Variant report

Variant	rs1556886
Chromosome Location	chr6:128645188-128645189
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 22 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:17)

rs_ID	r²[population]
rs1339190	0.94[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs1339192	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs1339194	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs1339195	1.00[YRI][hapmap];0.96[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs1738272	0.81[YRI][hapmap];0.96[AFR][1000 genomes]
rs1890544	1.00[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs2326681	1.00[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs4897254	0.92[YRI][hapmap];0.92[AFR][1000 genomes]
rs6914789	1.00[YRI][hapmap];0.98[AFR][1000 genomes]
rs6922127	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73596689	0.83[AFR][1000 genomes]
rs7738641	0.87[YRI][hapmap];0.96[AFR][1000 genomes]
rs7742250	0.81[YRI][hapmap];0.96[AFR][1000 genomes]
rs7745739	1.00[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs7774819	1.00[YRI][hapmap];0.98[AFR][1000 genomes]
rs9388630	1.00[YRI][hapmap];0.94[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs9402034	1.00[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes]

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:43 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:128609000-128646000	Weak transcription	NH-A	brain
2	chr6:128621800-128649000	Weak transcription	HSMMtube	muscle
3	chr6:128626200-128645800	Weak transcription	Duodenum Mucosa	Duodenum
4	chr6:128627800-128649000	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
5	chr6:128631400-128645200	Weak transcription	Muscle Satellite Cultured Cells	--
6	chr6:128631600-128648600	Weak transcription	Fetal Intestine Small	intestine
7	chr6:128631800-128649000	Weak transcription	Aorta	Aorta
8	chr6:128632000-128649000	Weak transcription	Sigmoid Colon	Sigmoid Colon
9	chr6:128632000-128650600	Weak transcription	Psoas Muscle	Psoas
10	chr6:128632000-128650800	Weak transcription	Right Ventricle	heart
11	chr6:128632000-128658000	Weak transcription	Ovary	ovary
12	chr6:128632200-128665200	Weak transcription	Gastric	stomach
13	chr6:128633600-128649000	Weak transcription	Fetal Thymus	thymus
14	chr6:128635600-128672000	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
15	chr6:128635800-128654200	Weak transcription	Liver	Liver
16	chr6:128639000-128660600	Weak transcription	Rectal Mucosa Donor 31	rectum
17	chr6:128639000-128660800	Weak transcription	Small Intestine	intestine
18	chr6:128639400-128648800	Weak transcription	HUVEC	blood vessel
19	chr6:128639800-128659000	Weak transcription	Fetal Stomach	stomach
20	chr6:128640000-128653200	Weak transcription	HUES64 Cell Line	embryonic stem cell
21	chr6:128640000-128660600	Weak transcription	Rectal Mucosa Donor 29	rectum
22	chr6:128640200-128645200	Enhancers	Brain Hippocampus Middle	brain
23	chr6:128640600-128649000	Weak transcription	HUES6 Cell Line	embryonic stem cell
24	chr6:128640600-128649000	Weak transcription	Primary T cells from cord blood	blood
25	chr6:128641200-128645400	Enhancers	Brain Substantia Nigra	brain
26	chr6:128641400-128649000	Weak transcription	Fetal Lung	lung
27	chr6:128641400-128661400	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
28	chr6:128641600-128645400	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
29	chr6:128641800-128657600	Weak transcription	HUES48 Cell Line	embryonic stem cell
30	chr6:128642000-128649000	Weak transcription	Left Ventricle	heart
31	chr6:128642000-128657000	Weak transcription	HepG2	liver
32	chr6:128642200-128645600	Weak transcription	Fetal Heart	heart
33	chr6:128643200-128645600	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
34	chr6:128643400-128648600	Weak transcription	Fetal Intestine Large	intestine
35	chr6:128643400-128649000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
36	chr6:128643400-128649000	Weak transcription	HSMM	muscle
37	chr6:128643400-128659000	Weak transcription	NHEK	skin
38	chr6:128643400-128660600	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
39	chr6:128643600-128653400	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
40	chr6:128643800-128648800	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
41	chr6:128644600-128646000	Enhancers	Brain Inferior Temporal Lobe	brain
42	chr6:128644800-128646000	Weak transcription	Brain Anterior Caudate	brain
43	chr6:128645000-128654800	Weak transcription	Brain Cingulate Gyrus	brain

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