Variant report

Variant	rs10954233
Chromosome Location	chr7:129086128-129086129
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 32 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:28)

rs_ID	r²[population]
rs10500117	0.90[AFR][1000 genomes];0.86[AMR][1000 genomes];0.94[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs10954234	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12155142	0.86[EUR][1000 genomes]
rs12667232	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12671604	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2305326	0.95[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs34000750	0.85[AFR][1000 genomes];0.86[AMR][1000 genomes];0.93[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs34794308	0.92[AFR][1000 genomes];0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs34916100	0.85[AFR][1000 genomes];0.92[EUR][1000 genomes]
rs35131522	0.89[AMR][1000 genomes];0.95[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs35277123	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35544616	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4728165	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4731578	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4731579	0.95[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4731580	0.90[AFR][1000 genomes];0.86[AMR][1000 genomes];0.93[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs4731581	0.90[AFR][1000 genomes];0.84[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs4731582	0.81[AFR][1000 genomes];0.83[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs4731583	0.90[AFR][1000 genomes];0.83[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs62489110	0.95[AFR][1000 genomes];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs644723	0.86[JPT][hapmap]
rs691124	0.86[JPT][hapmap]
rs691158	0.86[JPT][hapmap]
rs691435	0.86[JPT][hapmap]
rs692697	0.86[JPT][hapmap]
rs6943021	0.95[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs753336	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs966481	0.96[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv428508	chr7:128946738-129114691	Enhancers Active TSS Weak transcription Strong transcription Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	11 gene(s)	inside rSNPs	diseases
2	nsv1015550	chr7:128992460-129111060	Enhancers Weak transcription Flanking Active TSS Strong transcription Bivalent/Poised TSS Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	9 gene(s)	inside rSNPs	diseases
3	nsv539122	chr7:128992460-129111060	Strong transcription Weak transcription ZNF genes & repeats Enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Active TSS Bivalent Enhancer Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	9 gene(s)	inside rSNPs	diseases
4	nsv831128	chr7:129063040-129240800	Weak transcription Active TSS Strong transcription Enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Genic enhancers Flanking Active TSS Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	14 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:64 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:129075200-129088200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
2	chr7:129075200-129096000	Weak transcription	Brain Inferior Temporal Lobe	brain
3	chr7:129075200-129100600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
4	chr7:129075200-129108400	Weak transcription	Gastric	stomach
5	chr7:129075400-129093200	Weak transcription	Brain Angular Gyrus	brain
6	chr7:129075400-129102800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
7	chr7:129075400-129105800	Weak transcription	Ovary	ovary
8	chr7:129075600-129087600	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
9	chr7:129075800-129087400	Weak transcription	Cortex derived primary cultured neurospheres	brain
10	chr7:129075800-129091800	Weak transcription	HepG2	liver
11	chr7:129076000-129088800	Weak transcription	Fetal Lung	lung
12	chr7:129076000-129095000	Weak transcription	Dnd41	blood
13	chr7:129076000-129110000	Weak transcription	Brain Cingulate Gyrus	brain
14	chr7:129076400-129088000	Weak transcription	HUES64 Cell Line	embryonic stem cell
15	chr7:129077400-129109400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
16	chr7:129078600-129087800	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
17	chr7:129078800-129086800	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
18	chr7:129079200-129090200	Weak transcription	HSMM	muscle
19	chr7:129079200-129095200	Weak transcription	NHLF	lung
20	chr7:129079600-129107200	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
21	chr7:129079800-129106400	Weak transcription	NHDF-Ad	bronchial
22	chr7:129080000-129087200	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
23	chr7:129080000-129091800	Weak transcription	Osteobl	bone
24	chr7:129080000-129094600	Weak transcription	Hela-S3	cervix
25	chr7:129080000-129104800	Weak transcription	A549	lung
26	chr7:129080000-129128000	Weak transcription	HUVEC	blood vessel
27	chr7:129080400-129094000	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
28	chr7:129080600-129101800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
29	chr7:129082000-129091400	Weak transcription	iPS-15b Cell Line	embryonic stem cell
30	chr7:129082600-129087600	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
31	chr7:129082600-129108400	Weak transcription	Thymus	Thymus
32	chr7:129083400-129086200	Strong transcription	Muscle Satellite Cultured Cells	--
33	chr7:129083400-129086400	Strong transcription	HUES48 Cell Line	embryonic stem cell
34	chr7:129083400-129088400	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
35	chr7:129083400-129092400	Weak transcription	HMEC	breast
36	chr7:129083600-129086800	Strong transcription	HUES6 Cell Line	embryonic stem cell
37	chr7:129083600-129087200	Weak transcription	Psoas Muscle	Psoas
38	chr7:129083800-129086200	Weak transcription	Stomach Smooth Muscle	stomach
39	chr7:129083800-129086600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
40	chr7:129083800-129087000	Strong transcription	iPS-20b Cell Line	embryonic stem cell
41	chr7:129083800-129091400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
42	chr7:129083800-129112800	Strong transcription	K562	blood
43	chr7:129084000-129087400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
44	chr7:129084200-129088000	Strong transcription	Brain Anterior Caudate	brain
45	chr7:129084400-129086800	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
46	chr7:129084400-129092000	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
47	chr7:129084400-129092200	Weak transcription	Left Ventricle	heart
48	chr7:129084400-129093000	Weak transcription	Right Ventricle	heart
49	chr7:129084800-129086400	Strong transcription	H1 Cell Line	embryonic stem cell
50	chr7:129085400-129086200	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived

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