Variant report

Variant	rs13202835
Chromosome Location	chr6:4461250-4461251
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr6:4458091..4459630-chr6:4459877..4462370,2	MCF-7	breast:

Extended variants
information (count: 79 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:46)

rs_ID	r²[population]
rs10485314	0.81[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13193502	0.94[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs13195311	1.00[ASN][1000 genomes]
rs13195598	0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13195767	1.00[ASN][1000 genomes]
rs13199395	1.00[YRI][hapmap];0.81[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13200803	0.94[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs13202454	0.82[EUR][1000 genomes]
rs13203709	0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13204463	1.00[ASN][1000 genomes]
rs13204714	0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13204863	0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13208005	1.00[MEX][hapmap];1.00[ASN][1000 genomes]
rs13209392	1.00[ASN][1000 genomes]
rs13210174	0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13210434	0.94[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13210994	0.94[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13214243	0.81[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13214540	1.00[ASN][1000 genomes]
rs13215112	0.82[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13215125	0.82[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13218058	0.94[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13220119	1.00[ASN][1000 genomes]
rs1330790	0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1330793	0.81[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1411653	1.00[ASN][1000 genomes]
rs17138183	1.00[ASN][1000 genomes]
rs17511568	0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34908924	0.94[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs34971804	1.00[ASN][1000 genomes]
rs35364338	0.91[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4959967	1.00[ASN][1000 genomes]
rs6899991	1.00[ASN][1000 genomes]
rs6901275	1.00[ASN][1000 genomes]
rs6901445	1.00[ASN][1000 genomes]
rs6933015	0.82[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6937849	0.94[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6938854	1.00[ASN][1000 genomes]
rs7742092	1.00[ASN][1000 genomes]
rs7744183	0.81[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7755347	1.00[ASN][1000 genomes]
rs7761922	0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9392600	1.00[ASN][1000 genomes]
rs9504097	1.00[ASN][1000 genomes]
rs9504099	1.00[ASN][1000 genomes]
rs9766812	1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:33 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv600861	chr6:4238488-4469641	Enhancers Weak transcription Flanking Bivalent TSS/Enh Active TSS Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases
2	nsv462618	chr6:4238488-4472587	Enhancers Flanking Active TSS Weak transcription Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases
3	nsv600862	chr6:4238488-4472587	Weak transcription Enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Active TSS Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases
4	nsv949364	chr6:4253413-4466981	Weak transcription Enhancers Flanking Active TSS Active TSS Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases
5	nsv600863	chr6:4255387-4472587	Weak transcription Enhancers Flanking Active TSS Genic enhancers Bivalent Enhancer Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases
6	nsv1027498	chr6:4255640-4471635	Flanking Active TSS Enhancers Flanking Bivalent TSS/Enh Weak transcription Active TSS ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases
7	esv2763995	chr6:4255640-4474114	Bivalent/Poised TSS Enhancers Weak transcription Bivalent Enhancer Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Strong transcription Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases
8	nsv1020205	chr6:4255640-4474114	Enhancers Flanking Active TSS Weak transcription ZNF genes & repeats Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Genic enhancers Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases
9	nsv600864	chr6:4255708-4464630	Enhancers Flanking Active TSS Weak transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Active TSS ZNF genes & repeats Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases
10	nsv516402	chr6:4255708-4472587	Enhancers Flanking Active TSS Weak transcription Active TSS Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases
11	nsv462619	chr6:4255708-4472587	Weak transcription Enhancers Flanking Active TSS Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases
12	nsv600865	chr6:4255708-4472587	Enhancers Weak transcription Flanking Active TSS Flanking Bivalent TSS/Enh Active TSS Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases
13	nsv462620	chr6:4255708-4481421	Weak transcription Enhancers Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases
14	nsv600866	chr6:4255708-4481421	Enhancers Weak transcription Flanking Active TSS Bivalent Enhancer Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Genic enhancers Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases
15	nsv600867	chr6:4255725-4464630	Enhancers Flanking Active TSS Weak transcription Active TSS Bivalent Enhancer Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases
16	nsv462621	chr6:4255725-4472587	Weak transcription Active TSS Enhancers Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases
17	nsv600868	chr6:4255725-4472587	Enhancers Flanking Active TSS Weak transcription ZNF genes & repeats Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases
18	nsv1029501	chr6:4255745-4471635	Enhancers Active TSS Flanking Active TSS Weak transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases
19	nsv432845	chr6:4255905-4471472	Weak transcription Enhancers Flanking Active TSS Active TSS ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases
20	nsv1030655	chr6:4257190-4473701	Enhancers Weak transcription Flanking Active TSS Active TSS Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Genic enhancers Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases
21	nsv538108	chr6:4257190-4473701	Weak transcription Bivalent Enhancer Enhancers Flanking Active TSS Active TSS Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Genic enhancers Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases
22	nsv1030840	chr6:4257390-4473562	Bivalent Enhancer Enhancers Weak transcription Flanking Active TSS Flanking Bivalent TSS/Enh Active TSS ZNF genes & repeats Bivalent/Poised TSS Genic enhancers Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases
23	nsv538109	chr6:4257390-4473562	Enhancers Weak transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent/Poised TSS Active TSS ZNF genes & repeats Genic enhancers Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases
24	nsv1026890	chr6:4259075-4471635	Enhancers Weak transcription Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Genic enhancers Active TSS Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases
25	nsv1021257	chr6:4264933-4473384	Active TSS Enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer Weak transcription Flanking Active TSS ZNF genes & repeats Strong transcription Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases
26	nsv538110	chr6:4264933-4473384	Enhancers Active TSS Weak transcription Bivalent Enhancer Flanking Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Strong transcription Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases
27	nsv1016621	chr6:4277411-4473384	Flanking Active TSS Enhancers Weak transcription Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Strong transcription Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases
28	nsv883413	chr6:4371622-4474114	Enhancers Weak transcription Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Active TSS ZNF genes & repeats Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
29	nsv1021743	chr6:4382308-4494308	Enhancers Weak transcription Active TSS Bivalent Enhancer Flanking Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
30	nsv538111	chr6:4382308-4494308	Enhancers Flanking Active TSS Weak transcription ZNF genes & repeats Active TSS Bivalent Enhancer Strong transcription Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
31	esv3421990	chr6:4446933-4659639	Enhancers Bivalent Enhancer Weak transcription Flanking Active TSS Active TSS ZNF genes & repeats Strong transcription Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
32	nsv830576	chr6:4447554-4610604	Enhancers Weak transcription Flanking Active TSS Active TSS ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
33	nsv981355	chr6:4455801-4466820	Enhancers Flanking Active TSS Active TSS Weak transcription Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats	Chromatin interactive region lncRNA	n/a	inside rSNPs	n/a

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs13202835	RPP40	cis	cerebellum	SCAN
rs13202835	EEF1E1	cis	cerebellum	SCAN

Chromatin state (count:53 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:4458800-4461600	Enhancers	HMEC	breast
2	chr6:4459000-4461400	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
3	chr6:4459000-4461400	Enhancers	Placenta	Placenta
4	chr6:4459000-4461600	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
5	chr6:4459000-4461600	Enhancers	HSMM	muscle
6	chr6:4459000-4461800	Enhancers	NH-A	brain
7	chr6:4459200-4461400	Enhancers	Esophagus	oesophagus
8	chr6:4459200-4461400	Enhancers	Left Ventricle	heart
9	chr6:4459200-4461400	Enhancers	Psoas Muscle	Psoas
10	chr6:4459200-4461600	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
11	chr6:4459200-4462200	Enhancers	Fetal Muscle Leg	muscle
12	chr6:4459200-4462200	Enhancers	Skeletal Muscle Female	skeletal muscle
13	chr6:4459400-4461400	Enhancers	Fetal Adrenal Gland	Adrenal Gland
14	chr6:4459600-4461400	Enhancers	Ovary	ovary
15	chr6:4460000-4472400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
16	chr6:4460400-4461400	Enhancers	Fetal Lung	lung
17	chr6:4460400-4461600	Flanking Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
18	chr6:4460400-4465800	Weak transcription	Spleen	Spleen
19	chr6:4460600-4461400	Enhancers	NHLF	lung
20	chr6:4460600-4461800	Weak transcription	HUVEC	blood vessel
21	chr6:4460800-4461400	Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
22	chr6:4460800-4461400	Flanking Active TSS	Skeletal Muscle Male	skeletal muscle
23	chr6:4460800-4461600	Enhancers	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
24	chr6:4460800-4461800	Flanking Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
25	chr6:4460800-4461800	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
26	chr6:4460800-4461800	Flanking Active TSS	Stomach Smooth Muscle	stomach
27	chr6:4461000-4461400	Enhancers	H1 Cell Line	embryonic stem cell
28	chr6:4461000-4461400	Active TSS	Adipose Nuclei	Adipose
29	chr6:4461000-4461400	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
30	chr6:4461000-4461400	Active TSS	Brain Substantia Nigra	brain
31	chr6:4461000-4461400	Flanking Bivalent TSS/Enh	Fetal Muscle Trunk	muscle
32	chr6:4461000-4461400	Bivalent Enhancer	Fetal Stomach	stomach
33	chr6:4461000-4461600	Flanking Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
34	chr6:4461000-4461600	Flanking Active TSS	Breast Myoepithelial Primary Cells	Breast
35	chr6:4461000-4461600	Flanking Active TSS	Cortex derived primary cultured neurospheres	brain
36	chr6:4461000-4461600	Flanking Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
37	chr6:4461000-4461600	Flanking Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
38	chr6:4461000-4461600	Flanking Active TSS	Brain Germinal Matrix	brain
39	chr6:4461000-4461600	Weak transcription	Colon Smooth Muscle	Colon
40	chr6:4461000-4461600	Flanking Active TSS	NHDF-Ad	bronchial
41	chr6:4461000-4461800	Active TSS	Brain Angular Gyrus	brain
42	chr6:4461000-4461800	Active TSS	Brain Inferior Temporal Lobe	brain
43	chr6:4461000-4462000	Enhancers	ES-I3 Cell Line	embryonic stem cell
44	chr6:4461200-4461400	Flanking Active TSS	Muscle Satellite Cultured Cells	--
45	chr6:4461200-4461600	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
46	chr6:4461200-4461600	Flanking Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
47	chr6:4461200-4461600	Flanking Active TSS	Brain Anterior Caudate	brain
48	chr6:4461200-4461600	Active TSS	Brain Cingulate Gyrus	brain
49	chr6:4461200-4461600	Active TSS	Brain Hippocampus Middle	brain
50	chr6:4461200-4461600	Active TSS	Fetal Brain Female	brain

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