Variant report

Variant	rs1265297
Chromosome Location	chr6:4460050-4460051
allele	A/C
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: 98 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:65)

rs_ID	r²[population]
rs1010638	0.82[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs10447477	0.81[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs10447478	0.83[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs10447479	0.82[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10458172	0.81[CEU][hapmap]
rs10458173	0.90[CEU][hapmap];0.84[EUR][1000 genomes]
rs10900958	0.83[EUR][1000 genomes]
rs10900959	0.83[EUR][1000 genomes]
rs10900960	0.83[EUR][1000 genomes]
rs10900961	0.83[EUR][1000 genomes]
rs11242924	1.00[ASW][hapmap];0.82[CEU][hapmap];0.88[GIH][hapmap];0.89[TSI][hapmap]
rs11242933	0.83[EUR][1000 genomes]
rs11242934	0.83[EUR][1000 genomes]
rs11242935	0.83[EUR][1000 genomes]
rs11242936	0.83[EUR][1000 genomes]
rs11242937	0.84[EUR][1000 genomes]
rs11242939	0.84[EUR][1000 genomes]
rs11242944	0.88[CEU][hapmap];0.84[EUR][1000 genomes]
rs11242945	0.89[CEU][hapmap]
rs11242948	0.87[EUR][1000 genomes]
rs11242951	0.81[AFR][1000 genomes];0.82[AMR][1000 genomes];0.89[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs11755069	0.83[EUR][1000 genomes]
rs12191559	0.84[EUR][1000 genomes]
rs12194925	0.81[AFR][1000 genomes];0.83[AMR][1000 genomes];0.91[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12200144	0.81[CEU][hapmap]
rs12203267	0.81[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs12207060	0.81[AFR][1000 genomes];0.83[AMR][1000 genomes];0.91[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12207864	0.81[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs12210818	0.85[EUR][1000 genomes]
rs12211520	0.88[EUR][1000 genomes]
rs12211781	0.87[EUR][1000 genomes]
rs1265299	0.81[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs1265300	0.90[AFR][1000 genomes];0.88[AMR][1000 genomes];0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1265303	0.83[EUR][1000 genomes]
rs1265304	0.83[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs1265305	0.83[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs12660869	0.81[EUR][1000 genomes]
rs12661792	0.81[AFR][1000 genomes];0.82[AMR][1000 genomes];0.90[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs12663036	0.87[EUR][1000 genomes]
rs12664576	0.81[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs12665814	0.88[EUR][1000 genomes]
rs1590939	0.84[EUR][1000 genomes]
rs17510496	0.88[EUR][1000 genomes]
rs17510539	0.88[EUR][1000 genomes]
rs17570029	0.81[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs17570071	0.81[AFR][1000 genomes];0.83[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs2026185	0.82[CEU][hapmap];0.88[GIH][hapmap];0.89[TSI][hapmap]
rs2183497	0.84[EUR][1000 genomes]
rs2326491	0.81[AFR][1000 genomes];0.83[AMR][1000 genomes];0.89[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2875944	0.80[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs4403297	0.87[EUR][1000 genomes]
rs4513847	0.84[EUR][1000 genomes]
rs4621669	0.84[EUR][1000 genomes]
rs59075559	0.83[EUR][1000 genomes]
rs60109220	0.88[EUR][1000 genomes]
rs61498839	0.80[EUR][1000 genomes]
rs61711492	0.85[EUR][1000 genomes]
rs66815625	0.88[EUR][1000 genomes]
rs67284074	0.88[EUR][1000 genomes]
rs67655715	0.88[EUR][1000 genomes]
rs6902044	0.84[EUR][1000 genomes]
rs6920549	0.84[EUR][1000 genomes]
rs911568	0.83[EUR][1000 genomes]
rs911569	0.83[EUR][1000 genomes]
rs953323	0.81[AFR][1000 genomes];0.81[AMR][1000 genomes];0.88[EUR][1000 genomes];0.82[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
rs1265297	TUBB2A	cis	cerebellum	SCAN
rs1265297	ZBTB5	trans	brain	seeQTL

Chromatin state (count:48 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:4457800-4460400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
2	chr6:4458800-4461000	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
3	chr6:4458800-4461600	Enhancers	HMEC	breast
4	chr6:4459000-4460200	Enhancers	HSMMtube	muscle
5	chr6:4459000-4460200	Enhancers	NHLF	lung
6	chr6:4459000-4460400	Enhancers	Right Ventricle	heart
7	chr6:4459000-4460600	Enhancers	Hela-S3	cervix
8	chr6:4459000-4460600	Enhancers	HUVEC	blood vessel
9	chr6:4459000-4461000	Enhancers	Breast Myoepithelial Primary Cells	Breast
10	chr6:4459000-4461000	Enhancers	Right Atrium	heart
11	chr6:4459000-4461000	Enhancers	NHDF-Ad	bronchial
12	chr6:4459000-4461200	Enhancers	Muscle Satellite Cultured Cells	--
13	chr6:4459000-4461200	Enhancers	NHEK	skin
14	chr6:4459000-4461400	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
15	chr6:4459000-4461400	Enhancers	Placenta	Placenta
16	chr6:4459000-4461600	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
17	chr6:4459000-4461600	Enhancers	HSMM	muscle
18	chr6:4459000-4461800	Enhancers	NH-A	brain
19	chr6:4459200-4460200	Enhancers	Stomach Smooth Muscle	stomach
20	chr6:4459200-4460400	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
21	chr6:4459200-4460400	Weak transcription	Brain Germinal Matrix	brain
22	chr6:4459200-4460400	Enhancers	Rectal Smooth Muscle	rectum
23	chr6:4459200-4460600	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
24	chr6:4459200-4461000	Enhancers	Cortex derived primary cultured neurospheres	brain
25	chr6:4459200-4461000	Enhancers	Fetal Muscle Trunk	muscle
26	chr6:4459200-4461400	Enhancers	Esophagus	oesophagus
27	chr6:4459200-4461400	Enhancers	Left Ventricle	heart
28	chr6:4459200-4461400	Enhancers	Psoas Muscle	Psoas
29	chr6:4459200-4461600	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
30	chr6:4459200-4462200	Enhancers	Fetal Muscle Leg	muscle
31	chr6:4459200-4462200	Enhancers	Skeletal Muscle Female	skeletal muscle
32	chr6:4459400-4460800	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
33	chr6:4459400-4460800	Enhancers	Skeletal Muscle Male	skeletal muscle
34	chr6:4459400-4461000	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
35	chr6:4459400-4461000	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
36	chr6:4459400-4461000	Enhancers	Colon Smooth Muscle	Colon
37	chr6:4459400-4461400	Enhancers	Fetal Adrenal Gland	Adrenal Gland
38	chr6:4459600-4460200	Weak transcription	Spleen	Spleen
39	chr6:4459600-4461000	Enhancers	Brain Dorsolateral Prefrontal Cortex	brain
40	chr6:4459600-4461000	Enhancers	Fetal Stomach	stomach
41	chr6:4459600-4461400	Enhancers	Ovary	ovary
42	chr6:4459800-4461000	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
43	chr6:4459800-4461000	Enhancers	Adipose Nuclei	Adipose
44	chr6:4459800-4461200	Enhancers	Brain Hippocampus Middle	brain
45	chr6:4459800-4461200	Weak transcription	Osteobl	bone
46	chr6:4460000-4460800	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
47	chr6:4460000-4461200	Enhancers	Brain Cingulate Gyrus	brain
48	chr6:4460000-4472400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast

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