Variant report

Variant	rs1738291
Chromosome Location	chr6:128598519-128598520
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	chr6:128598470..128600441-chr6:128838939..128840470,2	MCF-7	breast:

Extended variants
information (count: 50 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:45)

rs_ID	r²[population]
rs11968696	0.85[AMR][1000 genomes]
rs1339188	1.00[MEX][hapmap]
rs1738276	0.87[AMR][1000 genomes]
rs1738277	0.87[AMR][1000 genomes]
rs1738278	1.00[MEX][hapmap];0.87[AMR][1000 genomes]
rs1738279	0.87[AMR][1000 genomes]
rs1738285	0.87[AMR][1000 genomes]
rs1738286	0.96[LWK][hapmap];1.00[MEX][hapmap];1.00[YRI][hapmap];1.00[AMR][1000 genomes]
rs1738289	0.85[AMR][1000 genomes]
rs1768347	0.81[YRI][hapmap]
rs1768348	0.87[YRI][hapmap];1.00[AMR][1000 genomes]
rs1768349	1.00[YRI][hapmap];0.84[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs1768350	0.87[YRI][hapmap];1.00[AMR][1000 genomes]
rs1768351	0.91[YRI][hapmap];0.81[AFR][1000 genomes];0.85[AMR][1000 genomes]
rs1768352	0.92[LWK][hapmap];1.00[MEX][hapmap];0.87[AMR][1000 genomes]
rs1768353	1.00[MEX][hapmap]
rs1768356	0.87[AMR][1000 genomes]
rs1768357	1.00[MEX][hapmap]
rs1768359	0.87[AMR][1000 genomes]
rs55958764	0.87[AMR][1000 genomes]
rs6900798	1.00[MEX][hapmap]
rs73592688	0.87[AMR][1000 genomes]
rs73592691	0.87[AMR][1000 genomes]
rs73594656	1.00[AMR][1000 genomes]
rs73594666	0.85[AMR][1000 genomes]
rs73594668	0.85[AMR][1000 genomes]
rs73594673	0.85[AMR][1000 genomes]
rs73594676	0.85[AMR][1000 genomes]
rs73594679	0.85[AMR][1000 genomes]
rs73594681	0.83[AFR][1000 genomes];0.85[AMR][1000 genomes]
rs73594682	0.84[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73596645	1.00[AMR][1000 genomes]
rs73596648	0.84[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73596649	1.00[AMR][1000 genomes]
rs73596651	1.00[AMR][1000 genomes]
rs73596654	1.00[AMR][1000 genomes]
rs73596655	0.85[AMR][1000 genomes]
rs73596659	1.00[AMR][1000 genomes]
rs73596661	0.84[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73772021	0.87[AMR][1000 genomes]
rs981998	1.00[MEX][hapmap]
rs981999	0.87[AMR][1000 genomes]
rs982000	0.87[AMR][1000 genomes]
rs982001	0.87[AMR][1000 genomes]
rs982002	0.86[LWK][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:34 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:128585200-128617600	Weak transcription	Sigmoid Colon	Sigmoid Colon
2	chr6:128586400-128602000	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
3	chr6:128587600-128602200	Weak transcription	Fetal Intestine Large	intestine
4	chr6:128588000-128608200	Weak transcription	Aorta	Aorta
5	chr6:128592600-128599200	Weak transcription	Fetal Brain Male	brain
6	chr6:128592800-128602200	Weak transcription	Psoas Muscle	Psoas
7	chr6:128592800-128605200	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
8	chr6:128593000-128600000	Weak transcription	Fetal Heart	heart
9	chr6:128593000-128600000	Weak transcription	Ovary	ovary
10	chr6:128593000-128603200	Weak transcription	Stomach Mucosa	stomach
11	chr6:128593000-128609000	Weak transcription	Fetal Lung	lung
12	chr6:128593000-128631600	Weak transcription	Left Ventricle	heart
13	chr6:128593200-128600000	Weak transcription	Duodenum Smooth Muscle	Duodenum
14	chr6:128594200-128601000	Weak transcription	H1 Cell Line	embryonic stem cell
15	chr6:128595800-128608800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
16	chr6:128596000-128598800	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
17	chr6:128596200-128599000	Enhancers	Osteobl	bone
18	chr6:128596600-128608800	Weak transcription	NH-A	brain
19	chr6:128596800-128602800	Weak transcription	Brain Hippocampus Middle	brain
20	chr6:128596800-128607400	Weak transcription	HSMMtube	muscle
21	chr6:128596800-128623600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
22	chr6:128597400-128598800	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
23	chr6:128597600-128598800	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
24	chr6:128597600-128598800	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
25	chr6:128597800-128598600	Weak transcription	Brain Substantia Nigra	brain
26	chr6:128597800-128598800	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
27	chr6:128597800-128599200	Enhancers	Liver	Liver
28	chr6:128597800-128625000	Weak transcription	HSMM	muscle
29	chr6:128598200-128598600	Enhancers	Fetal Stomach	stomach
30	chr6:128598200-128599000	Enhancers	HepG2	liver
31	chr6:128598200-128600400	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
32	chr6:128598200-128613800	Weak transcription	HUVEC	blood vessel
33	chr6:128598400-128598600	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
34	chr6:128598400-128598800	Enhancers	Brain Cingulate Gyrus	brain

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