Variant report

Variant	rs17218566
Chromosome Location	chr2:161054748-161054749
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	chr2:161052648..161055115-chr2:161348196..161351144,2	MCF-7	breast:
2	chr2:161033297..161035700-chr2:161053449..161055429,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000153250	Chromatin interaction

Extended variants
information (count: 72 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:69)

rs_ID	r²[population]
rs10497209	1.00[YRI][hapmap]
rs10497210	1.00[YRI][hapmap]
rs10497213	0.82[CHB][hapmap];0.95[JPT][hapmap]
rs10929965	1.00[ASW][hapmap];0.84[CEU][hapmap];0.90[JPT][hapmap];1.00[LWK][hapmap];1.00[MKK][hapmap];0.89[TSI][hapmap];1.00[YRI][hapmap]
rs13001911	0.83[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs16844715	1.00[ASW][hapmap];0.85[CEU][hapmap];1.00[LWK][hapmap];1.00[MKK][hapmap];0.83[TSI][hapmap];1.00[YRI][hapmap]
rs16844848	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.95[ASN][1000 genomes]
rs16844863	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.99[ASN][1000 genomes]
rs16844866	1.00[CHB][hapmap];1.00[JPT][hapmap];0.98[ASN][1000 genomes]
rs16844875	0.85[JPT][hapmap]
rs17216980	0.88[CEU][hapmap];0.82[CHB][hapmap];0.95[JPT][hapmap];1.00[YRI][hapmap]
rs17241282	0.81[JPT][hapmap];1.00[YRI][hapmap]
rs17341301	0.85[CEU][hapmap];0.86[JPT][hapmap];0.89[TSI][hapmap]
rs17829873	1.00[YRI][hapmap]
rs17830307	1.00[YRI][hapmap]
rs17830558	1.00[YRI][hapmap]
rs17830904	0.84[ASW][hapmap];0.81[JPT][hapmap];1.00[YRI][hapmap]
rs17831161	0.84[CEU][hapmap];0.90[JPT][hapmap];1.00[YRI][hapmap]
rs17831191	0.85[CEU][hapmap];0.90[JPT][hapmap];1.00[YRI][hapmap]
rs17831251	1.00[ASW][hapmap];0.85[CEU][hapmap];0.90[JPT][hapmap];1.00[LWK][hapmap];1.00[MKK][hapmap];0.89[TSI][hapmap];1.00[YRI][hapmap]
rs1870102	0.81[AFR][1000 genomes];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1870104	0.90[AFR][1000 genomes];0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2124969	0.91[CEU][hapmap];0.81[CHB][hapmap];0.95[JPT][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];0.85[EUR][1000 genomes]
rs2175416	0.83[CEU][hapmap];0.86[CHB][hapmap];0.89[JPT][hapmap];1.00[YRI][hapmap]
rs2198918	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[AFR][1000 genomes];0.91[AMR][1000 genomes];0.93[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2221808	1.00[YRI][hapmap]
rs2305818	1.00[ASW][hapmap];0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];0.92[TSI][hapmap];1.00[YRI][hapmap];0.90[AFR][1000 genomes];0.92[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2305819	0.87[CHB][hapmap];0.94[JPT][hapmap]
rs3749117	0.81[JPT][hapmap];1.00[YRI][hapmap]
rs3749119	0.90[JPT][hapmap];1.00[YRI][hapmap]
rs3792175	1.00[YRI][hapmap]
rs3792192	0.84[ASW][hapmap];0.81[JPT][hapmap];1.00[YRI][hapmap]
rs4292050	0.88[CEU][hapmap];0.82[CHB][hapmap];0.95[JPT][hapmap];1.00[YRI][hapmap]
rs4664308	1.00[ASW][hapmap];0.85[CEU][hapmap];0.90[JPT][hapmap];1.00[LWK][hapmap];1.00[MKK][hapmap];0.89[TSI][hapmap];1.00[YRI][hapmap]
rs4664317	0.83[ASN][1000 genomes]
rs4665138	0.84[ASW][hapmap];0.81[JPT][hapmap];1.00[YRI][hapmap]
rs4665140	0.81[JPT][hapmap];1.00[YRI][hapmap]
rs4665141	0.81[JPT][hapmap];1.00[YRI][hapmap]
rs4665147	1.00[ASW][hapmap];0.85[CEU][hapmap];0.90[JPT][hapmap];1.00[LWK][hapmap];1.00[MKK][hapmap];0.88[TSI][hapmap];1.00[YRI][hapmap]
rs4665161	1.00[CHB][hapmap];1.00[JPT][hapmap];0.98[ASN][1000 genomes]
rs4665162	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.91[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs55959207	0.90[AFR][1000 genomes];0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs57993273	0.95[ASN][1000 genomes]
rs59019419	0.85[AFR][1000 genomes];0.91[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs59541669	0.85[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs60608133	0.87[ASN][1000 genomes]
rs60801510	0.96[ASN][1000 genomes]
rs60908067	0.90[AFR][1000 genomes];0.80[AMR][1000 genomes];0.87[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs61330151	0.92[ASN][1000 genomes]
rs62175395	0.90[AFR][1000 genomes];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6705574	0.86[JPT][hapmap]
rs6707458	1.00[ASW][hapmap];0.85[CEU][hapmap];0.90[JPT][hapmap];1.00[LWK][hapmap];1.00[MKK][hapmap];0.89[TSI][hapmap];1.00[YRI][hapmap]
rs6719686	0.84[CEU][hapmap];0.90[JPT][hapmap];1.00[YRI][hapmap]
rs6722275	0.84[ASW][hapmap];0.81[JPT][hapmap];1.00[YRI][hapmap]
rs6731260	1.00[ASW][hapmap];0.88[CEU][hapmap];0.82[CHB][hapmap];0.91[CHD][hapmap];0.92[GIH][hapmap];0.95[JPT][hapmap];1.00[LWK][hapmap];1.00[MKK][hapmap];0.91[TSI][hapmap];1.00[YRI][hapmap];0.80[AFR][1000 genomes];0.86[EUR][1000 genomes]
rs6732107	1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[ASN][1000 genomes]
rs6739867	0.88[CEU][hapmap];0.82[CHB][hapmap];0.95[JPT][hapmap];1.00[YRI][hapmap]
rs6759836	0.84[CEU][hapmap];0.90[JPT][hapmap];1.00[YRI][hapmap]
rs6759924	1.00[YRI][hapmap]
rs72623108	0.91[ASN][1000 genomes]
rs72623109	0.96[ASN][1000 genomes]
rs72623111	0.98[ASN][1000 genomes]
rs733810	0.89[ASN][1000 genomes]
rs7567781	0.95[AFR][1000 genomes];0.87[EUR][1000 genomes]
rs7589820	0.87[AMR][1000 genomes];0.92[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7595859	0.90[AFR][1000 genomes];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs877200	0.87[CEU][hapmap];0.89[JPT][hapmap]
rs925410	1.00[ASW][hapmap];0.85[CEU][hapmap];0.90[JPT][hapmap];1.00[LWK][hapmap];1.00[MKK][hapmap];0.89[TSI][hapmap];1.00[YRI][hapmap]
rs983916	1.00[LWK][hapmap];1.00[YRI][hapmap]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv459929	chr2:160963603-161079435	Enhancers Active TSS Genic enhancers Flanking Active TSS Strong transcription Weak transcription Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
2	nsv583497	chr2:160963603-161079435	Enhancers Weak transcription Strong transcription Genic enhancers Active TSS ZNF genes & repeats Flanking Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
3	nsv1001502	chr2:160967864-161079450	Weak transcription Enhancers Strong transcription Flanking Active TSS ZNF genes & repeats Active TSS Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs17218566	LY75	cis	Esophagus Mucosa	GTEx
rs17218566	TANK	cis	parietal	SCAN

Chromatin state (count:29 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:161029400-161063200	Weak transcription	Fetal Muscle Leg	muscle
2	chr2:161047200-161058800	Weak transcription	Psoas Muscle	Psoas
3	chr2:161048600-161061600	Weak transcription	Sigmoid Colon	Sigmoid Colon
4	chr2:161049600-161055600	Weak transcription	Fetal Stomach	stomach
5	chr2:161049800-161055200	Weak transcription	Colonic Mucosa	Colon
6	chr2:161050400-161061200	Weak transcription	Esophagus	oesophagus
7	chr2:161051800-161056600	Weak transcription	Pancreas	Pancrea
8	chr2:161051800-161064600	Weak transcription	Lung	lung
9	chr2:161052000-161058400	Weak transcription	HSMM	muscle
10	chr2:161052200-161054800	Weak transcription	Fetal Intestine Small	intestine
11	chr2:161052200-161064600	Weak transcription	Gastric	stomach
12	chr2:161052400-161054800	Weak transcription	Rectal Mucosa Donor 31	rectum
13	chr2:161052800-161055000	Weak transcription	Duodenum Mucosa	Duodenum
14	chr2:161052800-161055000	Weak transcription	Rectal Mucosa Donor 29	rectum
15	chr2:161053200-161064600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
16	chr2:161053600-161055000	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
17	chr2:161053800-161055200	Enhancers	Skeletal Muscle Male	skeletal muscle
18	chr2:161053800-161055400	Enhancers	Skeletal Muscle Female	skeletal muscle
19	chr2:161054000-161055000	Flanking Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
20	chr2:161054000-161055400	Flanking Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
21	chr2:161054000-161055400	Flanking Active TSS	NHEK	skin
22	chr2:161054000-161057200	Active TSS	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
23	chr2:161054200-161055000	Enhancers	Stomach Mucosa	stomach
24	chr2:161054200-161055600	Enhancers	Fetal Intestine Large	intestine
25	chr2:161054400-161054800	Active TSS	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
26	chr2:161054400-161056800	Active TSS	Placenta Amnion	Placenta Amnion
27	chr2:161054400-161057000	Active TSS	Breast Myoepithelial Primary Cells	Breast
28	chr2:161054400-161057400	Weak transcription	HSMMtube	muscle
29	chr2:161054600-161057000	Active TSS	HMEC	breast

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