Variant report

Variant	rs9897954
Chromosome Location	chr17:18243638-18243639
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	chr17:18229628..18231978-chr17:18243132..18244767,2	MCF-7	breast:

Extended variants
information (count: 40 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:25)

rs_ID	r²[population]
rs16961060	1.00[YRI][hapmap];0.82[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs2125154	1.00[CEU][hapmap];1.00[MEX][hapmap]
rs28523978	0.82[ASW][hapmap];1.00[MEX][hapmap];0.91[YRI][hapmap];0.83[AMR][1000 genomes]
rs28630807	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs4924848	1.00[CEU][hapmap]
rs4925170	1.00[CEU][hapmap]
rs4925173	1.00[CEU][hapmap]
rs4925174	1.00[ASW][hapmap];1.00[CEU][hapmap];0.86[LWK][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs4925180	1.00[CEU][hapmap];0.84[YRI][hapmap]
rs6502648	1.00[CEU][hapmap];1.00[MEX][hapmap]
rs7215491	1.00[CEU][hapmap]
rs73980863	0.83[AMR][1000 genomes]
rs8080285	1.00[CEU][hapmap];1.00[MEX][hapmap]
rs9893653	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs9897239	1.00[YRI][hapmap];0.84[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs9898548	0.82[ASW][hapmap];0.93[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[YRI][hapmap];0.87[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs9902011	1.00[CEU][hapmap]
rs9902498	1.00[ASW][hapmap];1.00[CEU][hapmap];0.87[LWK][hapmap];1.00[MEX][hapmap]
rs9903762	1.00[MEX][hapmap]
rs9904323	1.00[CEU][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs9907277	1.00[AMR][1000 genomes]
rs9907337	0.89[AFR][1000 genomes]
rs9909732	0.82[ASW][hapmap];0.91[YRI][hapmap];1.00[AMR][1000 genomes]
rs9911649	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs9941377	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:15 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv916653	chr17:17651916-18454952	Enhancers Strong transcription Active TSS Genic enhancers Flanking Active TSS Weak transcription ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	144 gene(s)	inside rSNPs	diseases
2	nsv1061162	chr17:17978838-18259234	Flanking Active TSS Weak transcription Genic enhancers Active TSS Enhancers Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	47 gene(s)	inside rSNPs	diseases
3	nsv492305	chr17:17980441-18424702	Flanking Active TSS Enhancers Strong transcription Transcr. at gene 5' and 3' Weak transcription Active TSS Genic enhancers ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	68 gene(s)	inside rSNPs	diseases
4	nsv833386	chr17:18170261-18332726	Strong transcription Weak transcription Enhancers Genic enhancers Active TSS Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	30 gene(s)	inside rSNPs	diseases
5	nsv1057081	chr17:18171516-18256347	Active TSS Strong transcription Weak transcription ZNF genes & repeats Enhancers Genic enhancers Flanking Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	15 gene(s)	inside rSNPs	diseases
6	nsv543247	chr17:18171516-18256347	Weak transcription Active TSS Genic enhancers Strong transcription Enhancers Flanking Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	15 gene(s)	inside rSNPs	diseases
7	nsv1062368	chr17:18180747-18259234	Weak transcription Strong transcription Genic enhancers Transcr. at gene 5' and 3' Flanking Active TSS Active TSS Enhancers ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	14 gene(s)	inside rSNPs	diseases
8	nsv833387	chr17:18200081-18378155	Active TSS Genic enhancers Weak transcription Strong transcription Transcr. at gene 5' and 3' Enhancers Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	34 gene(s)	inside rSNPs	diseases
9	esv1806346	chr17:18200081-18446384	Active TSS Weak transcription Strong transcription Flanking Active TSS Transcr. at gene 5' and 3' Enhancers Genic enhancers Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	39 gene(s)	inside rSNPs	diseases
10	esv1812661	chr17:18200081-18446384	Genic enhancers Active TSS Transcr. at gene 5' and 3' Strong transcription Weak transcription Enhancers Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	39 gene(s)	inside rSNPs	diseases
11	nsv428333	chr17:18200081-18446384	Flanking Active TSS Enhancers Weak transcription Strong transcription Active TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	39 gene(s)	inside rSNPs	diseases
12	nsv427992	chr17:18200081-19192047	Strong transcription Genic enhancers Enhancers Flanking Active TSS Weak transcription Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	100 gene(s)	inside rSNPs	diseases
13	esv2758443	chr17:18234525-18446384	Weak transcription Strong transcription Flanking Active TSS Enhancers Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA	30 gene(s)	inside rSNPs	diseases
14	esv2758677	chr17:18234525-18446384	Flanking Active TSS Weak transcription Enhancers Strong transcription Bivalent/Poised TSS Active TSS Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	30 gene(s)	inside rSNPs	diseases
15	esv1829832	chr17:18235992-18405148	Active TSS Flanking Active TSS Enhancers Weak transcription Strong transcription Bivalent Enhancer Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA	26 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:124 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr17:18219400-18266000	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
2	chr17:18222400-18266200	Weak transcription	Small Intestine	intestine
3	chr17:18223600-18265400	Strong transcription	Fetal Stomach	stomach
4	chr17:18223800-18253600	Strong transcription	Thymus	Thymus
5	chr17:18224200-18253000	Weak transcription	Fetal Heart	heart
6	chr17:18224400-18249400	Weak transcription	K562	blood
7	chr17:18227600-18243800	Weak transcription	HUVEC	blood vessel
8	chr17:18228200-18265800	Weak transcription	Fetal Brain Male	brain
9	chr17:18228600-18251400	Weak transcription	HSMMtube	muscle
10	chr17:18228600-18266000	Weak transcription	HSMM	muscle
11	chr17:18228800-18249400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
12	chr17:18229000-18266000	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
13	chr17:18230000-18260000	Weak transcription	Muscle Satellite Cultured Cells	--
14	chr17:18230200-18260200	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
15	chr17:18230200-18265600	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
16	chr17:18231000-18266000	Weak transcription	Psoas Muscle	Psoas
17	chr17:18231200-18260600	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
18	chr17:18234600-18243800	Weak transcription	Fetal Kidney	kidney
19	chr17:18234600-18249400	Weak transcription	Osteobl	bone
20	chr17:18235400-18256600	Weak transcription	Primary T helper naive cells from peripheral blood	blood
21	chr17:18235800-18245800	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
22	chr17:18235800-18265400	Weak transcription	Primary T killer memory cells from peripheral blood	blood
23	chr17:18236400-18250000	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
24	chr17:18236600-18250400	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
25	chr17:18237400-18244600	Strong transcription	Foreskin Fibroblast Primary Cells skin01	Skin
26	chr17:18237600-18246200	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
27	chr17:18237600-18246200	Strong transcription	Lung	lung
28	chr17:18237600-18260200	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
29	chr17:18238000-18246600	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
30	chr17:18239000-18244000	Weak transcription	NHLF	lung
31	chr17:18239000-18249800	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
32	chr17:18239000-18250200	Weak transcription	NHDF-Ad	bronchial
33	chr17:18239400-18247200	Weak transcription	Rectal Smooth Muscle	rectum
34	chr17:18239400-18248200	Weak transcription	Right Ventricle	heart
35	chr17:18239800-18249600	Weak transcription	Placenta Amnion	Placenta Amnion
36	chr17:18240000-18246200	Strong transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
37	chr17:18241200-18246000	Strong transcription	Spleen	Spleen
38	chr17:18242000-18244000	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
39	chr17:18242000-18244800	Strong transcription	Fetal Intestine Large	intestine
40	chr17:18242200-18260400	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
41	chr17:18242400-18243800	ZNF genes & repeats	HUES64 Cell Line	embryonic stem cell
42	chr17:18242400-18244000	ZNF genes & repeats	HUES48 Cell Line	embryonic stem cell
43	chr17:18242400-18244200	Strong transcription	Fetal Brain Female	brain
44	chr17:18242400-18244200	ZNF genes & repeats	Fetal Intestine Small	intestine
45	chr17:18242400-18244400	ZNF genes & repeats	H9 Derived Neuron Cultured Cells	ES cell derived
46	chr17:18242400-18244400	ZNF genes & repeats	HUES6 Cell Line	embryonic stem cell
47	chr17:18242400-18244400	Strong transcription	iPS-15b Cell Line	embryonic stem cell
48	chr17:18242400-18244400	Strong transcription	Primary T cells fromperipheralblood	blood
49	chr17:18242400-18244400	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
50	chr17:18242400-18244400	Strong transcription	Brain Germinal Matrix	brain

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