Variant report

Variant	rs2555111
Chromosome Location	chr17:46648899-46648900
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	chr17:46648452..46650597-chr17:46655694..46657382,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000120093	Chromatin interaction
ENSG00000257178	Chromatin interaction

Extended variants
information (count: 26 )
Associated
traits (count: 6 )

rSNPs within LD-proxies of this variant (count:4)

rs_ID	r²[population]
rs11652860	0.84[AFR][1000 genomes]
rs2740760	0.84[TSI][hapmap];1.00[YRI][hapmap]
rs4793944	0.85[CEU][hapmap];0.90[CHB][hapmap];0.92[CHD][hapmap];0.84[JPT][hapmap];0.90[LWK][hapmap];0.82[TSI][hapmap];0.80[AFR][1000 genomes];0.81[ASN][1000 genomes]
rs999493	0.85[CHB][hapmap]

Variant overlapped rSNPs/rCNVs (count:22 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv833469	chr17:46491849-46709406	Bivalent Enhancer Flanking Bivalent TSS/Enh Weak transcription Enhancers Flanking Active TSS Bivalent/Poised TSS Active TSS Genic enhancers Transcr. at gene 5' and 3' Strong transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	349 gene(s)	inside rSNPs	diseases
2	esv3420538	chr17:46504944-46861553	Active TSS Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Weak transcription Enhancers Transcr. at gene 5' and 3' Genic enhancers Strong transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	369 gene(s)	inside rSNPs	diseases
3	nsv908577	chr17:46584900-46704536	Flanking Bivalent TSS/Enh Weak transcription Bivalent Enhancer Active TSS Flanking Active TSS Strong transcription Enhancers Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	343 gene(s)	inside rSNPs	diseases
4	nsv908578	chr17:46592413-46698710	Flanking Bivalent TSS/Enh Enhancers Active TSS Flanking Active TSS Bivalent Enhancer Weak transcription Bivalent/Poised TSS Transcr. at gene 5' and 3' Genic enhancers Strong transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	335 gene(s)	inside rSNPs	diseases
5	nsv908579	chr17:46592413-46727289	Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer Enhancers Active TSS Flanking Active TSS Weak transcription Transcr. at gene 5' and 3' Strong transcription Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	349 gene(s)	inside rSNPs	diseases
6	nsv532113	chr17:46598247-47588570	Genic enhancers Weak transcription Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Flanking Active TSS Enhancers Bivalent/Poised TSS Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	453 gene(s)	inside rSNPs	diseases
7	esv2758459	chr17:46602673-46836837	Active TSS Enhancers Weak transcription Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3' Strong transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	364 gene(s)	inside rSNPs	diseases
8	esv2758694	chr17:46602673-46836837	Active TSS Bivalent Enhancer Bivalent/Poised TSS Weak transcription Flanking Bivalent TSS/Enh Enhancers Genic enhancers Flanking Active TSS Transcr. at gene 5' and 3' Strong transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	364 gene(s)	inside rSNPs	diseases
9	nsv908580	chr17:46609103-46698710	Bivalent Enhancer Flanking Bivalent TSS/Enh Flanking Active TSS Genic enhancers Enhancers Bivalent/Poised TSS Active TSS Transcr. at gene 5' and 3' Weak transcription Strong transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	335 gene(s)	inside rSNPs	diseases
10	nsv908581	chr17:46610646-46735520	Bivalent Enhancer Enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Active TSS Flanking Active TSS Weak transcription Transcr. at gene 5' and 3' Genic enhancers Strong transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	349 gene(s)	inside rSNPs	diseases
11	nsv575480	chr17:46617019-46684929	Flanking Active TSS Flanking Bivalent TSS/Enh Active TSS Bivalent Enhancer Strong transcription Enhancers Weak transcription Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	322 gene(s)	inside rSNPs	diseases
12	nsv908582	chr17:46617019-46698710	Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Flanking Active TSS Bivalent/Poised TSS Enhancers Genic enhancers Weak transcription Strong transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	334 gene(s)	inside rSNPs	diseases
13	nsv908583	chr17:46617019-46704536	Bivalent Enhancer Flanking Bivalent TSS/Enh Flanking Active TSS Enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Weak transcription Strong transcription Genic enhancers Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	342 gene(s)	inside rSNPs	diseases
14	nsv833471	chr17:46617787-46783345	Bivalent Enhancer Flanking Bivalent TSS/Enh Active TSS Weak transcription Bivalent/Poised TSS Flanking Active TSS Enhancers Genic enhancers Transcr. at gene 5' and 3' Strong transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	356 gene(s)	inside rSNPs	diseases
15	nsv908584	chr17:46618926-46735520	Bivalent Enhancer Flanking Bivalent TSS/Enh Enhancers Active TSS Flanking Active TSS Weak transcription Bivalent/Poised TSS Transcr. at gene 5' and 3' Strong transcription Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	348 gene(s)	inside rSNPs	diseases
16	nsv457822	chr17:46620402-46698710	Flanking Active TSS Weak transcription Bivalent Enhancer Transcr. at gene 5' and 3' Enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Active TSS Strong transcription Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	334 gene(s)	inside rSNPs	diseases
17	nsv575481	chr17:46620402-46698710	Bivalent/Poised TSS Active TSS Flanking Active TSS Bivalent Enhancer Enhancers Flanking Bivalent TSS/Enh Weak transcription Transcr. at gene 5' and 3' Genic enhancers Strong transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	334 gene(s)	inside rSNPs	diseases
18	nsv457823	chr17:46620402-46704536	Enhancers Active TSS Bivalent Enhancer Flanking Active TSS Weak transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3' Strong transcription Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	342 gene(s)	inside rSNPs	diseases
19	nsv575482	chr17:46620402-46704536	Active TSS Flanking Bivalent TSS/Enh Weak transcription Enhancers Bivalent Enhancer Bivalent/Poised TSS Flanking Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	342 gene(s)	inside rSNPs	diseases
20	nsv457824	chr17:46625519-46693491	Bivalent Enhancer Flanking Bivalent TSS/Enh Active TSS Flanking Active TSS Enhancers Bivalent/Poised TSS Weak transcription Transcr. at gene 5' and 3' Genic enhancers Strong transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	332 gene(s)	inside rSNPs	diseases
21	nsv575483	chr17:46625519-46693491	Flanking Active TSS Bivalent Enhancer Active TSS Enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3' Strong transcription Weak transcription Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	332 gene(s)	inside rSNPs	diseases
22	esv1007307	chr17:46638901-46653131	Transcr. at gene 5' and 3' Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh Flanking Active TSS Weak transcription Enhancers Bivalent/Poised TSS Strong transcription Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases

mRNA abundance (count:6)

SNP	Gene	Cis/trans	Tissue	Source
rs2555111	KLHL11	cis	parietal	SCAN
rs2555111	PNPO	cis	parietal	SCAN
rs2555111	RUNDC3A	cis	parietal	SCAN
rs2555111	ACLY	cis	parietal	SCAN
rs2555111	RPRML	cis	parietal	SCAN
rs2555111	HOXB2	cis	Whole Blood	GTEx

Chromatin state (count:55 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr17:46635000-46654600	Weak transcription	Hela-S3	cervix
2	chr17:46641200-46649000	Bivalent Enhancer	ES-UCSF4 Cell Line	embryonic stem cell
3	chr17:46644600-46652200	Transcr. at gene 5' and 3'	IMR90 fetal lung fibroblasts Cell Line	lung
4	chr17:46644600-46654200	Weak transcription	Spleen	Spleen
5	chr17:46645200-46650200	Weak transcription	A549	lung
6	chr17:46645800-46649600	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
7	chr17:46645800-46649600	Bivalent Enhancer	Fetal Muscle Leg	muscle
8	chr17:46645800-46652200	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
9	chr17:46646400-46652000	Bivalent Enhancer	Fetal Adrenal Gland	Adrenal Gland
10	chr17:46646400-46654800	Transcr. at gene 5' and 3'	Fetal Stomach	stomach
11	chr17:46646600-46650200	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
12	chr17:46647200-46649600	Flanking Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
13	chr17:46647200-46649600	Flanking Active TSS	HUVEC	blood vessel
14	chr17:46647400-46649000	Flanking Bivalent TSS/Enh	HUES6 Cell Line	embryonic stem cell
15	chr17:46647400-46649200	Flanking Active TSS	Adipose Nuclei	Adipose
16	chr17:46647400-46649200	Bivalent/Poised TSS	Duodenum Smooth Muscle	Duodenum
17	chr17:46647400-46649200	Flanking Bivalent TSS/Enh	Fetal Intestine Small	intestine
18	chr17:46647400-46649600	Flanking Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
19	chr17:46647400-46653600	Bivalent/Poised TSS	iPS-15b Cell Line	embryonic stem cell
20	chr17:46647600-46649000	Bivalent Enhancer	H1 Cell Line	embryonic stem cell
21	chr17:46647600-46649000	Flanking Active TSS	Muscle Satellite Cultured Cells	--
22	chr17:46647600-46649000	Strong transcription	Foreskin Melanocyte Primary Cells skin01	Skin
23	chr17:46647600-46649000	Active TSS	Aorta	Aorta
24	chr17:46647600-46649400	Transcr. at gene 5' and 3'	Primary hematopoietic stem cells G-CSF-mobilized Male	--
25	chr17:46647600-46650000	Active TSS	Rectal Mucosa Donor 29	rectum
26	chr17:46647800-46649600	Transcr. at gene 5' and 3'	Primary hematopoietic stem cells G-CSF-mobilized Female	--
27	chr17:46648000-46649200	Bivalent Enhancer	Fetal Muscle Trunk	muscle
28	chr17:46648000-46649200	Transcr. at gene 5' and 3'	K562	blood
29	chr17:46648000-46651000	Transcr. at gene 5' and 3'	NHLF	lung
30	chr17:46648200-46649000	Active TSS	Colon Smooth Muscle	Colon
31	chr17:46648200-46649400	Transcr. at gene 5' and 3'	Fetal Kidney	kidney
32	chr17:46648200-46649800	Bivalent/Poised TSS	Fetal Intestine Large	intestine
33	chr17:46648200-46650200	Weak transcription	Sigmoid Colon	Sigmoid Colon
34	chr17:46648200-46650400	Weak transcription	Placenta Amnion	Placenta Amnion
35	chr17:46648400-46649400	Flanking Active TSS	Rectal Mucosa Donor 31	rectum
36	chr17:46648400-46650000	Flanking Bivalent TSS/Enh	Fetal Lung	lung
37	chr17:46648400-46651000	Genic enhancers	Primary hematopoietic stem cells short term culture	blood
38	chr17:46648400-46652400	Weak transcription	HSMMtube	muscle
39	chr17:46648600-46649000	Flanking Active TSS	Colonic Mucosa	Colon
40	chr17:46648600-46650800	Flanking Active TSS	Stomach Smooth Muscle	stomach
41	chr17:46648600-46650800	Bivalent Enhancer	NH-A	brain
42	chr17:46648600-46651200	Flanking Active TSS	Rectal Smooth Muscle	rectum
43	chr17:46648600-46651600	Bivalent Enhancer	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
44	chr17:46648600-46652800	Weak transcription	Primary hematopoietic stem cells	blood
45	chr17:46648800-46649000	Flanking Active TSS	HSMM	muscle
46	chr17:46648800-46649200	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
47	chr17:46648800-46650000	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
48	chr17:46648800-46650200	Weak transcription	Primary T cells fromperipheralblood	blood
49	chr17:46648800-46650200	Weak transcription	Esophagus	oesophagus
50	chr17:46648800-46650600	Weak transcription	Lung	lung

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