Variant report

Variant	rs2954775
Chromosome Location	chr17:15352224-15352225
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr17:15349124..15352004-chr17:15352182..15355070,2	K562	blood:
2	chr17:15350797..15353355-chr17:15356720..15358516,2	MCF-7	breast:

Extended variants
information (count: 55 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:46)

rs_ID	r²[population]
rs1019092	1.00[CEU][hapmap];0.91[CHB][hapmap];0.95[JPT][hapmap];0.84[AMR][1000 genomes];0.97[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs10432020	0.97[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs1548679	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1548680	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17842195	1.00[CEU][hapmap];0.91[CHB][hapmap];0.91[JPT][hapmap];0.97[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2108757	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.94[MEX][hapmap];1.00[TSI][hapmap];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2190914	0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2323734	0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2875140	1.00[CEU][hapmap];0.91[CHB][hapmap];0.98[CHD][hapmap];0.97[GIH][hapmap];0.95[JPT][hapmap];0.89[MEX][hapmap];1.00[TSI][hapmap];0.86[AMR][1000 genomes];0.97[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2906973	1.00[CEU][hapmap];0.85[JPT][hapmap];0.97[EUR][1000 genomes]
rs2906977	0.89[CHB][hapmap];0.94[JPT][hapmap];0.87[AMR][1000 genomes];0.97[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2906978	0.91[CHB][hapmap];0.84[ASN][1000 genomes]
rs2906979	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2906980	1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2906981	0.93[ASN][1000 genomes]
rs2906982	1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2906983	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2906984	0.81[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2906985	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2954749	0.81[AMR][1000 genomes]
rs2954750	0.81[AMR][1000 genomes]
rs2954753	0.84[AMR][1000 genomes]
rs2954759	0.93[GIH][hapmap];0.91[JPT][hapmap]
rs2954760	0.90[GIH][hapmap];0.80[MEX][hapmap]
rs2954761	0.90[JPT][hapmap]
rs2954762	0.90[GIH][hapmap];0.85[MEX][hapmap]
rs2954765	0.86[ASN][1000 genomes]
rs2954767	0.96[AMR][1000 genomes]
rs2954768	0.93[AMR][1000 genomes]
rs2954770	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2954771	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2954772	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2954773	0.91[AFR][1000 genomes];0.83[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2954774	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2954776	0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2954777	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2954778	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.94[MEX][hapmap];1.00[TSI][hapmap];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2954779	1.00[CEU][hapmap];0.91[CHB][hapmap];0.98[CHD][hapmap];0.97[GIH][hapmap];0.95[JPT][hapmap];0.85[MEX][hapmap];1.00[TSI][hapmap];0.85[AMR][1000 genomes];0.94[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs56055931	0.97[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs6502450	0.96[AMR][1000 genomes]
rs728854	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[TSI][hapmap];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs729355	1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs729356	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs729357	0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs887033	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs887034	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:9 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv492304	chr17:15043353-15611753	Active TSS Enhancers Weak transcription Flanking Active TSS Bivalent/Poised TSS Strong transcription Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	58 gene(s)	inside rSNPs	diseases
2	nsv916652	chr17:15093600-15856310	Strong transcription Weak transcription Enhancers Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	73 gene(s)	inside rSNPs	diseases
3	nsv427990	chr17:15154329-15434020	Flanking Active TSS Enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Strong transcription Active TSS Weak transcription Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	31 gene(s)	inside rSNPs	diseases
4	nsv907703	chr17:15199907-15370701	Enhancers Flanking Active TSS Weak transcription Active TSS Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Genic enhancers Strong transcription Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	10 gene(s)	inside rSNPs	diseases
5	nsv949172	chr17:15206970-15416808	Active TSS Flanking Active TSS Enhancers Weak transcription Strong transcription Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	14 gene(s)	inside rSNPs	diseases
6	nsv1055677	chr17:15294011-15561130	Enhancers Flanking Active TSS Weak transcription Genic enhancers Active TSS Strong transcription Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	34 gene(s)	inside rSNPs	diseases
7	nsv1059056	chr17:15294011-15856861	Strong transcription Weak transcription Active TSS Enhancers Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	55 gene(s)	inside rSNPs	diseases
8	nsv1058286	chr17:15315763-15561130	Strong transcription Enhancers Weak transcription Flanking Active TSS Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	33 gene(s)	inside rSNPs	diseases
9	nsv543213	chr17:15315763-15561130	Weak transcription Enhancers Genic enhancers Strong transcription Active TSS Flanking Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	33 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	chr17:15333600-15361000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
2	chr17:15338400-15362200	Weak transcription	HUES48 Cell Line	embryonic stem cell
3	chr17:15339400-15354800	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
4	chr17:15339400-15358800	Weak transcription	Pancreatic Islets	Pancreatic Islet
5	chr17:15339600-15367000	Weak transcription	A549	lung
6	chr17:15340000-15355400	Weak transcription	Hela-S3	cervix
7	chr17:15340000-15355800	Weak transcription	iPS-18 Cell Line	embryonic stem cell
8	chr17:15340000-15357400	Weak transcription	Rectal Mucosa Donor 29	rectum
9	chr17:15340200-15354800	Weak transcription	Osteobl	bone
10	chr17:15340200-15355600	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
11	chr17:15340400-15355600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
12	chr17:15340400-15356000	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
13	chr17:15340400-15359000	Weak transcription	Colon Smooth Muscle	Colon
14	chr17:15340600-15359800	Weak transcription	Duodenum Smooth Muscle	Duodenum
15	chr17:15340600-15360200	Weak transcription	Primary T killer memory cells from peripheral blood	blood
16	chr17:15340600-15360200	Weak transcription	Fetal Thymus	thymus
17	chr17:15340600-15366200	Weak transcription	Gastric	stomach
18	chr17:15340600-15366800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
19	chr17:15340600-15399600	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
20	chr17:15341200-15355600	Weak transcription	iPS-20b Cell Line	embryonic stem cell
21	chr17:15341200-15356200	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
22	chr17:15341200-15359800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
23	chr17:15341400-15355400	Weak transcription	HUES64 Cell Line	embryonic stem cell
24	chr17:15341400-15356000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
25	chr17:15341400-15359600	Weak transcription	Stomach Smooth Muscle	stomach
26	chr17:15341400-15360200	Weak transcription	Aorta	Aorta
27	chr17:15341400-15360800	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
28	chr17:15341400-15366800	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
29	chr17:15341400-15366800	Weak transcription	Esophagus	oesophagus
30	chr17:15341400-15368400	Weak transcription	H9 Cell Line	embryonic stem cell
31	chr17:15341400-15375800	Weak transcription	H1 Cell Line	embryonic stem cell
32	chr17:15341600-15357200	Weak transcription	Sigmoid Colon	Sigmoid Colon
33	chr17:15341800-15354800	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
34	chr17:15343000-15353600	Weak transcription	HepG2	liver
35	chr17:15343000-15356600	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
36	chr17:15346400-15355400	Weak transcription	Brain Germinal Matrix	brain
37	chr17:15346400-15355800	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
38	chr17:15346400-15357600	Weak transcription	Fetal Brain Male	brain
39	chr17:15346400-15357600	Weak transcription	Fetal Brain Female	brain
40	chr17:15346600-15355000	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
41	chr17:15347000-15352400	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
42	chr17:15347000-15358600	Weak transcription	Placenta	Placenta
43	chr17:15347200-15352400	Enhancers	HUVEC	blood vessel
44	chr17:15348000-15352400	Enhancers	Adipose Nuclei	Adipose
45	chr17:15348400-15355400	Weak transcription	Primary T cells fromperipheralblood	blood
46	chr17:15348400-15355800	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
47	chr17:15348400-15356800	Weak transcription	Ovary	ovary
48	chr17:15348400-15360400	Weak transcription	Primary hematopoietic stem cells short term culture	blood
49	chr17:15348400-15361400	Weak transcription	Primary T helper cells PMA-I stimulated	--
50	chr17:15348600-15355400	Weak transcription	Primary T cells from cord blood	blood

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