Variant report

Variant	rs3002008
Chromosome Location	chr6:56622325-56622326
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:0)
CpG islands
(count:0)
Chromatin interactive
region (count:9)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:9 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr6:56573542..56574688-chr6:56622197..56623128,5	MCF-7	breast:
2	chr6:56620669..56623205-chr6:56923260..56926182,2	K562	blood:
3	chr6:56621954..56624540-chr6:56707900..56710066,2	MCF-7	breast:
4	chr6:56575600..56578099-chr6:56621546..56624732,3	MCF-7	breast:
5	chr6:56575250..56576343-chr6:56622212..56623158,6	MCF-7	breast:
6	chr17:59470558..59471536-chr6:56622198..56623124,2	MCF-7	breast:
7	chr6:56502427..56503029-chr6:56622069..56623096,3	K562	blood:
8	chr6:56575844..56576434-chr6:56621965..56622686,2	MCF-7	breast:
9	chr12:67848196..67848927-chr6:56622319..56622922,2	MCF-7	breast:

No data

Variant related genes	Relation type
ENSG00000231441	Chromatin interaction
ENSG00000267280	Chromatin interaction
ENSG00000151914	Chromatin interaction

Extended variants
information (count: 104 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:99)

rs_ID	r²[population]
rs10498811	0.83[EUR][1000 genomes]
rs11961141	0.86[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs11961342	0.98[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs11968575	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs11970648	0.89[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13191164	0.83[EUR][1000 genomes]
rs13192037	0.83[EUR][1000 genomes]
rs13192478	0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs13192567	0.86[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.89[ASN][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	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs13213878	0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs13217390	1.00[EUR][1000 genomes]
rs13219546	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs13219942	0.97[EUR][1000 genomes]
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	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.89[ASN][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[AMR][1000 genomes];0.99[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2967963	0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3002003	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs3002004	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs3002006	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs3002007	1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3002009	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs3002010	0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3002011	0.98[AFR][1000 genomes];0.94[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];0.96[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	0.94[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];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs34824960	0.98[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	0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs36068365	0.86[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs4072271	0.84[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	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs4574644	0.89[ASN][1000 genomes]
rs4640889	1.00[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]
rs59085778	0.87[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs59162324	0.89[ASN][1000 genomes]
rs59247267	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs60498201	0.86[AFR][1000 genomes];0.96[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];0.84[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs62412556	0.89[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs6901176	0.83[EUR][1000 genomes]
rs6904535	0.83[AMR][1000 genomes]
rs6924375	0.83[EUR][1000 genomes]
rs6926134	1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs6938003	0.98[AFR][1000 genomes];0.98[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]
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:95 , 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	chr6:56615000-56625000	Enhancers	iPS-15b Cell Line	embryonic stem cell
3	chr6:56615800-56624000	Enhancers	Fetal Heart	heart
4	chr6:56617200-56624400	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
5	chr6:56617200-56624800	Enhancers	Brain Angular Gyrus	brain
6	chr6:56617800-56624800	Enhancers	Brain Cingulate Gyrus	brain
7	chr6:56618000-56625800	Enhancers	HUES48 Cell Line	embryonic stem cell
8	chr6:56618200-56623800	Enhancers	NHLF	lung
9	chr6:56618200-56624200	Enhancers	ES-I3 Cell Line	embryonic stem cell
10	chr6:56618400-56625600	Enhancers	HUES64 Cell Line	embryonic stem cell
11	chr6:56618600-56625400	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
12	chr6:56619200-56623800	Enhancers	Fetal Stomach	stomach
13	chr6:56619800-56623200	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
14	chr6:56619800-56624200	Enhancers	HUES6 Cell Line	embryonic stem cell
15	chr6:56619800-56625400	Enhancers	Cortex derived primary cultured neurospheres	brain
16	chr6:56619800-56629200	Weak transcription	Pancreas	Pancrea
17	chr6:56620000-56622400	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
18	chr6:56620000-56623200	Enhancers	Fetal Lung	lung
19	chr6:56620000-56623800	Enhancers	Muscle Satellite Cultured Cells	--
20	chr6:56620000-56624000	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
21	chr6:56620000-56624000	Enhancers	Brain Dorsolateral Prefrontal Cortex	brain
22	chr6:56620000-56626200	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
23	chr6:56620200-56624800	Enhancers	Skeletal Muscle Female	skeletal muscle
24	chr6:56620200-56625200	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
25	chr6:56620400-56623800	Enhancers	HSMM	muscle
26	chr6:56620400-56626000	Enhancers	Colon Smooth Muscle	Colon
27	chr6:56620600-56622600	Enhancers	Fetal Intestine Small	intestine
28	chr6:56620600-56623200	Enhancers	Adipose Nuclei	Adipose
29	chr6:56620600-56623200	Enhancers	Fetal Brain Female	brain
30	chr6:56620600-56623800	Enhancers	Breast Myoepithelial Primary Cells	Breast
31	chr6:56620600-56624000	Enhancers	A549	lung
32	chr6:56620600-56624000	Enhancers	Osteobl	bone
33	chr6:56620600-56625600	Enhancers	Brain Germinal Matrix	brain
34	chr6:56620800-56622600	Enhancers	Fetal Brain Male	brain
35	chr6:56620800-56622800	Enhancers	Sigmoid Colon	Sigmoid Colon
36	chr6:56620800-56623000	Enhancers	Foreskin Melanocyte Primary Cells skin01	Skin
37	chr6:56620800-56623000	Enhancers	Liver	Liver
38	chr6:56620800-56623000	Enhancers	Placenta Amnion	Placenta Amnion
39	chr6:56620800-56623200	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
40	chr6:56620800-56623200	Enhancers	Stomach Mucosa	stomach
41	chr6:56620800-56623400	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
42	chr6:56620800-56623800	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
43	chr6:56620800-56623800	Enhancers	Rectal Mucosa Donor 29	rectum
44	chr6:56620800-56623800	Enhancers	NH-A	brain
45	chr6:56620800-56625200	Enhancers	iPS-20b Cell Line	embryonic stem cell
46	chr6:56620800-56625400	Enhancers	Skeletal Muscle Male	skeletal muscle
47	chr6:56621000-56622600	Enhancers	Rectal Mucosa Donor 31	rectum
48	chr6:56621000-56622800	Enhancers	H1 Cell Line	embryonic stem cell
49	chr6:56621000-56623000	Enhancers	Rectal Smooth Muscle	rectum
50	chr6:56621000-56623400	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--

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