Variant report

Variant	rs11655588
Chromosome Location	chr17:18107451-18107452
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr17:18085712..18088140-chr17:18106871..18109334,2	MCF-7	breast:
2	chr17:18088851..18092330-chr17:18106978..18109728,3	K562	blood:
3	chr17:18086176..18087752-chr17:18106920..18108922,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000091542	Chromatin interaction
ENSG00000266677	Chromatin interaction

Extended variants
information (count: 90 )
Associated
traits (count: 9 )

rSNPs within LD-proxies of this variant (count:79)

rs_ID	r²[population]
rs10048161	0.94[CEU][hapmap];1.00[CHB][hapmap];0.87[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10451244	0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11078411	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[GIH][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.91[AFR][1000 genomes];0.94[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11078412	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[GIH][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11652964	1.00[CHB][hapmap];0.85[EUR][1000 genomes]
rs11653988	0.91[AFR][1000 genomes];0.94[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11654146	0.89[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11654177	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11654741	0.90[AFR][1000 genomes];0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11655731	1.00[CHB][hapmap];0.90[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs11655797	0.99[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11656035	0.87[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs11657194	0.83[AFR][1000 genomes];0.94[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs11658477	0.94[CEU][hapmap];1.00[CHB][hapmap];0.87[GIH][hapmap];0.92[MEX][hapmap];0.90[TSI][hapmap];0.86[EUR][1000 genomes]
rs11868832	1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11868886	0.89[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs11869582	0.80[CEU][hapmap]
rs11871039	0.86[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs11871491	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12449313	0.94[GIH][hapmap]
rs12600694	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[GIH][hapmap];0.87[LWK][hapmap];0.93[MEX][hapmap];0.88[TSI][hapmap];0.96[YRI][hapmap];0.83[AFR][1000 genomes];0.91[AMR][1000 genomes];0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13284	1.00[ASW][hapmap];0.94[CEU][hapmap];1.00[GIH][hapmap];0.95[LWK][hapmap];0.80[MEX][hapmap];1.00[MKK][hapmap];0.97[TSI][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1563371	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[GIH][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];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1563373	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs16960980	0.94[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[GIH][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs16960983	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[GIH][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];0.98[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs16960986	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[GIH][hapmap];1.00[LWK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs16960990	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[GIH][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];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs16960996	0.94[CEU][hapmap];1.00[CHB][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs16961153	0.94[GIH][hapmap]
rs2015336	0.88[CEU][hapmap];1.00[CHB][hapmap];1.00[GIH][hapmap];0.92[MEX][hapmap];0.84[MKK][hapmap];0.97[TSI][hapmap];0.89[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2071242	0.90[GIH][hapmap]
rs2290502	0.90[GIH][hapmap]
rs2290503	0.90[GIH][hapmap]
rs2294913	0.94[GIH][hapmap]
rs28364628	0.90[GIH][hapmap]
rs28811342	0.88[AFR][1000 genomes];0.87[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3088233	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[GIH][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];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34474249	0.89[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs36058389	0.90[AFR][1000 genomes];0.92[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs3817992	0.94[GIH][hapmap]
rs3829956	0.94[GIH][hapmap]
rs55918833	0.83[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs58441148	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs59354912	0.88[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs60285171	0.95[AFR][1000 genomes];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62072464	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs62072465	0.96[AFR][1000 genomes];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62072466	0.96[AFR][1000 genomes];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62072467	0.95[EUR][1000 genomes]
rs62072468	0.90[AFR][1000 genomes];0.89[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62072496	0.84[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs62072497	0.84[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs62072498	0.88[AFR][1000 genomes];0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62072500	0.87[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62073602	0.84[EUR][1000 genomes]
rs62073603	0.87[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs62073604	0.87[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs62073605	0.86[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs62073606	0.86[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs62073607	0.86[AMR][1000 genomes];0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62073608	0.89[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62073609	0.89[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62073611	0.86[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs62073615	0.86[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs62073649	0.86[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62073650	0.86[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6502640	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[GIH][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7207276	0.87[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs7215678	0.90[GIH][hapmap]
rs735960	0.83[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs7498	0.90[GIH][hapmap]
rs8065026	0.88[CEU][hapmap];1.00[CHB][hapmap];0.87[GIH][hapmap];0.93[MEX][hapmap];0.90[TSI][hapmap];0.83[EUR][1000 genomes]
rs8069094	0.88[AFR][1000 genomes];0.92[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs8077577	0.88[CEU][hapmap];1.00[GIH][hapmap];0.92[MEX][hapmap];0.85[MKK][hapmap];0.87[TSI][hapmap];0.86[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs9909104	1.00[GIH][hapmap]
rs9913139	0.90[GIH][hapmap]
rs9916193	0.84[EUR][1000 genomes]
rs997315	0.94[CEU][hapmap];1.00[CHB][hapmap];0.87[AMR][1000 genomes];0.90[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:11 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv531183	chr17:17571035-18205309	Genic enhancers Weak transcription Enhancers Strong transcription Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	123 gene(s)	inside rSNPs	diseases
2	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
3	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
4	nsv482491	chr17:17959577-18153920	Enhancers Genic enhancers Flanking Active TSS Active TSS Weak transcription Strong transcription Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	38 gene(s)	inside rSNPs	diseases
5	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
6	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
7	nsv510702	chr17:18037676-18116801	Enhancers Strong transcription Genic enhancers Transcr. at gene 5' and 3' Flanking Active TSS Weak transcription Active TSS ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	24 gene(s)	inside rSNPs	diseases
8	nsv1062828	chr17:18098110-18136330	Flanking Active TSS Weak transcription Active TSS Genic enhancers Strong transcription Enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region	10 gene(s)	inside rSNPs	diseases
9	nsv543245	chr17:18098110-18136330	Flanking Active TSS Weak transcription Strong transcription Enhancers Active TSS Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region	10 gene(s)	inside rSNPs	diseases
10	nsv907773	chr17:18099962-18206234	Strong transcription Enhancers Weak transcription Flanking Active TSS Active TSS Genic enhancers ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	21 gene(s)	inside rSNPs	diseases
11	nsv907774	chr17:18103907-18206234	Transcr. at gene 5' and 3' Genic enhancers Weak transcription Flanking Active TSS Strong transcription Enhancers Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	21 gene(s)	inside rSNPs	diseases

mRNA abundance (count:9)

SNP	Gene	Cis/trans	Tissue	Source
rs11655588	SLC47A1	cis	cerebellum	SCAN
rs11655588	SHMT1	cis	lymphoblastoid	seeQTL
rs11655588	SHMT1	cis	cerebellum	SCAN
rs11655588	EPN2	cis	parietal	SCAN
rs11655588	TRPV2	cis	cerebellum	SCAN
rs11655588	LOC162632	cis	cerebellum	SCAN
rs11655588	FLII	cis	cerebellum	SCAN
rs11655588	PLD6	cis	cerebellum	SCAN
rs11655588	LOC162632	cis	parietal	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr17:18091400-18114000	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
2	chr17:18091800-18114400	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
3	chr17:18094200-18114600	Strong transcription	Primary hematopoietic stem cells short term culture	blood
4	chr17:18094400-18114600	Strong transcription	Monocytes-CD14+_RO01746	blood
5	chr17:18094600-18114600	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
6	chr17:18095000-18108600	Strong transcription	Cortex derived primary cultured neurospheres	brain
7	chr17:18095000-18114600	Strong transcription	Sigmoid Colon	Sigmoid Colon
8	chr17:18095000-18114800	Strong transcription	Fetal Thymus	thymus
9	chr17:18095400-18116000	Strong transcription	Fetal Stomach	stomach
10	chr17:18095600-18114600	Strong transcription	Dnd41	blood
11	chr17:18095800-18108600	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
12	chr17:18096200-18114400	Strong transcription	Primary T cells from cord blood	blood
13	chr17:18096200-18114600	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
14	chr17:18096800-18114600	Strong transcription	Primary monocytes fromperipheralblood	blood
15	chr17:18097000-18108600	Strong transcription	Brain Germinal Matrix	brain
16	chr17:18097000-18114600	Strong transcription	Primary neutrophils fromperipheralblood	blood
17	chr17:18097200-18114600	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
18	chr17:18097600-18114600	Strong transcription	Primary B cells from peripheral blood	blood
19	chr17:18097800-18114600	Strong transcription	Fetal Brain Female	brain
20	chr17:18098000-18114600	Strong transcription	Primary B cells from cord blood	blood
21	chr17:18098000-18114600	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
22	chr17:18098000-18114600	Strong transcription	Fetal Muscle Leg	muscle
23	chr17:18101000-18108600	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
24	chr17:18101200-18108400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
25	chr17:18101200-18114400	Strong transcription	Primary T helper 17 cells PMA-I stimulated	--
26	chr17:18101600-18114600	Strong transcription	Thymus	Thymus
27	chr17:18101600-18115400	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
28	chr17:18101800-18108200	Strong transcription	Foreskin Melanocyte Primary Cells skin01	Skin
29	chr17:18101800-18108400	Weak transcription	Fetal Brain Male	brain
30	chr17:18101800-18109400	Weak transcription	HSMMtube	muscle
31	chr17:18102000-18108200	Weak transcription	H9 Cell Line	embryonic stem cell
32	chr17:18102000-18108600	Weak transcription	K562	blood
33	chr17:18102000-18108800	Weak transcription	Colonic Mucosa	Colon
34	chr17:18102000-18114600	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
35	chr17:18102000-18116200	Strong transcription	Fetal Muscle Trunk	muscle
36	chr17:18102200-18109600	Weak transcription	HUVEC	blood vessel
37	chr17:18102200-18109800	Weak transcription	Small Intestine	intestine
38	chr17:18102200-18114600	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
39	chr17:18102400-18110000	Weak transcription	Pancreatic Islets	Pancreatic Islet
40	chr17:18102400-18114400	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
41	chr17:18102600-18108400	Strong transcription	Breast Myoepithelial Primary Cells	Breast
42	chr17:18102800-18108400	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
43	chr17:18103000-18108600	Weak transcription	H1 Cell Line	embryonic stem cell
44	chr17:18103000-18114600	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
45	chr17:18103000-18114800	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
46	chr17:18103200-18108800	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
47	chr17:18103400-18114400	Strong transcription	Primary T helper cells PMA-I stimulated	--
48	chr17:18104000-18108400	Weak transcription	Primary T helper naive cells from peripheral blood	blood
49	chr17:18104000-18109000	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
50	chr17:18104000-18109600	Weak transcription	Primary T killer naive cells fromperipheralblood	blood

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