Variant report

Variant	rs16961112
Chromosome Location	chr17:18210151-18210152
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr17:18161909..18165526-chr17:18209408..18212171,3	MCF-7	breast:
2	chr17:18162871..18165268-chr17:18208056..18210567,2	MCF-7	breast:
3	chr17:18207672..18211933-chr17:18214098..18218432,6	MCF-7	breast:

Variant related genes	Relation type
ENSG00000177731	Chromatin interaction
ENSG00000177302	Chromatin interaction
ENSG00000228000	Chromatin interaction
ENSG00000177427	Chromatin interaction
ENSG00000237382	Chromatin interaction

Extended variants
information (count: 51 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:38)

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];0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs16961060	1.00[CEU][hapmap]
rs2125154	0.87[YRI][hapmap];0.90[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs28523978	1.00[CEU][hapmap]
rs28671051	0.93[YRI][hapmap];0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4924848	0.82[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs4925170	1.00[CEU][hapmap];0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs4925173	1.00[YRI][hapmap];0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs4925175	0.89[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	1.00[YRI][hapmap];0.85[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];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs8080285	1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs8082574	1.00[ASN][1000 genomes]
rs9893254	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9894005	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]
rs9894616	1.00[CEU][hapmap];1.00[YRI][hapmap];0.97[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];0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs9902498	0.86[YRI][hapmap];0.89[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs9903235	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs9903762	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]
rs9907337	1.00[CEU][hapmap]
rs9913916	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9915858	0.80[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:13 , 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

No data

Chromatin state (count:126 , 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	chr17:18173000-18213800	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
3	chr17:18184800-18217000	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
4	chr17:18194600-18215600	Weak transcription	Fetal Heart	heart
5	chr17:18196800-18217000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
6	chr17:18200600-18211400	Strong transcription	Lung	lung
7	chr17:18201800-18216200	Strong transcription	H1 Cell Line	embryonic stem cell
8	chr17:18202000-18210600	Strong transcription	H9 Cell Line	embryonic stem cell
9	chr17:18202000-18212600	Strong transcription	iPS-20b Cell Line	embryonic stem cell
10	chr17:18202000-18213000	Strong transcription	Placenta	Placenta
11	chr17:18202200-18216600	Strong transcription	HUES64 Cell Line	embryonic stem cell
12	chr17:18202400-18210600	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
13	chr17:18202400-18210800	Strong transcription	Brain Germinal Matrix	brain
14	chr17:18202400-18211200	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
15	chr17:18202400-18211200	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
16	chr17:18202400-18211200	Strong transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
17	chr17:18202400-18211200	Strong transcription	Ovary	ovary
18	chr17:18202400-18211200	Strong transcription	Placenta Amnion	Placenta Amnion
19	chr17:18202400-18211200	Strong transcription	Sigmoid Colon	Sigmoid Colon
20	chr17:18202400-18211200	Strong transcription	Stomach Smooth Muscle	stomach
21	chr17:18202400-18211400	Strong transcription	Breast Myoepithelial Primary Cells	Breast
22	chr17:18202400-18211400	Strong transcription	Fetal Muscle Leg	muscle
23	chr17:18202400-18211400	Strong transcription	Left Ventricle	heart
24	chr17:18202400-18211600	Strong transcription	Fetal Intestine Small	intestine
25	chr17:18202400-18211600	Strong transcription	Thymus	Thymus
26	chr17:18202400-18211600	Strong transcription	Osteobl	bone
27	chr17:18202400-18211800	Strong transcription	Primary T helper naive cells fromperipheralblood	blood
28	chr17:18202400-18211800	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
29	chr17:18202400-18212000	Strong transcription	Fetal Intestine Large	intestine
30	chr17:18202400-18212200	Strong transcription	Liver	Liver
31	chr17:18202400-18212200	Strong transcription	Rectal Mucosa Donor 29	rectum
32	chr17:18202400-18212400	Strong transcription	Primary T helper cells PMA-I stimulated	--
33	chr17:18202400-18212400	Strong transcription	A549	lung
34	chr17:18202400-18212600	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
35	chr17:18202400-18212600	Strong transcription	Duodenum Mucosa	Duodenum
36	chr17:18202400-18212800	Strong transcription	Primary T cells fromperipheralblood	blood
37	chr17:18202400-18213600	Strong transcription	Dnd41	blood
38	chr17:18202400-18214200	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
39	chr17:18202400-18215400	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
40	chr17:18202400-18215600	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
41	chr17:18202400-18215600	Strong transcription	Fetal Thymus	thymus
42	chr17:18202400-18216000	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
43	chr17:18202400-18216000	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
44	chr17:18202400-18216000	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
45	chr17:18202400-18216200	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
46	chr17:18202400-18216400	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
47	chr17:18202400-18216400	Strong transcription	Fetal Stomach	stomach
48	chr17:18202400-18216600	Strong transcription	HUES48 Cell Line	embryonic stem cell
49	chr17:18202400-18216600	Strong transcription	HUES6 Cell Line	embryonic stem cell
50	chr17:18202400-18216600	Strong transcription	iPS-18 Cell Line	embryonic stem cell

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