSS Enhancers Active TSS Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	24 gene(s)	inside rSNPs	diseases
2	nsv535984	chr2:152361972-153059840	Active TSS Weak transcription Enhancers Strong transcription Flanking Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	24 gene(s)	inside rSNPs	diseases
3	esv3693431	chr2:152683731-152981827	Enhancers Active TSS Weak transcription Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Strong transcription ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	11 gene(s)	inside rSNPs	diseases
4	nsv875287	chr2:152714680-153110573	Enhancers Strong transcription Weak transcription Active TSS Genic enhancers Bivalent/Poised TSS Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	20 gene(s)	inside rSNPs	diseases
5	nsv875288	chr2:152716628-153183646	Weak transcription Enhancers Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Strong transcription Flanking Active TSS Bivalent Enhancer Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	21 gene(s)	inside rSNPs	diseases
6	nsv875289	chr2:152720030-153183646	Enhancers Weak transcription ZNF genes & repeats Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent/Poised TSS Strong transcription Active TSS Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	21 gene(s)	inside rSNPs	diseases
7	nsv875290	chr2:152803129-152920126	Enhancers Flanking Active TSS Weak transcription Bivalent Enhancer Active TSS Bivalent/Poised TSS ZNF genes & repeats Strong transcription Flanking Bivalent TSS/Enh Genic enhancers	TF binding region CpG island Chromatin interactive region	6 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:66 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:152799600-152804800	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
2	chr2:152799800-152804800	Enhancers	HMEC	breast
3	chr2:152801200-152805000	Enhancers	Placenta	Placenta
4	chr2:152801800-152804600	Enhancers	Fetal Adrenal Gland	Adrenal Gland
5	chr2:152801800-152805000	Enhancers	NHEK	skin
6	chr2:152802000-152809800	Weak transcription	HepG2	liver
7	chr2:152802800-152804400	Enhancers	Fetal Brain Male	brain
8	chr2:152802800-152805000	Enhancers	Fetal Muscle Leg	muscle
9	chr2:152802800-152805000	Enhancers	Fetal Thymus	thymus
10	chr2:152803000-152805400	Enhancers	Brain Substantia Nigra	brain
11	chr2:152803400-152804400	Enhancers	Primary B cells from peripheral blood	blood
12	chr2:152803600-152804400	Enhancers	HUES48 Cell Line	embryonic stem cell
13	chr2:152803600-152804400	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
14	chr2:152803600-152804400	Enhancers	Pancreas	Pancrea
15	chr2:152803600-152804400	Enhancers	Psoas Muscle	Psoas
16	chr2:152803600-152804600	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
17	chr2:152803600-152804600	Enhancers	iPS-15b Cell Line	embryonic stem cell
18	chr2:152803600-152804600	Flanking Active TSS	Adipose Nuclei	Adipose
19	chr2:152803600-152804600	Flanking Active TSS	Brain Anterior Caudate	brain
20	chr2:152803600-152804600	Enhancers	Lung	lung
21	chr2:152803600-152804600	Flanking Active TSS	Skeletal Muscle Male	skeletal muscle
22	chr2:152803600-152804600	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
23	chr2:152803600-152804800	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
24	chr2:152803600-152804800	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
25	chr2:152803600-152804800	Weak transcription	Fetal Brain Female	brain
26	chr2:152803600-152805200	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
27	chr2:152803800-152804400	Flanking Active TSS	H9 Derived Neuron Cultured Cells	ES cell derived
28	chr2:152803800-152804400	Active TSS	Brain Hippocampus Middle	brain
29	chr2:152803800-152804400	Active TSS	Duodenum Mucosa	Duodenum
30	chr2:152803800-152804400	Flanking Active TSS	Fetal Muscle Trunk	muscle
31	chr2:152803800-152804400	Active TSS	Rectal Mucosa Donor 29	rectum
32	chr2:152803800-152804400	Active TSS	Rectal Smooth Muscle	rectum
33	chr2:152803800-152804400	Flanking Active TSS	Right Atrium	heart
34	chr2:152803800-152804600	Flanking Active TSS	Primary monocytes fromperipheralblood	blood
35	chr2:152803800-152804800	Enhancers	Cortex derived primary cultured neurospheres	brain
36	chr2:152803800-152805000	Enhancers	Fetal Lung	lung
37	chr2:152804000-152804400	Flanking Active TSS	ES-I3 Cell Line	embryonic stem cell
38	chr2:152804000-152804400	Flanking Active TSS	H1 Cell Line	embryonic stem cell
39	chr2:152804000-152804400	Enhancers	HUES6 Cell Line	embryonic stem cell
40	chr2:152804000-152804400	Enhancers	HUES64 Cell Line	embryonic stem cell
41	chr2:152804000-152804400	Flanking Active TSS	iPS-18 Cell Line	embryonic stem cell
42	chr2:152804000-152804400	Flanking Active TSS	iPS-20b Cell Line	embryonic stem cell
43	chr2:152804000-152804400	Flanking Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
44	chr2:152804000-152804400	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
45	chr2:152804000-152804400	Active TSS	Breast Myoepithelial Primary Cells	Breast
46	chr2:152804000-152804400	Flanking Active TSS	Primary hematopoietic stem cells short term culture	blood
47	chr2:152804000-152804400	Active TSS	Brain Angular Gyrus	brain
48	chr2:152804000-152804400	Flanking Active TSS	Brain Inferior Temporal Lobe	brain
49	chr2:152804000-152804400	Flanking Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
50	chr2:152804000-152804400	Active TSS	Colon Smooth Muscle	Colon

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