Variant report

Variant	rs3002011
Chromosome Location	chr6:56625123-56625124
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr6:56592975..56595181-chr6:56623797..56627807,3	MCF-7	breast:
2	chr6:56624772..56628939-chr6:56706585..56709491,3	MCF-7	breast:
3	chr6:56625069..56627235-chr6:56628459..56631328,2	K562	blood:

Variant related genes	Relation type
ENSG00000151914	Chromatin interaction
ENSG00000231441	Chromatin interaction

Extended variants
information (count: 141 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:136)

rs_ID	r²[population]
rs10498811	0.83[EUR][1000 genomes]
rs10498812	0.81[CEU][hapmap]
rs10498813	0.81[CEU][hapmap]
rs11961141	0.86[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs11961342	0.96[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs11968575	1.00[CEU][hapmap];0.92[YRI][hapmap];0.94[AFR][1000 genomes];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs11970648	0.80[CEU][hapmap];1.00[CHB][hapmap];0.91[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13190784	1.00[CHB][hapmap]
rs13191164	0.83[EUR][1000 genomes]
rs13192037	0.83[EUR][1000 genomes]
rs13192478	0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs13192567	0.86[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs13194625	0.81[CEU][hapmap]
rs13194904	0.81[CEU][hapmap]
rs13196211	0.82[EUR][1000 genomes]
rs13198399	0.99[EUR][1000 genomes]
rs13198938	0.99[EUR][1000 genomes]
rs13200166	0.80[CEU][hapmap]
rs13203000	1.00[CEU][hapmap];1.00[EUR][1000 genomes]
rs13203681	0.81[CEU][hapmap]
rs13204466	0.81[CEU][hapmap]
rs13205013	0.83[EUR][1000 genomes]
rs13205667	0.81[CEU][hapmap]
rs13206849	0.83[EUR][1000 genomes]
rs13207768	0.80[CEU][hapmap]
rs13208409	0.82[EUR][1000 genomes]
rs13210876	0.97[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs13213878	0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs13217390	1.00[CEU][hapmap];1.00[EUR][1000 genomes]
rs13218913	0.80[CEU][hapmap]
rs13219546	0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs13219942	0.97[EUR][1000 genomes]
rs13220618	0.81[CEU][hapmap]
rs13220628	0.85[CEU][hapmap]
rs16888118	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	0.97[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs16888171	0.80[CEU][hapmap]
rs16888186	1.00[CHB][hapmap]
rs17684511	0.83[EUR][1000 genomes]
rs17684553	0.84[EUR][1000 genomes]
rs17684571	0.84[EUR][1000 genomes]
rs17684748	0.81[CEU][hapmap]
rs17684772	0.81[CEU][hapmap]
rs17684784	0.80[CEU][hapmap]
rs17684802	0.80[CEU][hapmap]
rs17684878	0.80[CEU][hapmap]
rs17684884	0.81[CEU][hapmap]
rs17751682	0.83[EUR][1000 genomes]
rs17751695	0.83[EUR][1000 genomes]
rs17751977	0.81[CEU][hapmap]
rs17752046	0.81[CEU][hapmap]
rs17752106	0.81[CEU][hapmap]
rs1903332	1.00[CHB][hapmap]
rs2967960	0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2967963	0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3002003	0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs3002004	0.98[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs3002006	0.94[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs3002007	0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3002008	0.98[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3002009	0.94[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs3002010	1.00[CEU][hapmap];1.00[CHB][hapmap];0.90[YRI][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34138864	0.83[EUR][1000 genomes]
rs34429594	0.86[AFR][1000 genomes];0.94[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	0.93[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs34724718	0.83[EUR][1000 genomes]
rs34803237	1.00[EUR][1000 genomes]
rs34812826	0.86[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs34824960	0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs34832779	0.99[EUR][1000 genomes]
rs35089136	0.80[EUR][1000 genomes];0.89[ASN][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	0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs36068365	0.86[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs4072271	0.82[AMR][1000 genomes];0.84[EUR][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	0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs4299824	0.80[CEU][hapmap]
rs4348308	0.81[CEU][hapmap]
rs4371846	0.81[CEU][hapmap]
rs4415160	0.80[CEU][hapmap]
rs4457154	0.81[CEU][hapmap]
rs4574644	0.89[ASN][1000 genomes]
rs4640889	0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs5024547	0.83[EUR][1000 genomes]
rs55742092	0.82[EUR][1000 genomes]
rs56094263	0.89[ASN][1000 genomes]
rs56101897	0.83[EUR][1000 genomes]
rs58980183	0.82[AMR][1000 genomes]
rs59085778	0.88[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs59162324	0.89[ASN][1000 genomes]
rs59247267	0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs60498201	0.86[AFR][1000 genomes];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.89[ASN][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	0.82[AFR][1000 genomes];0.83[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs62412556	0.88[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs6901176	0.83[EUR][1000 genomes]
rs6904535	0.85[AMR][1000 genomes]
rs6905603	0.81[CEU][hapmap]
rs6918949	0.80[CEU][hapmap]
rs6924375	0.83[EUR][1000 genomes]
rs6926134	0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs6934714	0.81[CEU][hapmap];1.00[CHB][hapmap]
rs6938003	0.97[AFR][1000 genomes];0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs71564848	0.81[EUR][1000 genomes]
rs71564849	0.84[EUR][1000 genomes]
rs7758867	0.80[CEU][hapmap];1.00[CHB][hapmap]
rs7761501	0.80[CEU][hapmap]
rs7761729	0.80[CEU][hapmap]
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:83 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:56611600-56625800	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
2	chr6:56618000-56625800	Enhancers	HUES48 Cell Line	embryonic stem cell
3	chr6:56618400-56625600	Enhancers	HUES64 Cell Line	embryonic stem cell
4	chr6:56618600-56625400	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
5	chr6:56619800-56625400	Enhancers	Cortex derived primary cultured neurospheres	brain
6	chr6:56619800-56629200	Weak transcription	Pancreas	Pancrea
7	chr6:56620000-56626200	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
8	chr6:56620200-56625200	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
9	chr6:56620400-56626000	Enhancers	Colon Smooth Muscle	Colon
10	chr6:56620600-56625600	Enhancers	Brain Germinal Matrix	brain
11	chr6:56620800-56625200	Enhancers	iPS-20b Cell Line	embryonic stem cell
12	chr6:56620800-56625400	Enhancers	Skeletal Muscle Male	skeletal muscle
13	chr6:56621000-56625200	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
14	chr6:56621000-56625400	Enhancers	iPS-18 Cell Line	embryonic stem cell
15	chr6:56621000-56626200	Enhancers	NHDF-Ad	bronchial
16	chr6:56621200-56626200	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
17	chr6:56621400-56626000	Enhancers	Brain Substantia Nigra	brain
18	chr6:56621400-56629000	Weak transcription	Aorta	Aorta
19	chr6:56621400-56634200	Weak transcription	Spleen	Spleen
20	chr6:56622200-56625400	Weak transcription	Pancreatic Islets	Pancreatic Islet
21	chr6:56622400-56637600	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
22	chr6:56622600-56626000	Enhancers	Brain Anterior Caudate	brain
23	chr6:56622800-56627800	Weak transcription	Stomach Smooth Muscle	stomach
24	chr6:56622800-56628800	Weak transcription	Ovary	ovary
25	chr6:56622800-56631000	Weak transcription	Sigmoid Colon	Sigmoid Colon
26	chr6:56623000-56625200	Weak transcription	Rectal Smooth Muscle	rectum
27	chr6:56623000-56631000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
28	chr6:56623200-56625800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
29	chr6:56623200-56626000	Enhancers	Brain Hippocampus Middle	brain
30	chr6:56623200-56628200	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
31	chr6:56623200-56628800	Weak transcription	HepG2	liver
32	chr6:56623200-56629000	Weak transcription	Primary monocytes fromperipheralblood	blood
33	chr6:56623200-56629000	Weak transcription	HUVEC	blood vessel
34	chr6:56623200-56629200	Weak transcription	Stomach Mucosa	stomach
35	chr6:56623200-56631000	Weak transcription	Fetal Lung	lung
36	chr6:56623400-56625200	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
37	chr6:56623400-56625400	Weak transcription	NHEK	skin
38	chr6:56623400-56625800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
39	chr6:56623400-56628600	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
40	chr6:56623600-56626400	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
41	chr6:56623600-56628600	Weak transcription	Duodenum Smooth Muscle	Duodenum
42	chr6:56623600-56631000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
43	chr6:56623600-56637200	Weak transcription	H9 Cell Line	embryonic stem cell
44	chr6:56623600-56637600	Weak transcription	Fetal Muscle Leg	muscle
45	chr6:56623800-56625200	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
46	chr6:56623800-56625200	Weak transcription	HMEC	breast
47	chr6:56623800-56625400	Weak transcription	Breast Myoepithelial Primary Cells	Breast
48	chr6:56623800-56625800	Weak transcription	Right Ventricle	heart
49	chr6:56623800-56628400	Weak transcription	Right Atrium	heart
50	chr6:56623800-56628600	Weak transcription	Muscle Satellite Cultured Cells	--

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