Variant report

Variant	rs494954
Chromosome Location	chr6:143127078-143127079
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr6:143125289..143128187-chr6:143130624..143132976,2	MCF-7	breast:
2	chr6:143125446..143128291-chr6:143134651..143136662,2	K562	blood:

Extended variants
information (count: 39 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:36)

rs_ID	r²[population]
rs11155264	0.86[ASN][1000 genomes]
rs197494	0.87[JPT][hapmap];0.81[YRI][hapmap]
rs197496	0.87[JPT][hapmap];0.87[YRI][hapmap]
rs197497	0.87[JPT][hapmap];0.82[YRI][hapmap]
rs197511	0.86[JPT][hapmap];0.86[YRI][hapmap]
rs2328388	0.85[ASN][1000 genomes]
rs472185	0.91[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs472288	0.90[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs473497	0.96[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs478768	0.91[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs487754	0.99[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs491414	0.94[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs491953	0.99[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs492156	0.92[ASN][1000 genomes]
rs494038	0.93[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs507404	0.91[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs511565	0.82[ASN][1000 genomes]
rs512808	0.90[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs516300	0.86[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.89[AFR][1000 genomes];0.94[ASN][1000 genomes]
rs519874	0.93[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs525928	0.99[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs527870	0.90[AFR][1000 genomes];0.81[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs533117	0.87[ASN][1000 genomes]
rs533173	0.91[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs541274	0.99[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs550149	0.96[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs552004	0.85[AFR][1000 genomes];0.92[ASN][1000 genomes]
rs552928	0.93[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs557004	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs559818	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs561642	0.96[ASN][1000 genomes]
rs576657	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.99[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs576760	0.86[ASN][1000 genomes]
rs9376708	0.82[ASN][1000 genomes]
rs9386009	0.82[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs9403407	0.81[AMR][1000 genomes];0.93[EUR][1000 genomes];0.92[ASN][1000 genomes]

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	nsv949088	chr6:142561402-143128849	Weak transcription Enhancers Strong transcription Genic enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Active TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	16 gene(s)	inside rSNPs	diseases
2	nsv830829	chr6:143058408-143218077	Active TSS Weak transcription Enhancers Flanking Active TSS Genic enhancers Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	4 gene(s)	inside rSNPs	diseases
3	nsv1019558	chr6:143121577-143154554	Enhancers Active TSS Weak transcription Genic enhancers Strong transcription Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3'	Chromatin interactive region	1 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:72 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:143096200-143140800	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
2	chr6:143105800-143140400	Weak transcription	Primary hematopoietic stem cells short term culture	blood
3	chr6:143106000-143128200	Weak transcription	Primary hematopoietic stem cells	blood
4	chr6:143106000-143140400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
5	chr6:143112200-143139400	Weak transcription	HepG2	liver
6	chr6:143113200-143140400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
7	chr6:143114200-143140800	Weak transcription	Fetal Muscle Leg	muscle
8	chr6:143116000-143139600	Weak transcription	Small Intestine	intestine
9	chr6:143116200-143132200	Weak transcription	Fetal Brain Female	brain
10	chr6:143117000-143129400	Enhancers	Primary T helper naive cells fromperipheralblood	blood
11	chr6:143117000-143140800	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
12	chr6:143118000-143132200	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
13	chr6:143118000-143137600	Weak transcription	Right Atrium	heart
14	chr6:143119600-143129600	Weak transcription	Brain Inferior Temporal Lobe	brain
15	chr6:143119800-143130000	Weak transcription	Brain Substantia Nigra	brain
16	chr6:143121000-143133000	Weak transcription	Pancreas	Pancrea
17	chr6:143121200-143138400	Weak transcription	Primary B cells from peripheral blood	blood
18	chr6:143121600-143129400	Weak transcription	Brain Anterior Caudate	brain
19	chr6:143123400-143128400	Enhancers	Primary T helper cells fromperipheralblood	blood
20	chr6:143123400-143132000	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
21	chr6:143123400-143140600	Weak transcription	HSMM	muscle
22	chr6:143123400-143144000	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
23	chr6:143123600-143129400	Weak transcription	HSMMtube	muscle
24	chr6:143123600-143130200	Weak transcription	Brain Cingulate Gyrus	brain
25	chr6:143123600-143132000	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
26	chr6:143123600-143132000	Weak transcription	Fetal Brain Male	brain
27	chr6:143123600-143132200	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
28	chr6:143123600-143139400	Weak transcription	Fetal Intestine Small	intestine
29	chr6:143123800-143132000	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
30	chr6:143123800-143132400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
31	chr6:143124000-143132000	Weak transcription	NHDF-Ad	bronchial
32	chr6:143124000-143132200	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
33	chr6:143124000-143137400	Weak transcription	NH-A	brain
34	chr6:143124000-143140600	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
35	chr6:143124000-143140800	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
36	chr6:143124200-143132000	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
37	chr6:143124200-143132000	Weak transcription	NHLF	lung
38	chr6:143124200-143137400	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
39	chr6:143124200-143140600	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
40	chr6:143124400-143128200	Weak transcription	Osteobl	bone
41	chr6:143124400-143140800	Weak transcription	NHEK	skin
42	chr6:143124600-143137200	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
43	chr6:143124800-143127200	Enhancers	Psoas Muscle	Psoas
44	chr6:143124800-143129200	Enhancers	Primary T regulatory cells fromperipheralblood	blood
45	chr6:143124800-143129600	Enhancers	Primary T helper naive cells from peripheral blood	blood
46	chr6:143125000-143130200	Weak transcription	Brain Angular Gyrus	brain
47	chr6:143125000-143130600	Strong transcription	Primary B cells from cord blood	blood
48	chr6:143125000-143131600	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
49	chr6:143125000-143141000	Weak transcription	Breast Myoepithelial Primary Cells	Breast
50	chr6:143125200-143130200	Genic enhancers	Primary T helper cells PMA-I stimulated	--

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