Variant report

Variant	rs10935839
Chromosome Location	chr3:151070692-151070693
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 36 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:33)

rs_ID	r²[population]
rs10513391	0.82[CEU][hapmap]
rs10935831	0.83[CEU][hapmap]
rs10935832	0.87[CEU][hapmap]
rs10935833	0.83[CEU][hapmap]
rs10935835	0.87[CEU][hapmap]
rs11925037	0.87[CEU][hapmap]
rs11926145	0.87[CEU][hapmap]
rs12107539	0.87[CEU][hapmap]
rs12497019	0.87[CEU][hapmap]
rs12497330	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12637988	0.87[CEU][hapmap]
rs13095610	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs16863287	0.82[CEU][hapmap]
rs2307020	1.00[CEU][hapmap];0.91[CHB][hapmap];1.00[JPT][hapmap];0.97[YRI][hapmap];0.82[AFR][1000 genomes];0.86[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2904430	0.87[YRI][hapmap]
rs3732759	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs3732760	0.83[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs3773621	0.87[CEU][hapmap]
rs4680307	0.87[CEU][hapmap];0.87[YRI][hapmap]
rs4680356	0.87[CEU][hapmap]
rs6440737	0.83[AFR][1000 genomes];0.87[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6440738	1.00[CEU][hapmap];0.91[CHB][hapmap];1.00[JPT][hapmap];0.87[YRI][hapmap];0.84[AFR][1000 genomes];0.87[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6767192	1.00[CEU][hapmap];0.91[CHB][hapmap];1.00[JPT][hapmap];0.87[YRI][hapmap];0.84[AFR][1000 genomes];0.87[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6784934	0.87[CEU][hapmap]
rs6785930	0.87[CEU][hapmap]
rs6790448	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[YRI][hapmap];0.92[AFR][1000 genomes];0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6793898	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.91[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6801273	1.00[CEU][hapmap];0.90[CHB][hapmap];1.00[JPT][hapmap];0.85[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6804769	1.00[CEU][hapmap];0.90[CHB][hapmap];1.00[JPT][hapmap];0.86[YRI][hapmap];0.84[AFR][1000 genomes];0.87[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7428575	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7641645	0.83[AFR][1000 genomes];0.87[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7644001	1.00[CEU][hapmap];0.90[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.83[AFR][1000 genomes];0.86[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7648875	0.87[CEU][hapmap]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv460894	chr3:150770614-151095093	Enhancers Flanking Bivalent TSS/Enh Weak transcription Strong transcription Genic enhancers Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Active TSS Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases
2	nsv592045	chr3:150770614-151095093	Flanking Active TSS Weak transcription Enhancers Bivalent Enhancer Bivalent/Poised TSS Active TSS Flanking Bivalent TSS/Enh Strong transcription Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases
3	nsv829757	chr3:151044880-151226442	Enhancers Genic enhancers Weak transcription Flanking Bivalent TSS/Enh Active TSS Flanking Active TSS Strong transcription Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	8 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:34 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:151063800-151099800	Weak transcription	Fetal Intestine Small	intestine
2	chr3:151064400-151089200	Weak transcription	NHLF	lung
3	chr3:151064600-151075200	Weak transcription	Adipose Nuclei	Adipose
4	chr3:151064600-151112400	Weak transcription	Breast Myoepithelial Primary Cells	Breast
5	chr3:151065400-151079600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
6	chr3:151065600-151109400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
7	chr3:151065600-151115200	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
8	chr3:151065800-151082200	Weak transcription	Fetal Thymus	thymus
9	chr3:151066000-151074800	Weak transcription	Brain Anterior Caudate	brain
10	chr3:151066400-151075000	Weak transcription	Brain Hippocampus Middle	brain
11	chr3:151066800-151074600	Weak transcription	Cortex derived primary cultured neurospheres	brain
12	chr3:151067800-151083600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
13	chr3:151068000-151075000	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
14	chr3:151068000-151078800	Weak transcription	iPS-18 Cell Line	embryonic stem cell
15	chr3:151068000-151079600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
16	chr3:151068000-151082600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
17	chr3:151068200-151073600	Weak transcription	H1 Cell Line	embryonic stem cell
18	chr3:151068400-151075000	Weak transcription	Aorta	Aorta
19	chr3:151068600-151073800	Weak transcription	iPS-20b Cell Line	embryonic stem cell
20	chr3:151069200-151073400	Weak transcription	HUES64 Cell Line	embryonic stem cell
21	chr3:151069200-151078800	Weak transcription	HUES48 Cell Line	embryonic stem cell
22	chr3:151069200-151078800	Weak transcription	HUES6 Cell Line	embryonic stem cell
23	chr3:151069400-151129800	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
24	chr3:151069800-151073600	Weak transcription	H9 Cell Line	embryonic stem cell
25	chr3:151070000-151071000	Enhancers	Primary B cells from cord blood	blood
26	chr3:151070000-151071400	Enhancers	Primary neutrophils fromperipheralblood	blood
27	chr3:151070200-151071400	Enhancers	Primary monocytes fromperipheralblood	blood
28	chr3:151070400-151070800	Enhancers	Primary hematopoietic stem cells short term culture	blood
29	chr3:151070400-151071200	Enhancers	GM12878-XiMat	blood
30	chr3:151070400-151082800	Weak transcription	Primary hematopoietic stem cells	blood
31	chr3:151070600-151071000	Enhancers	Monocytes-CD14+_RO01746	blood
32	chr3:151070600-151072400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
33	chr3:151070600-151072600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
34	chr3:151070600-151075000	Weak transcription	Primary B cells from peripheral blood	blood

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