Variant report

Variant	rs12629887
Chromosome Location	chr3:194807856-194807857
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 16 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:9)

rs_ID	r²[population]
rs12631520	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12637385	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.90[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs12638373	1.00[AMR][1000 genomes];0.90[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs12638577	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs12639591	0.89[GIH][hapmap];0.81[JPT][hapmap];0.84[TSI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.90[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs34303305	0.81[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs3959148	0.82[GIH][hapmap]
rs59469498	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs60982146	0.95[AMR][1000 genomes];0.81[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	nsv1007697	chr3:194554814-195009930	Weak transcription Enhancers Flanking Active TSS Strong transcription Active TSS ZNF genes & repeats Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA	28 gene(s)	inside rSNPs	diseases
2	nsv536873	chr3:194554814-195009930	Weak transcription Enhancers Genic enhancers Flanking Active TSS Active TSS Bivalent Enhancer Strong transcription ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	28 gene(s)	inside rSNPs	diseases
3	nsv997779	chr3:194687093-194885936	Enhancers Weak transcription Flanking Active TSS Active TSS Strong transcription Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	14 gene(s)	inside rSNPs	diseases
4	nsv536874	chr3:194687093-194885936	Weak transcription Enhancers Flanking Active TSS Active TSS Strong transcription Bivalent Enhancer ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA	14 gene(s)	inside rSNPs	diseases
5	nsv1009796	chr3:194737333-195124248	Weak transcription Enhancers Flanking Active TSS Bivalent Enhancer Active TSS Genic enhancers ZNF genes & repeats Strong transcription Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA	22 gene(s)	inside rSNPs	diseases
6	esv1813153	chr3:194754532-194851746	Weak transcription Genic enhancers Enhancers ZNF genes & repeats Flanking Active TSS Bivalent Enhancer Strong transcription Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
7	nsv878136	chr3:194779412-194845226	Genic enhancers Weak transcription Enhancers Flanking Active TSS Strong transcription Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:67 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:194779000-194808000	Weak transcription	H9 Cell Line	embryonic stem cell
2	chr3:194781000-194808000	Weak transcription	Colonic Mucosa	Colon
3	chr3:194790400-194808000	Weak transcription	Primary T helper cells fromperipheralblood	blood
4	chr3:194791000-194821800	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
5	chr3:194797200-194808200	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
6	chr3:194801000-194814600	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
7	chr3:194801200-194808200	Weak transcription	Rectal Mucosa Donor 29	rectum
8	chr3:194801200-194814800	Weak transcription	Primary T cells from cord blood	blood
9	chr3:194801200-194814800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
10	chr3:194801600-194808400	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
11	chr3:194802000-194826800	Weak transcription	Brain Cingulate Gyrus	brain
12	chr3:194803000-194814400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
13	chr3:194803200-194808000	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
14	chr3:194803200-194815800	Weak transcription	Stomach Smooth Muscle	stomach
15	chr3:194803600-194808000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
16	chr3:194804000-194818200	Weak transcription	Right Ventricle	heart
17	chr3:194805400-194809200	Enhancers	Fetal Thymus	thymus
18	chr3:194806200-194808000	Weak transcription	Fetal Muscle Leg	muscle
19	chr3:194806600-194808200	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
20	chr3:194806600-194808200	Enhancers	Fetal Adrenal Gland	Adrenal Gland
21	chr3:194806600-194808800	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
22	chr3:194806800-194808000	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
23	chr3:194806800-194808400	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
24	chr3:194806800-194808400	Enhancers	Thymus	Thymus
25	chr3:194806800-194808800	Enhancers	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
26	chr3:194806800-194826400	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
27	chr3:194807000-194808000	Enhancers	HUES6 Cell Line	embryonic stem cell
28	chr3:194807000-194808400	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
29	chr3:194807000-194808400	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
30	chr3:194807000-194808800	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
31	chr3:194807200-194808000	Enhancers	H1 Cell Line	embryonic stem cell
32	chr3:194807200-194808000	Enhancers	HUES48 Cell Line	embryonic stem cell
33	chr3:194807200-194808000	Enhancers	iPS-15b Cell Line	embryonic stem cell
34	chr3:194807200-194808000	Enhancers	iPS-18 Cell Line	embryonic stem cell
35	chr3:194807200-194808000	Enhancers	Breast Myoepithelial Primary Cells	Breast
36	chr3:194807200-194808200	Enhancers	ES-I3 Cell Line	embryonic stem cell
37	chr3:194807200-194808400	Enhancers	Pancreas	Pancrea
38	chr3:194807200-194808600	Enhancers	Fetal Heart	heart
39	chr3:194807400-194808000	Genic enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
40	chr3:194807400-194808000	Enhancers	HUES64 Cell Line	embryonic stem cell
41	chr3:194807400-194808000	Enhancers	iPS-20b Cell Line	embryonic stem cell
42	chr3:194807400-194808200	Enhancers	iPS DF 6.9 Cell Line	embryonic stem cell
43	chr3:194807400-194808600	Enhancers	K562	blood
44	chr3:194807600-194808200	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
45	chr3:194807600-194808200	Enhancers	Stomach Mucosa	stomach
46	chr3:194807600-194808800	Enhancers	Esophagus	oesophagus
47	chr3:194807600-194814400	Weak transcription	Primary hematopoietic stem cells short term culture	blood
48	chr3:194807800-194808000	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
49	chr3:194807800-194808000	Enhancers	Brain Dorsolateral Prefrontal Cortex	brain
50	chr3:194807800-194808000	Enhancers	Duodenum Mucosa	Duodenum

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