Variant report

Variant	rs7629357
Chromosome Location	chr3:105570818-105570819
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 67 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:63)

rs_ID	r²[population]
rs1021858	0.90[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs1021859	0.90[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs1039544	0.90[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs10511246	0.93[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1075739	0.90[CHB][hapmap];0.91[JPT][hapmap];0.81[ASN][1000 genomes]
rs11921710	0.91[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11924742	1.00[CEU][hapmap];0.83[CHB][hapmap];0.90[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs12633654	0.84[ASN][1000 genomes]
rs12633854	0.90[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs12635232	0.86[CHB][hapmap];0.86[JPT][hapmap];0.81[ASN][1000 genomes]
rs12637560	0.91[CHB][hapmap];0.87[JPT][hapmap];0.89[ASN][1000 genomes]
rs12637809	0.91[CHB][hapmap];0.87[JPT][hapmap];0.82[ASN][1000 genomes]
rs12639271	0.81[ASN][1000 genomes]
rs1503921	0.90[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs1561922	0.86[JPT][hapmap];0.85[ASN][1000 genomes]
rs16851523	0.83[CHB][hapmap];0.86[JPT][hapmap];0.81[ASN][1000 genomes]
rs16851539	0.91[CHB][hapmap];0.86[JPT][hapmap];0.81[ASN][1000 genomes]
rs16851563	0.91[CHB][hapmap];0.87[JPT][hapmap];0.83[ASN][1000 genomes]
rs16851570	0.90[CHB][hapmap];0.86[JPT][hapmap];0.83[ASN][1000 genomes]
rs16851587	0.87[CHB][hapmap];0.83[JPT][hapmap];0.81[ASN][1000 genomes]
rs16851630	0.86[CHB][hapmap];0.86[JPT][hapmap];0.89[ASN][1000 genomes]
rs1867192	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1867195	0.81[CEU][hapmap]
rs1910499	1.00[CEU][hapmap];0.82[CHB][hapmap];0.90[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs1947000	0.90[CHB][hapmap];0.86[JPT][hapmap];0.83[ASN][1000 genomes]
rs2089091	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2197208	0.86[CHB][hapmap];0.86[JPT][hapmap];0.82[ASN][1000 genomes]
rs2197209	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3996189	0.88[CEU][hapmap]
rs4447799	0.86[CEU][hapmap]
rs4894840	0.90[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs4894957	0.88[CEU][hapmap]
rs57520912	1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs58340800	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs59534462	0.89[ASN][1000 genomes]
rs59611997	0.84[ASN][1000 genomes]
rs60619938	0.82[ASN][1000 genomes]
rs6437620	0.97[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6437621	1.00[CEU][hapmap];0.95[YRI][hapmap];0.89[AFR][1000 genomes];0.97[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6437624	0.87[CEU][hapmap]
rs6437626	0.88[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs6767627	1.00[CEU][hapmap];0.82[CHB][hapmap];1.00[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs6788366	0.88[CEU][hapmap]
rs6804152	0.94[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs6807382	0.88[CEU][hapmap]
rs73854891	0.85[ASN][1000 genomes]
rs73854894	0.89[ASN][1000 genomes]
rs73857222	0.88[ASN][1000 genomes]
rs7619449	0.97[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs7624400	0.90[CHB][hapmap];0.86[JPT][hapmap];0.82[ASN][1000 genomes]
rs7634844	0.90[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs7641825	0.93[CEU][hapmap];0.82[CHB][hapmap];0.81[AFR][1000 genomes];0.85[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs7648842	0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7649466	0.93[CEU][hapmap];0.81[YRI][hapmap];0.81[AFR][1000 genomes];0.87[EUR][1000 genomes]
rs7651784	0.87[CEU][hapmap]
rs9631436	0.95[AFR][1000 genomes];0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9657904	1.00[CEU][hapmap];0.82[CHB][hapmap];0.94[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs9789988	0.82[ASN][1000 genomes]
rs9826886	0.89[AFR][1000 genomes];0.97[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9841500	0.87[CEU][hapmap]
rs9846534	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.90[AFR][1000 genomes];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9869648	1.00[CEU][hapmap];0.90[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs9874600	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[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	esv2755185	chr3:105378310-105597310	Strong transcription Weak transcription Enhancers Genic enhancers ZNF genes & repeats Flanking Active TSS Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
2	nsv1008564	chr3:105554580-105643435	Enhancers Weak transcription Active TSS Strong transcription Transcr. at gene 5' and 3' Flanking Active TSS Genic enhancers Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
3	nsv1008876	chr3:105554580-105645373	Active TSS Strong transcription Weak transcription Flanking Active TSS Enhancers Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
4	nsv877312	chr3:105560638-105916506	Enhancers ZNF genes & repeats Flanking Active TSS Strong transcription Weak transcription Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:121 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:105543400-105581200	Weak transcription	Gastric	stomach
2	chr3:105543800-105571000	Weak transcription	Lung	lung
3	chr3:105544200-105584600	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
4	chr3:105546600-105586200	Weak transcription	Esophagus	oesophagus
5	chr3:105549000-105571800	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
6	chr3:105555800-105576600	Weak transcription	Psoas Muscle	Psoas
7	chr3:105556200-105571600	Weak transcription	Monocytes-CD14+_RO01746	blood
8	chr3:105556200-105579000	Weak transcription	Stomach Mucosa	stomach
9	chr3:105557800-105579200	Weak transcription	H1 Cell Line	embryonic stem cell
10	chr3:105557800-105586200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
11	chr3:105558200-105571800	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
12	chr3:105558600-105586600	Weak transcription	Placenta Amnion	Placenta Amnion
13	chr3:105561600-105586200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
14	chr3:105562000-105586000	Weak transcription	K562	blood
15	chr3:105563000-105584600	Weak transcription	Stomach Smooth Muscle	stomach
16	chr3:105563000-105586800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
17	chr3:105563200-105571600	Weak transcription	Fetal Intestine Small	intestine
18	chr3:105563200-105572000	Weak transcription	HUVEC	blood vessel
19	chr3:105563200-105572200	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
20	chr3:105563400-105583000	Weak transcription	Spleen	Spleen
21	chr3:105563800-105584400	Weak transcription	Brain Angular Gyrus	brain
22	chr3:105564800-105585000	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
23	chr3:105565600-105572000	Weak transcription	HMEC	breast
24	chr3:105565600-105584800	Weak transcription	NHEK	skin
25	chr3:105566000-105571800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
26	chr3:105566000-105574800	Strong transcription	Placenta	Placenta
27	chr3:105566200-105584800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
28	chr3:105566200-105585000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
29	chr3:105566400-105574000	Genic enhancers	Primary T helper cells PMA-I stimulated	--
30	chr3:105566600-105572000	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
31	chr3:105566600-105581200	Weak transcription	Aorta	Aorta
32	chr3:105566600-105584600	Weak transcription	Fetal Stomach	stomach
33	chr3:105567000-105571800	Weak transcription	Colon Smooth Muscle	Colon
34	chr3:105567000-105576600	Weak transcription	Right Ventricle	heart
35	chr3:105567000-105578800	Weak transcription	Fetal Brain Male	brain
36	chr3:105567000-105583000	Weak transcription	Brain Substantia Nigra	brain
37	chr3:105567000-105584200	Weak transcription	Brain Inferior Temporal Lobe	brain
38	chr3:105567200-105571800	Weak transcription	Skeletal Muscle Male	skeletal muscle
39	chr3:105567200-105576600	Weak transcription	Ovary	ovary
40	chr3:105567200-105583200	Weak transcription	Brain Hippocampus Middle	brain
41	chr3:105567200-105584000	Weak transcription	Brain Anterior Caudate	brain
42	chr3:105567200-105584600	Weak transcription	Rectal Smooth Muscle	rectum
43	chr3:105567400-105574000	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
44	chr3:105567600-105571800	Weak transcription	Fetal Heart	heart
45	chr3:105567600-105573000	Strong transcription	Primary T cells fromperipheralblood	blood
46	chr3:105567600-105574200	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
47	chr3:105567600-105574600	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
48	chr3:105567800-105572600	Strong transcription	HUES64 Cell Line	embryonic stem cell
49	chr3:105567800-105575400	Strong transcription	NH-A	brain
50	chr3:105568000-105573000	Strong transcription	HSMM	muscle

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