Variant report

Variant	rs9894005
Chromosome Location	chr17:18216131-18216132
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr17:18204042..18206073-chr17:18215565..18218215,2	MCF-7	breast:
2	chr17:18207672..18211933-chr17:18214098..18218432,6	MCF-7	breast:
3	chr17:18185665..18188160-chr17:18215584..18219242,3	MCF-7	breast:
4	chr17:18159194..18166260-chr17:18215929..18222740,16	MCF-7	breast:
5	chr17:18156705..18166530-chr17:18215131..18220177,19	MCF-7	breast:

Variant related genes	Relation type
ENSG00000177427	Chromatin interaction
ENSG00000177731	Chromatin interaction
ENSG00000177302	Chromatin interaction

Extended variants
information (count: 53 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:39)

rs_ID	r²[population]
rs11540888	1.00[ASN][1000 genomes]
rs11870681	1.00[ASN][1000 genomes]
rs16961058	1.00[CEU][hapmap];1.00[YRI][hapmap];0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs16961060	1.00[CEU][hapmap]
rs16961112	1.00[CEU][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2125154	0.86[ASW][hapmap];1.00[GIH][hapmap];0.88[YRI][hapmap];0.81[AFR][1000 genomes];0.90[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs28523978	1.00[CEU][hapmap]
rs28671051	1.00[ASW][hapmap];1.00[GIH][hapmap];1.00[LWK][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];0.94[YRI][hapmap];0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4924848	0.84[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs4925170	1.00[CEU][hapmap];0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs4925173	1.00[YRI][hapmap];0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs4925175	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs4925180	0.89[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs55973639	1.00[ASN][1000 genomes]
rs61753153	1.00[ASN][1000 genomes]
rs6502648	0.86[ASW][hapmap];1.00[GIH][hapmap];0.83[LWK][hapmap];1.00[YRI][hapmap];0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs7215491	1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs7222589	1.00[ASN][1000 genomes]
rs73980813	1.00[ASN][1000 genomes]
rs73980819	1.00[ASN][1000 genomes]
rs73980849	1.00[ASN][1000 genomes]
rs73980856	1.00[ASN][1000 genomes]
rs73980857	1.00[ASN][1000 genomes]
rs8074858	1.00[CEU][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs8075915	1.00[CHB][hapmap]
rs8080285	1.00[GIH][hapmap];1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs8082574	1.00[ASN][1000 genomes]
rs9893254	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9894616	1.00[CEU][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs9897239	1.00[CEU][hapmap]
rs9898548	1.00[CEU][hapmap]
rs9900382	1.00[CEU][hapmap]
rs9902011	1.00[YRI][hapmap];0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs9902498	1.00[GIH][hapmap];0.81[YRI][hapmap];0.89[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs9903235	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs9903762	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[LWK][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9907337	1.00[CEU][hapmap];1.00[CHB][hapmap]
rs9913916	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9915858	0.83[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:14 , 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	nsv533142	chr17:17691726-18236686	Active TSS Flanking Active TSS Enhancers Strong transcription Weak transcription Genic enhancers Transcr. at gene 5' and 3' 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	116 gene(s)	inside rSNPs	diseases
3	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
4	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
5	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
6	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
7	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
8	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
9	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
10	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
11	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
12	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
13	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
14	nsv962274	chr17:18215705-18216580	Active TSS Flanking Active TSS Weak transcription Enhancers Transcr. at gene 5' and 3' Strong transcription Genic enhancers ZNF genes & repeats	TF binding region Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:127 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr17:18172200-18217400	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
2	chr17:18184800-18217000	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
3	chr17:18196800-18217000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
4	chr17:18201800-18216200	Strong transcription	H1 Cell Line	embryonic stem cell
5	chr17:18202200-18216600	Strong transcription	HUES64 Cell Line	embryonic stem cell
6	chr17:18202400-18216200	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
7	chr17:18202400-18216400	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
8	chr17:18202400-18216400	Strong transcription	Fetal Stomach	stomach
9	chr17:18202400-18216600	Strong transcription	HUES48 Cell Line	embryonic stem cell
10	chr17:18202400-18216600	Strong transcription	HUES6 Cell Line	embryonic stem cell
11	chr17:18202400-18216600	Strong transcription	iPS-18 Cell Line	embryonic stem cell
12	chr17:18202400-18216600	Strong transcription	Fetal Muscle Trunk	muscle
13	chr17:18203200-18216800	Weak transcription	Pancreatic Islets	Pancreatic Islet
14	chr17:18206800-18217000	Weak transcription	Stomach Mucosa	stomach
15	chr17:18208800-18217000	Weak transcription	Right Ventricle	heart
16	chr17:18210200-18217000	Weak transcription	Psoas Muscle	Psoas
17	chr17:18210600-18216400	Weak transcription	Small Intestine	intestine
18	chr17:18210600-18216600	Weak transcription	Rectal Mucosa Donor 31	rectum
19	chr17:18210600-18217200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
20	chr17:18211200-18216200	Weak transcription	Skeletal Muscle Male	skeletal muscle
21	chr17:18211200-18216400	Weak transcription	Primary B cells from cord blood	blood
22	chr17:18211200-18216800	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
23	chr17:18211200-18217000	Weak transcription	Ovary	ovary
24	chr17:18211200-18217200	Weak transcription	Aorta	Aorta
25	chr17:18212000-18216200	Weak transcription	HUVEC	blood vessel
26	chr17:18212200-18216400	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
27	chr17:18212600-18216600	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
28	chr17:18213600-18216200	Strong transcription	iPS-15b Cell Line	embryonic stem cell
29	chr17:18213800-18216400	Genic enhancers	Monocytes-CD14+_RO01746	blood
30	chr17:18214600-18216400	Strong transcription	Fetal Intestine Small	intestine
31	chr17:18214800-18216200	Strong transcription	Muscle Satellite Cultured Cells	--
32	chr17:18214800-18216400	Strong transcription	NHEK	skin
33	chr17:18214800-18216600	Strong transcription	Brain Anterior Caudate	brain
34	chr17:18215000-18216200	Strong transcription	H9 Cell Line	embryonic stem cell
35	chr17:18215000-18216200	Genic enhancers	Spleen	Spleen
36	chr17:18215000-18216400	Genic enhancers	Primary neutrophils fromperipheralblood	blood
37	chr17:18215000-18216400	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
38	chr17:18215000-18216600	Genic enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
39	chr17:18215200-18216200	Genic enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
40	chr17:18215200-18216200	Genic enhancers	HepG2	liver
41	chr17:18215200-18216400	Genic enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
42	chr17:18215200-18216600	Transcr. at gene 5' and 3'	Hela-S3	cervix
43	chr17:18215200-18216800	Transcr. at gene 5' and 3'	Foreskin Fibroblast Primary Cells skin01	Skin
44	chr17:18215200-18217000	Strong transcription	ES-I3 Cell Line	embryonic stem cell
45	chr17:18215400-18216200	Strong transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
46	chr17:18215400-18216200	Genic enhancers	Primary T cells from cord blood	blood
47	chr17:18215400-18216200	Genic enhancers	Adipose Nuclei	Adipose
48	chr17:18215400-18216400	Genic enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
49	chr17:18215400-18216400	Genic enhancers	Esophagus	oesophagus
50	chr17:18215400-18216400	Genic enhancers	Fetal Brain Male	brain

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