Variant report

Variant	rs1416517
Chromosome Location	chr6:128653599-128653600
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 102 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:97)

rs_ID	r²[population]
rs11964875	1.00[CEU][hapmap];0.91[EUR][1000 genomes]
rs11965122	1.00[CEU][hapmap];0.91[EUR][1000 genomes]
rs11965141	1.00[CEU][hapmap];0.91[EUR][1000 genomes]
rs11966128	1.00[CEU][hapmap];0.91[EUR][1000 genomes]
rs1339189	1.00[CEU][hapmap];0.98[EUR][1000 genomes]
rs1339196	1.00[CEU][hapmap];0.89[EUR][1000 genomes]
rs1538498	0.89[EUR][1000 genomes]
rs1612415	1.00[CEU][hapmap];0.86[AMR][1000 genomes]
rs17055564	1.00[CEU][hapmap];0.91[EUR][1000 genomes]
rs17055574	1.00[CEU][hapmap];0.89[EUR][1000 genomes]
rs17055596	1.00[CEU][hapmap];0.89[EUR][1000 genomes]
rs17055597	1.00[CEU][hapmap];0.91[EUR][1000 genomes]
rs17055601	1.00[CEU][hapmap];0.89[EUR][1000 genomes]
rs17055604	1.00[CEU][hapmap];0.91[EUR][1000 genomes]
rs17055608	1.00[CEU][hapmap];0.91[EUR][1000 genomes]
rs17055611	1.00[CEU][hapmap];0.89[EUR][1000 genomes]
rs17055612	1.00[CEU][hapmap];0.91[EUR][1000 genomes]
rs17055616	1.00[CEU][hapmap];0.91[EUR][1000 genomes]
rs17055617	0.83[CEU][hapmap];0.91[EUR][1000 genomes]
rs17055618	1.00[CEU][hapmap];0.91[EUR][1000 genomes]
rs17055619	1.00[CEU][hapmap];0.91[EUR][1000 genomes]
rs17055628	0.84[EUR][1000 genomes]
rs17055630	0.89[EUR][1000 genomes]
rs17055679	0.89[EUR][1000 genomes]
rs17055689	1.00[CEU][hapmap];0.98[EUR][1000 genomes]
rs17055706	1.00[CEU][hapmap];0.98[EUR][1000 genomes]
rs17055717	1.00[CEU][hapmap];1.00[EUR][1000 genomes]
rs17055719	1.00[CEU][hapmap];0.89[EUR][1000 genomes]
rs17055727	1.00[CEU][hapmap];1.00[EUR][1000 genomes]
rs17055733	1.00[CEU][hapmap];0.98[EUR][1000 genomes]
rs17343887	1.00[CEU][hapmap];0.89[EUR][1000 genomes]
rs17353545	1.00[CEU][hapmap];1.00[EUR][1000 genomes]
rs17430131	1.00[CEU][hapmap]
rs17430452	1.00[CEU][hapmap];0.89[EUR][1000 genomes]
rs17456343	1.00[CEU][hapmap];0.89[EUR][1000 genomes]
rs17456385	1.00[CEU][hapmap];0.89[EUR][1000 genomes]
rs17456601	1.00[CEU][hapmap];0.89[EUR][1000 genomes]
rs1768360	1.00[CEU][hapmap]
rs2027311	1.00[CEU][hapmap];1.00[YRI][hapmap];0.91[AFR][1000 genomes];0.90[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs4267969	0.89[EUR][1000 genomes]
rs4466261	1.00[CEU][hapmap];0.91[EUR][1000 genomes]
rs55969073	0.89[EUR][1000 genomes]
rs56095177	0.83[EUR][1000 genomes]
rs56241890	0.89[EUR][1000 genomes]
rs57318936	0.89[EUR][1000 genomes]
rs59132771	0.89[EUR][1000 genomes]
rs6420738	0.98[EUR][1000 genomes]
rs6913718	0.91[EUR][1000 genomes]
rs6931769	1.00[CEU][hapmap];0.91[EUR][1000 genomes]
rs6933821	1.00[CEU][hapmap]
rs72967026	0.89[EUR][1000 genomes]
rs72967039	0.89[EUR][1000 genomes]
rs72967046	0.89[EUR][1000 genomes]
rs72967053	0.91[EUR][1000 genomes]
rs72967056	0.91[EUR][1000 genomes]
rs72967058	0.89[EUR][1000 genomes]
rs72967074	0.89[EUR][1000 genomes]
rs72967078	0.91[EUR][1000 genomes]
rs72967081	0.91[EUR][1000 genomes]
rs72967087	0.91[EUR][1000 genomes]
rs72967090	0.91[EUR][1000 genomes]
rs72969051	0.98[EUR][1000 genomes]
rs72969054	0.89[EUR][1000 genomes]
rs72969059	0.89[EUR][1000 genomes]
rs72969061	0.89[EUR][1000 genomes]
rs72969063	0.89[EUR][1000 genomes]
rs72969067	0.89[EUR][1000 genomes]
rs72969070	0.89[EUR][1000 genomes]
rs72969074	0.89[EUR][1000 genomes]
rs72969075	0.91[EUR][1000 genomes]
rs72969078	0.91[EUR][1000 genomes]
rs72969081	0.93[EUR][1000 genomes]
rs72969088	0.98[EUR][1000 genomes]
rs72969090	0.98[EUR][1000 genomes]
rs72969093	0.98[EUR][1000 genomes]
rs72969097	0.89[EUR][1000 genomes]
rs72969098	0.91[EUR][1000 genomes]
rs72971103	0.89[EUR][1000 genomes]
rs72971104	0.98[EUR][1000 genomes]
rs72972078	0.98[EUR][1000 genomes]
rs72972082	0.89[EUR][1000 genomes]
rs72972084	0.89[EUR][1000 genomes]
rs72972086	0.89[EUR][1000 genomes]
rs72972090	1.00[EUR][1000 genomes]
rs72972091	0.98[EUR][1000 genomes]
rs72974006	0.82[EUR][1000 genomes]
rs7748155	0.93[YRI][hapmap]
rs7764930	0.93[YRI][hapmap]
rs7771630	1.00[CEU][hapmap];0.91[EUR][1000 genomes]
rs7773248	1.00[CEU][hapmap];1.00[EUR][1000 genomes]
rs7776405	0.89[EUR][1000 genomes]
rs9321114	1.00[CEU][hapmap];0.91[EUR][1000 genomes]
rs9372888	1.00[YRI][hapmap];0.91[AFR][1000 genomes]
rs9375562	0.85[CEU][hapmap]
rs9402035	0.92[CEU][hapmap];0.80[YRI][hapmap];0.81[AFR][1000 genomes];0.83[EUR][1000 genomes]
rs9491938	0.91[AFR][1000 genomes]
rs9491939	0.85[CEU][hapmap]

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	nsv1033443	chr6:128306654-128899203	Enhancers Weak transcription Flanking Active TSS Active TSS Strong transcription Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	8 gene(s)	inside rSNPs	diseases
2	nsv538440	chr6:128306654-128899203	Weak transcription Enhancers Strong transcription Flanking Active TSS Active TSS Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	8 gene(s)	inside rSNPs	diseases
3	nsv886649	chr6:128399657-128808054	Weak transcription Enhancers Active TSS Flanking Active TSS Genic enhancers Strong transcription ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	4 gene(s)	inside rSNPs	diseases
4	nsv1020071	chr6:128579774-129048919	Weak transcription Enhancers Flanking Active TSS Active TSS Strong transcription ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	15 gene(s)	inside rSNPs	diseases
5	nsv538441	chr6:128579774-129048919	Flanking Active TSS Weak transcription Strong transcription Enhancers Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	15 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:35 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:128632000-128658000	Weak transcription	Ovary	ovary
2	chr6:128632200-128665200	Weak transcription	Gastric	stomach
3	chr6:128635600-128672000	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
4	chr6:128635800-128654200	Weak transcription	Liver	Liver
5	chr6:128639000-128660600	Weak transcription	Rectal Mucosa Donor 31	rectum
6	chr6:128639000-128660800	Weak transcription	Small Intestine	intestine
7	chr6:128639800-128659000	Weak transcription	Fetal Stomach	stomach
8	chr6:128640000-128660600	Weak transcription	Rectal Mucosa Donor 29	rectum
9	chr6:128641400-128661400	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
10	chr6:128641800-128657600	Weak transcription	HUES48 Cell Line	embryonic stem cell
11	chr6:128642000-128657000	Weak transcription	HepG2	liver
12	chr6:128643400-128659000	Weak transcription	NHEK	skin
13	chr6:128643400-128660600	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
14	chr6:128645000-128654800	Weak transcription	Brain Cingulate Gyrus	brain
15	chr6:128646200-128657000	Weak transcription	Brain Anterior Caudate	brain
16	chr6:128648800-128654400	Weak transcription	A549	lung
17	chr6:128649200-128661400	Weak transcription	Pancreas	Pancrea
18	chr6:128649200-128665600	Weak transcription	Left Ventricle	heart
19	chr6:128649400-128654600	Weak transcription	Fetal Thymus	thymus
20	chr6:128649400-128658600	Weak transcription	Fetal Lung	lung
21	chr6:128649400-128659800	Weak transcription	Fetal Intestine Small	intestine
22	chr6:128649400-128660800	Weak transcription	HSMMtube	muscle
23	chr6:128649400-128671800	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
24	chr6:128649400-128678600	Weak transcription	HSMM	muscle
25	chr6:128649600-128654800	Weak transcription	Pancreatic Islets	Pancreatic Islet
26	chr6:128649600-128661600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
27	chr6:128651000-128656400	Weak transcription	Rectal Smooth Muscle	rectum
28	chr6:128651000-128660400	Weak transcription	Stomach Smooth Muscle	stomach
29	chr6:128651200-128657800	Weak transcription	HUES6 Cell Line	embryonic stem cell
30	chr6:128651800-128656400	Weak transcription	Brain Substantia Nigra	brain
31	chr6:128652000-128653800	Weak transcription	Duodenum Smooth Muscle	Duodenum
32	chr6:128652400-128654400	Weak transcription	Colon Smooth Muscle	Colon
33	chr6:128653200-128653600	Enhancers	HUES64 Cell Line	embryonic stem cell
34	chr6:128653400-128654400	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
35	chr6:128653400-128657600	Weak transcription	iPS-18 Cell Line	embryonic stem cell

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