Variant report

Variant	rs12196
Chromosome Location	chr2:74441799-74441800
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 25 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:20)

rs_ID	r²[population]
rs1095968	0.91[AMR][1000 genomes];0.90[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs13426653	0.87[EUR][1000 genomes]
rs1667601	0.84[CEU][hapmap]
rs1723281	0.94[AMR][1000 genomes];0.90[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1723285	0.93[CEU][hapmap];1.00[CHB][hapmap];0.82[JPT][hapmap];0.91[AMR][1000 genomes];0.90[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs3108164	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[AMR][1000 genomes];0.91[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs4853016	0.96[AMR][1000 genomes];0.91[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs6546893	0.82[EUR][1000 genomes]
rs6546894	0.89[EUR][1000 genomes]
rs702462	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7340453	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[AMR][1000 genomes];0.94[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7587117	1.00[CHB][hapmap]
rs8001	0.88[EUR][1000 genomes]
rs828853	0.87[EUR][1000 genomes]
rs828855	0.89[AMR][1000 genomes];0.88[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs828856	0.81[EUR][1000 genomes]
rs828857	0.96[AMR][1000 genomes];0.91[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs828858	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[AMR][1000 genomes];0.91[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs828859	0.86[AMR][1000 genomes];0.89[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs828903	0.88[CEU][hapmap];0.87[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	esv3427010	chr2:74351730-74813541	Enhancers Weak transcription Active TSS Flanking Active TSS Strong transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	140 gene(s)	inside rSNPs	diseases
2	nsv834261	chr2:74391709-74613720	Strong transcription Enhancers Weak transcription Genic enhancers Flanking Active TSS Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	81 gene(s)	inside rSNPs	diseases
3	esv3401140	chr2:74439333-74533696	Strong transcription Weak transcription Bivalent Enhancer Enhancers Flanking Active TSS Active TSS Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	12 gene(s)	inside rSNPs	diseases
4	esv3380034	chr2:74439354-74533666	Weak transcription Strong transcription Flanking Active TSS Enhancers ZNF genes & repeats Genic enhancers Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	12 gene(s)	inside rSNPs	diseases
5	nsv961419	chr2:74441222-74443074	Strong transcription Weak transcription	Chromatin interactive region miRNA target site	1 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:122 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:74427400-74448400	Weak transcription	Brain Anterior Caudate	brain
2	chr2:74427400-74453000	Weak transcription	Stomach Smooth Muscle	stomach
3	chr2:74427400-74453200	Weak transcription	Rectal Smooth Muscle	rectum
4	chr2:74427400-74460200	Weak transcription	Brain Substantia Nigra	brain
5	chr2:74427400-74462000	Weak transcription	Brain Angular Gyrus	brain
6	chr2:74427400-74484400	Weak transcription	Fetal Lung	lung
7	chr2:74427600-74442600	Weak transcription	Cortex derived primary cultured neurospheres	brain
8	chr2:74427800-74494200	Weak transcription	Brain Germinal Matrix	brain
9	chr2:74428000-74448600	Weak transcription	Brain Inferior Temporal Lobe	brain
10	chr2:74428600-74449600	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
11	chr2:74429000-74450600	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
12	chr2:74429000-74453200	Weak transcription	Ovary	ovary
13	chr2:74429200-74452800	Weak transcription	Fetal Heart	heart
14	chr2:74432600-74444600	Strong transcription	H9 Cell Line	embryonic stem cell
15	chr2:74432800-74441800	Strong transcription	Fetal Muscle Leg	muscle
16	chr2:74433600-74441800	Strong transcription	Fetal Stomach	stomach
17	chr2:74433600-74443000	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
18	chr2:74433600-74444200	Strong transcription	ES-I3 Cell Line	embryonic stem cell
19	chr2:74433600-74447200	Strong transcription	iPS-18 Cell Line	embryonic stem cell
20	chr2:74433600-74447400	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
21	chr2:74433600-74447600	Strong transcription	HUES48 Cell Line	embryonic stem cell
22	chr2:74433600-74447600	Strong transcription	iPS-20b Cell Line	embryonic stem cell
23	chr2:74433600-74448400	Weak transcription	Brain Hippocampus Middle	brain
24	chr2:74433800-74447400	Strong transcription	H1 Cell Line	embryonic stem cell
25	chr2:74433800-74447400	Strong transcription	Dnd41	blood
26	chr2:74433800-74447600	Strong transcription	HUES64 Cell Line	embryonic stem cell
27	chr2:74433800-74447600	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
28	chr2:74433800-74448400	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
29	chr2:74433800-74449200	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
30	chr2:74433800-74449200	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
31	chr2:74433800-74449400	Strong transcription	NHEK	skin
32	chr2:74433800-74449600	Strong transcription	HUES6 Cell Line	embryonic stem cell
33	chr2:74433800-74449800	Strong transcription	Breast Myoepithelial Primary Cells	Breast
34	chr2:74433800-74461800	Weak transcription	Brain Cingulate Gyrus	brain
35	chr2:74434000-74444800	Strong transcription	Hela-S3	cervix
36	chr2:74434000-74453000	Weak transcription	Psoas Muscle	Psoas
37	chr2:74434200-74442000	Strong transcription	Foreskin Fibroblast Primary Cells skin01	Skin
38	chr2:74434200-74447600	Strong transcription	HMEC	breast
39	chr2:74434200-74449400	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
40	chr2:74434200-74449800	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
41	chr2:74434400-74447600	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
42	chr2:74434600-74447600	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
43	chr2:74434600-74448800	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
44	chr2:74434800-74446800	Strong transcription	HSMM	muscle
45	chr2:74434800-74447200	Strong transcription	Primary monocytes fromperipheralblood	blood
46	chr2:74434800-74449000	Strong transcription	Primary hematopoietic stem cells short term culture	blood
47	chr2:74434800-74449400	Strong transcription	Monocytes-CD14+_RO01746	blood
48	chr2:74434800-74449600	Strong transcription	A549	lung
49	chr2:74435000-74441800	Strong transcription	Foreskin Fibroblast Primary Cells skin02	Skin
50	chr2:74435000-74441800	Strong transcription	Fetal Adrenal Gland	Adrenal Gland

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