Variant report

Variant	rs9388629
Chromosome Location	chr6:128666749-128666750
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr6:128666022..128668619-chr6:128842327..128844085,2	MCF-7	breast:

Extended variants
information (count: 33 )
Associated
traits (count: 0)

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

rs_ID	r²[population]
rs12055766	0.83[CHB][hapmap];0.90[JPT][hapmap];0.88[YRI][hapmap]
rs12175825	1.00[MEX][hapmap]
rs1339191	1.00[CHB][hapmap];0.94[JPT][hapmap];0.95[ASN][1000 genomes]
rs1339193	1.00[JPT][hapmap]
rs1339197	0.89[CHB][hapmap];0.80[JPT][hapmap]
rs17055441	1.00[MEX][hapmap]
rs3822945	0.83[CHB][hapmap]
rs4243494	1.00[MEX][hapmap]
rs4296904	1.00[JPT][hapmap];0.82[MKK][hapmap];1.00[TSI][hapmap];0.87[YRI][hapmap];0.91[AMR][1000 genomes]
rs57546390	0.85[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6934873	0.83[CHB][hapmap];0.94[JPT][hapmap]
rs7744436	1.00[CHB][hapmap];0.94[JPT][hapmap];1.00[YRI][hapmap];0.85[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs9321115	0.94[ASN][1000 genomes]
rs9372887	1.00[MEX][hapmap]
rs9372889	0.93[JPT][hapmap];0.87[YRI][hapmap];0.91[AMR][1000 genomes];0.81[ASN][1000 genomes]
rs9375552	1.00[MEX][hapmap]
rs9375554	1.00[ASW][hapmap];1.00[MEX][hapmap]
rs9385452	1.00[MEX][hapmap]
rs9385457	0.83[CHB][hapmap];0.82[CHD][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.95[MKK][hapmap];1.00[TSI][hapmap];0.87[YRI][hapmap];0.91[AMR][1000 genomes]
rs9385461	1.00[MEX][hapmap]
rs9388623	1.00[MEX][hapmap]
rs9398865	1.00[MEX][hapmap]
rs9398867	1.00[MEX][hapmap]
rs9402025	1.00[MEX][hapmap]
rs9402033	0.82[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs9491939	1.00[CHB][hapmap];0.90[CHD][hapmap];1.00[JPT][hapmap];0.94[ASN][1000 genomes]
rs953549	0.82[CHB][hapmap];1.00[JPT][hapmap]
rs964179	0.83[CHB][hapmap];1.00[JPT][hapmap];0.87[YRI][hapmap];0.84[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:32 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:128635600-128672000	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
2	chr6:128649400-128671800	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
3	chr6:128649400-128678600	Weak transcription	HSMM	muscle
4	chr6:128657800-128667800	Weak transcription	Fetal Kidney	kidney
5	chr6:128659800-128671400	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
6	chr6:128660000-128667400	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
7	chr6:128660000-128667800	Weak transcription	Ovary	ovary
8	chr6:128661200-128667800	Weak transcription	Brain Anterior Caudate	brain
9	chr6:128661400-128671800	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
10	chr6:128661400-128677200	Weak transcription	Brain Cingulate Gyrus	brain
11	chr6:128661600-128667800	Weak transcription	Fetal Intestine Large	intestine
12	chr6:128661600-128679400	Weak transcription	Osteobl	bone
13	chr6:128661800-128671200	Weak transcription	Duodenum Smooth Muscle	Duodenum
14	chr6:128663000-128670000	Weak transcription	Liver	Liver
15	chr6:128664800-128668800	Enhancers	Fetal Heart	heart
16	chr6:128665200-128667200	Enhancers	Brain Substantia Nigra	brain
17	chr6:128665200-128671400	Weak transcription	Rectal Smooth Muscle	rectum
18	chr6:128665400-128669800	Weak transcription	Stomach Mucosa	stomach
19	chr6:128665400-128670800	Weak transcription	Fetal Intestine Small	intestine
20	chr6:128665800-128667800	Weak transcription	Colon Smooth Muscle	Colon
21	chr6:128665800-128668600	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
22	chr6:128665800-128670200	Weak transcription	HepG2	liver
23	chr6:128666000-128678600	Weak transcription	Left Ventricle	heart
24	chr6:128666000-128679400	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
25	chr6:128666200-128667200	Enhancers	Brain Inferior Temporal Lobe	brain
26	chr6:128666200-128668600	Enhancers	Fetal Lung	lung
27	chr6:128666400-128667000	Enhancers	Stomach Smooth Muscle	stomach
28	chr6:128666400-128668400	Weak transcription	Small Intestine	intestine
29	chr6:128666600-128666800	Enhancers	Fetal Stomach	stomach
30	chr6:128666600-128667000	Enhancers	Brain Hippocampus Middle	brain
31	chr6:128666600-128667200	Enhancers	Brain Angular Gyrus	brain
32	chr6:128666600-128667800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain

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