Variant report

Variant	rs3002006
Chromosome Location	chr6:56615714-56615715
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr6:56614450..56616010-chr6:56617525..56619069,2	MCF-7	breast:
2	chr6:56613706..56615863-chr6:56618976..56621667,2	K562	blood:

Extended variants
information (count: 103 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:98)

rs_ID	r²[population]
rs10498811	0.83[EUR][1000 genomes]
rs11961141	0.98[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs11961342	0.90[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs11968575	0.90[YRI][hapmap];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs11970648	0.82[YRI][hapmap];0.90[AFR][1000 genomes];0.89[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs13191164	0.83[EUR][1000 genomes]
rs13192037	0.83[EUR][1000 genomes]
rs13192478	0.83[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs13192567	0.98[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs13196211	0.82[EUR][1000 genomes]
rs13198399	0.99[EUR][1000 genomes]
rs13198938	0.83[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs13203000	1.00[EUR][1000 genomes]
rs13205013	0.83[EUR][1000 genomes]
rs13206849	0.83[EUR][1000 genomes]
rs13208409	0.82[EUR][1000 genomes]
rs13210876	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs13213878	0.93[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs13217390	1.00[EUR][1000 genomes]
rs13219546	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs13219942	0.97[EUR][1000 genomes]
rs16888118	0.84[AFR][1000 genomes];0.83[EUR][1000 genomes]
rs16888124	0.83[EUR][1000 genomes]
rs16888126	0.80[EUR][1000 genomes]
rs16888128	0.84[EUR][1000 genomes]
rs16888130	0.84[EUR][1000 genomes]
rs16888133	0.82[EUR][1000 genomes]
rs16888135	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs17684511	0.83[EUR][1000 genomes]
rs17684553	0.84[EUR][1000 genomes]
rs17684571	0.84[EUR][1000 genomes]
rs17751682	0.83[EUR][1000 genomes]
rs17751695	0.83[EUR][1000 genomes]
rs2967960	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs2967963	0.93[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs3002003	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs3002004	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs3002007	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs3002008	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs3002009	0.98[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs3002010	0.84[YRI][hapmap];0.94[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs3002011	0.94[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs34138864	0.83[EUR][1000 genomes]
rs34429594	0.96[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs34455199	1.00[EUR][1000 genomes]
rs34463732	0.91[EUR][1000 genomes]
rs34465210	1.00[EUR][1000 genomes]
rs34566275	1.00[EUR][1000 genomes]
rs34576803	0.81[EUR][1000 genomes]
rs34587484	1.00[EUR][1000 genomes]
rs34623351	1.00[EUR][1000 genomes]
rs34703847	0.83[AFR][1000 genomes];0.94[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs34724718	0.83[EUR][1000 genomes]
rs34803237	1.00[EUR][1000 genomes]
rs34812826	0.98[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs34824960	0.93[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs34832779	0.99[EUR][1000 genomes]
rs35089136	0.80[EUR][1000 genomes]
rs35206656	0.84[EUR][1000 genomes]
rs35326806	0.97[EUR][1000 genomes]
rs35408048	0.83[EUR][1000 genomes]
rs35494794	0.97[EUR][1000 genomes]
rs35619924	0.83[EUR][1000 genomes]
rs35637749	0.83[EUR][1000 genomes]
rs35668437	0.83[EUR][1000 genomes]
rs35687635	0.84[EUR][1000 genomes]
rs35876418	1.00[EUR][1000 genomes]
rs35920751	0.90[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs36068365	0.98[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs4072271	0.84[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs4073960	0.84[AFR][1000 genomes]
rs4074101	0.83[EUR][1000 genomes]
rs4074102	0.83[EUR][1000 genomes]
rs4074103	0.80[EUR][1000 genomes]
rs41267675	1.00[EUR][1000 genomes]
rs4275049	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs4305712	1.00[ASN][1000 genomes]
rs4640889	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs5024547	0.83[EUR][1000 genomes]
rs55742092	0.82[EUR][1000 genomes]
rs56101897	0.83[EUR][1000 genomes]
rs59085778	0.98[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs59247267	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs60498201	0.96[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs62412526	0.83[EUR][1000 genomes]
rs62412528	0.83[EUR][1000 genomes]
rs62412531	0.83[EUR][1000 genomes]
rs62412532	0.83[EUR][1000 genomes]
rs62412544	0.84[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs62412556	0.89[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs6901176	0.84[AFR][1000 genomes];0.83[EUR][1000 genomes]
rs6904535	0.83[AMR][1000 genomes]
rs6924375	0.83[EUR][1000 genomes]
rs6926134	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs6938003	0.98[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs71564848	0.81[EUR][1000 genomes]
rs71564849	0.84[EUR][1000 genomes]
rs7767128	0.83[EUR][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	nsv491933	chr6:56177722-57171010	Active TSS Enhancers Strong transcription Weak transcription Genic enhancers Flanking Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	51 gene(s)	inside rSNPs	diseases
2	nsv934026	chr6:56382056-57184218	Flanking Bivalent TSS/Enh Strong transcription Weak transcription Enhancers Transcr. at gene 5' and 3' Flanking Active TSS Genic enhancers Bivalent/Poised TSS Active TSS ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	49 gene(s)	inside rSNPs	diseases
3	nsv533050	chr6:56504480-57297586	Active TSS Enhancers Weak transcription Strong transcription Genic enhancers Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	44 gene(s)	inside rSNPs	diseases
4	nsv1021651	chr6:56569444-56966319	Flanking Active TSS Enhancers Weak transcription Genic enhancers Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Strong transcription ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	28 gene(s)	inside rSNPs	diseases
5	nsv538228	chr6:56569444-56966319	Active TSS Weak transcription Enhancers Genic enhancers Flanking Active TSS Strong transcription Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	28 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:75 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:56593200-56621200	Weak transcription	Fetal Muscle Leg	muscle
2	chr6:56606600-56617600	Enhancers	HUES48 Cell Line	embryonic stem cell
3	chr6:56607200-56618200	Weak transcription	Brain Germinal Matrix	brain
4	chr6:56607600-56620600	Weak transcription	Fetal Intestine Small	intestine
5	chr6:56608200-56621000	Weak transcription	Duodenum Smooth Muscle	Duodenum
6	chr6:56608600-56618000	Weak transcription	Rectal Smooth Muscle	rectum
7	chr6:56609200-56617600	Enhancers	HMEC	breast
8	chr6:56609200-56619200	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
9	chr6:56611600-56625800	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
10	chr6:56611800-56616200	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
11	chr6:56612000-56616400	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
12	chr6:56612200-56616200	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
13	chr6:56612200-56616600	Weak transcription	Cortex derived primary cultured neurospheres	brain
14	chr6:56612200-56616600	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
15	chr6:56612200-56620800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
16	chr6:56612400-56616800	Weak transcription	Brain Substantia Nigra	brain
17	chr6:56612400-56621800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
18	chr6:56613000-56617400	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
19	chr6:56613400-56615800	Enhancers	Breast Myoepithelial Primary Cells	Breast
20	chr6:56613400-56615800	Enhancers	Skeletal Muscle Female	skeletal muscle
21	chr6:56613400-56617600	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
22	chr6:56613600-56615800	Enhancers	Colon Smooth Muscle	Colon
23	chr6:56613800-56617600	Enhancers	Brain Anterior Caudate	brain
24	chr6:56614000-56621400	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
25	chr6:56614200-56615800	Enhancers	NHLF	lung
26	chr6:56614200-56617000	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
27	chr6:56614200-56619200	Enhancers	iPS-20b Cell Line	embryonic stem cell
28	chr6:56614200-56619400	Enhancers	Osteobl	bone
29	chr6:56614400-56616600	Enhancers	Placenta Amnion	Placenta Amnion
30	chr6:56614400-56616600	Enhancers	HSMMtube	muscle
31	chr6:56614400-56617400	Enhancers	HUES64 Cell Line	embryonic stem cell
32	chr6:56614400-56618000	Weak transcription	Stomach Smooth Muscle	stomach
33	chr6:56614400-56619400	Enhancers	NHDF-Ad	bronchial
34	chr6:56614400-56619600	Enhancers	Brain Hippocampus Middle	brain
35	chr6:56614600-56616000	Enhancers	Brain Angular Gyrus	brain
36	chr6:56614600-56617400	Enhancers	HUES6 Cell Line	embryonic stem cell
37	chr6:56614600-56617400	Enhancers	Brain Cingulate Gyrus	brain
38	chr6:56614600-56617800	Enhancers	ES-I3 Cell Line	embryonic stem cell
39	chr6:56614800-56615800	Enhancers	Brain Dorsolateral Prefrontal Cortex	brain
40	chr6:56614800-56616000	Enhancers	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
41	chr6:56614800-56617400	Enhancers	iPS-18 Cell Line	embryonic stem cell
42	chr6:56614800-56620600	Weak transcription	Aorta	Aorta
43	chr6:56615000-56617400	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
44	chr6:56615000-56617400	Enhancers	A549	lung
45	chr6:56615000-56617600	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
46	chr6:56615000-56618000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
47	chr6:56615000-56618000	Weak transcription	Right Ventricle	heart
48	chr6:56615000-56618800	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
49	chr6:56615000-56620000	Weak transcription	Psoas Muscle	Psoas
50	chr6:56615000-56620600	Weak transcription	Left Ventricle	heart

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