Variant report

Variant	rs560051
Chromosome Location	chr6:149666977-149666978
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	chr6:149665295..149667971-chr6:149694420..149696243,2	MCF-7	breast:
2	chr6:149636797..149641190-chr6:149663953..149668102,4	K562	blood:

Variant related genes	Relation type
ENSG00000055208	Chromatin interaction

Extended variants
information (count: 67 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:64)

rs_ID	r²[population]
rs2143076	1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[ASN][1000 genomes]
rs2262617	0.80[EUR][1000 genomes]
rs2341783	0.86[JPT][hapmap]
rs2341784	0.87[JPT][hapmap]
rs2744427	0.87[JPT][hapmap]
rs2744434	0.86[JPT][hapmap]
rs2789488	0.95[CHB][hapmap];1.00[JPT][hapmap];0.80[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2789490	0.91[CHB][hapmap];0.95[JPT][hapmap]
rs2789492	0.85[ASN][1000 genomes]
rs2789500	0.87[JPT][hapmap]
rs3734296	0.86[JPT][hapmap]
rs472810	0.91[JPT][hapmap]
rs474369	0.87[JPT][hapmap]
rs478767	0.87[JPT][hapmap]
rs480526	0.87[JPT][hapmap]
rs489551	0.85[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4895788	0.81[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs4895789	0.95[CEU][hapmap]
rs4897124	0.80[EUR][1000 genomes]
rs492956	0.86[JPT][hapmap]
rs494340	0.82[JPT][hapmap]
rs501926	0.87[JPT][hapmap]
rs504762	0.87[JPT][hapmap]
rs504985	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs506268	0.81[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.90[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs511100	0.86[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs511105	0.86[JPT][hapmap]
rs514839	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs515133	0.82[JPT][hapmap]
rs521845	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[YRI][hapmap];0.91[AFR][1000 genomes];0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs527971	0.80[JPT][hapmap]
rs532250	0.83[JPT][hapmap]
rs536203	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs537354	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs538386	0.87[JPT][hapmap]
rs540538	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs544947	0.85[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs556335	0.86[JPT][hapmap]
rs559052	0.86[JPT][hapmap]
rs562428	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs564961	0.91[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs565825	0.86[JPT][hapmap]
rs570442	0.86[JPT][hapmap]
rs577001	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs579789	1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs580011	0.85[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs585022	0.87[CEU][hapmap];0.83[CHB][hapmap];0.83[JPT][hapmap]
rs600739	0.81[JPT][hapmap]
rs628488	0.86[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs638407	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs652807	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[YRI][hapmap];0.83[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs652921	0.86[JPT][hapmap]
rs6570965	0.80[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs663625	0.87[JPT][hapmap]
rs909793	0.81[CHB][hapmap];0.95[JPT][hapmap]
rs9285519	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[YRI][hapmap];1.00[AFR][1000 genomes];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9322178	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9373589	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9373592	0.85[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs9377212	0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9377218	0.87[CHB][hapmap];0.95[JPT][hapmap]
rs9390676	0.86[JPT][hapmap]
rs9390677	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9404034	0.86[JPT][hapmap]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1024106	chr6:149622349-149745053	Weak transcription Enhancers Flanking Active TSS Strong transcription Genic enhancers 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 target site	10 gene(s)	inside rSNPs	diseases
2	nsv522875	chr6:149643709-149762537	Strong transcription Weak transcription Enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Genic enhancers Flanking Active TSS Active TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	4 gene(s)	inside rSNPs	diseases
3	nsv530444	chr6:149654540-149848997	Enhancers Weak transcription Flanking Active TSS Genic enhancers Strong transcription Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	7 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:98 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:149641200-149681400	Weak transcription	Fetal Stomach	stomach
2	chr6:149649400-149689400	Weak transcription	Fetal Brain Female	brain
3	chr6:149654000-149674200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
4	chr6:149654600-149668600	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
5	chr6:149656200-149670800	Weak transcription	Esophagus	oesophagus
6	chr6:149656800-149681400	Weak transcription	Psoas Muscle	Psoas
7	chr6:149656800-149682400	Weak transcription	Lung	lung
8	chr6:149656800-149694400	Weak transcription	Placenta	Placenta
9	chr6:149657800-149673800	Weak transcription	Thymus	Thymus
10	chr6:149657800-149683800	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
11	chr6:149657800-149691200	Weak transcription	Rectal Mucosa Donor 29	rectum
12	chr6:149658000-149673800	Weak transcription	Fetal Intestine Large	intestine
13	chr6:149658000-149673800	Weak transcription	Rectal Mucosa Donor 31	rectum
14	chr6:149658000-149674000	Weak transcription	H1 Cell Line	embryonic stem cell
15	chr6:149658000-149679000	Weak transcription	K562	blood
16	chr6:149658000-149680800	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
17	chr6:149658000-149681400	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
18	chr6:149658000-149695400	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
19	chr6:149658200-149691000	Weak transcription	NHDF-Ad	bronchial
20	chr6:149658800-149674000	Weak transcription	HepG2	liver
21	chr6:149658800-149692400	Weak transcription	Fetal Kidney	kidney
22	chr6:149659200-149685200	Weak transcription	Ovary	ovary
23	chr6:149659200-149691400	Weak transcription	Fetal Muscle Trunk	muscle
24	chr6:149659400-149679000	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
25	chr6:149659600-149679200	Weak transcription	NH-A	brain
26	chr6:149659600-149684200	Weak transcription	iPS-20b Cell Line	embryonic stem cell
27	chr6:149660200-149667000	Weak transcription	Stomach Mucosa	stomach
28	chr6:149660200-149669600	Weak transcription	Brain Angular Gyrus	brain
29	chr6:149660400-149669200	Weak transcription	Fetal Intestine Small	intestine
30	chr6:149660400-149682200	Weak transcription	Fetal Muscle Leg	muscle
31	chr6:149660400-149682400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
32	chr6:149660400-149685600	Weak transcription	Pancreas	Pancrea
33	chr6:149660400-149699200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
34	chr6:149661000-149669400	Weak transcription	Primary T cells fromperipheralblood	blood
35	chr6:149661000-149674200	Weak transcription	Left Ventricle	heart
36	chr6:149662200-149694800	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
37	chr6:149663000-149674000	Weak transcription	Osteobl	bone
38	chr6:149663400-149668400	Strong transcription	Dnd41	blood
39	chr6:149663400-149685400	Weak transcription	Fetal Lung	lung
40	chr6:149663600-149667200	Weak transcription	Fetal Heart	heart
41	chr6:149663600-149673800	Weak transcription	iPS-15b Cell Line	embryonic stem cell
42	chr6:149663600-149674200	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
43	chr6:149663800-149667600	Genic enhancers	Primary T helper cells PMA-I stimulated	--
44	chr6:149663800-149685400	Weak transcription	Brain Anterior Caudate	brain
45	chr6:149664000-149667400	Genic enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
46	chr6:149664000-149668000	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
47	chr6:149664000-149668200	Weak transcription	Rectal Smooth Muscle	rectum
48	chr6:149664000-149673600	Weak transcription	HUES48 Cell Line	embryonic stem cell
49	chr6:149664000-149673800	Weak transcription	HUES64 Cell Line	embryonic stem cell
50	chr6:149664000-149673800	Weak transcription	Adipose Nuclei	Adipose

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