Variant report

Variant	rs16945801
Chromosome Location	chr17:60116387-60116388
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr17:60109548..60112572-chr17:60115056..60118748,3	MCF-7	breast:

Variant related genes	Relation type
ENSG00000108510	Chromatin interaction

Extended variants
information (count: 63 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:59)

rs_ID	r²[population]
rs10512492	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.80[AFR][1000 genomes];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11079459	0.80[AFR][1000 genomes]
rs12450223	0.84[ASN][1000 genomes]
rs12450560	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];0.91[AMR][1000 genomes];0.91[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12451910	0.89[CEU][hapmap];0.80[JPT][hapmap]
rs12452094	1.00[CEU][hapmap];0.81[JPT][hapmap];0.81[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs12452742	1.00[CEU][hapmap];0.81[JPT][hapmap];1.00[YRI][hapmap]
rs12600620	0.89[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs12600909	0.90[CEU][hapmap];0.81[JPT][hapmap]
rs12604037	0.89[CEU][hapmap];0.90[CHB][hapmap];0.95[JPT][hapmap];0.89[EUR][1000 genomes]
rs16945692	0.89[CEU][hapmap]
rs16945753	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];0.88[AMR][1000 genomes];0.93[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs16945756	0.96[AFR][1000 genomes];0.91[AMR][1000 genomes];0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs16945759	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];0.91[AMR][1000 genomes];0.91[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2271576	0.89[CEU][hapmap];1.00[YRI][hapmap]
rs2278812	1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[ASN][1000 genomes]
rs28654524	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs3744434	0.89[CEU][hapmap];0.80[JPT][hapmap]
rs3809753	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];1.00[YRI][hapmap];0.92[AFR][1000 genomes];0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs3826419	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.92[AFR][1000 genomes];0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4410139	0.85[EUR][1000 genomes]
rs4422036	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap]
rs4968408	0.89[CEU][hapmap];0.80[JPT][hapmap]
rs4968451	0.89[CEU][hapmap];0.85[YRI][hapmap]
rs4968455	0.90[CEU][hapmap];0.81[JPT][hapmap]
rs4968456	0.90[CEU][hapmap];0.81[JPT][hapmap]
rs4968457	0.90[CEU][hapmap];0.80[JPT][hapmap]
rs4968460	0.89[CEU][hapmap];0.80[JPT][hapmap];1.00[YRI][hapmap];0.80[AFR][1000 genomes]
rs4968461	1.00[CEU][hapmap];0.85[JPT][hapmap];1.00[YRI][hapmap];0.83[EUR][1000 genomes]
rs4968462	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.80[AFR][1000 genomes];0.83[ASN][1000 genomes]
rs4968463	0.80[AFR][1000 genomes];0.89[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs4968464	0.84[AFR][1000 genomes];0.83[ASN][1000 genomes]
rs4968467	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];0.93[AMR][1000 genomes];0.93[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4968468	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.92[AFR][1000 genomes];0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4968470	0.88[AFR][1000 genomes];0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs4968476	0.90[CEU][hapmap]
rs4988344	0.90[CEU][hapmap];0.85[YRI][hapmap]
rs56794817	0.81[AMR][1000 genomes]
rs57137451	0.96[AFR][1000 genomes];0.91[AMR][1000 genomes];0.93[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs57746689	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs57918684	0.83[EUR][1000 genomes]
rs58241345	0.96[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs58335059	0.98[ASN][1000 genomes]
rs59080342	0.80[AFR][1000 genomes];0.81[AMR][1000 genomes]
rs60053512	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs61469058	0.96[AFR][1000 genomes];0.91[AMR][1000 genomes];0.91[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs61658218	0.84[EUR][1000 genomes]
rs6504084	0.89[CEU][hapmap]
rs7218724	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7221089	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs72843781	0.85[AFR][1000 genomes];0.90[ASN][1000 genomes]
rs73334621	0.83[EUR][1000 genomes]
rs73336436	0.93[AMR][1000 genomes];0.93[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs8065778	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs8066964	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs8074890	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];0.90[AMR][1000 genomes];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs8080599	0.89[CEU][hapmap]
rs8081917	0.89[CEU][hapmap];0.80[JPT][hapmap]
rs9630736	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.90[AFR][1000 genomes];0.88[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv3378293	chr17:59744117-60124899	ZNF genes & repeats Strong transcription Weak transcription Flanking Active TSS Active TSS Enhancers Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	175 gene(s)	inside rSNPs	diseases
2	nsv1062816	chr17:60074670-60470465	Strong transcription Enhancers Weak transcription Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Active TSS Flanking Active TSS ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	42 gene(s)	inside rSNPs	diseases
3	esv2753884	chr17:60077852-60190630	Strong transcription Active TSS Weak transcription Transcr. at gene 5' and 3' Enhancers Genic enhancers Flanking Active TSS ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	27 gene(s)	inside rSNPs	diseases
4	esv2755037	chr17:60086508-60386211	Weak transcription Enhancers Active TSS Strong transcription Flanking Active TSS Bivalent/Poised TSS Bivalent Enhancer Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	35 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	chr17:60033000-60128400	Weak transcription	Stomach Mucosa	stomach
2	chr17:60074600-60123800	Weak transcription	Right Atrium	heart
3	chr17:60077200-60136800	Strong transcription	Fetal Thymus	thymus
4	chr17:60098600-60139200	Strong transcription	Monocytes-CD14+_RO01746	blood
5	chr17:60098800-60135000	Strong transcription	Dnd41	blood
6	chr17:60099000-60134200	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
7	chr17:60099400-60131000	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
8	chr17:60099400-60139000	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
9	chr17:60105600-60117600	Strong transcription	Fetal Intestine Small	intestine
10	chr17:60105600-60120800	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
11	chr17:60106000-60129800	Weak transcription	Pancreatic Islets	Pancreatic Islet
12	chr17:60108000-60117200	Weak transcription	Esophagus	oesophagus
13	chr17:60108000-60141400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
14	chr17:60108800-60139000	Weak transcription	Placenta Amnion	Placenta Amnion
15	chr17:60109000-60116600	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
16	chr17:60109000-60119000	Weak transcription	Brain Germinal Matrix	brain
17	chr17:60109000-60119000	Weak transcription	Colonic Mucosa	Colon
18	chr17:60109000-60120200	Weak transcription	Small Intestine	intestine
19	chr17:60109000-60128600	Weak transcription	iPS-15b Cell Line	embryonic stem cell
20	chr17:60109000-60141200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
21	chr17:60110400-60123800	Weak transcription	Psoas Muscle	Psoas
22	chr17:60110600-60135200	Weak transcription	Aorta	Aorta
23	chr17:60110600-60139800	Weak transcription	Spleen	Spleen
24	chr17:60111000-60118400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
25	chr17:60111000-60120200	Weak transcription	Ovary	ovary
26	chr17:60111000-60130600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
27	chr17:60111000-60133800	Weak transcription	Pancreas	Pancrea
28	chr17:60111200-60117200	Weak transcription	Rectal Smooth Muscle	rectum
29	chr17:60111200-60117600	Weak transcription	Fetal Brain Female	brain
30	chr17:60111200-60120200	Weak transcription	Brain Anterior Caudate	brain
31	chr17:60111200-60122600	Weak transcription	HMEC	breast
32	chr17:60111200-60123600	Weak transcription	Brain Hippocampus Middle	brain
33	chr17:60111200-60129000	Weak transcription	Brain Angular Gyrus	brain
34	chr17:60111200-60140200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
35	chr17:60111400-60117000	Weak transcription	Primary B cells from cord blood	blood
36	chr17:60111400-60117400	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
37	chr17:60111400-60117400	Weak transcription	Primary T killer memory cells from peripheral blood	blood
38	chr17:60111400-60118000	Weak transcription	Brain Inferior Temporal Lobe	brain
39	chr17:60111400-60118000	Weak transcription	HSMM	muscle
40	chr17:60111400-60119800	Weak transcription	Primary T cells from cord blood	blood
41	chr17:60111400-60119800	Weak transcription	Fetal Lung	lung
42	chr17:60111400-60122200	Weak transcription	Brain Cingulate Gyrus	brain
43	chr17:60111400-60122600	Weak transcription	Stomach Smooth Muscle	stomach
44	chr17:60111400-60123000	Weak transcription	Colon Smooth Muscle	Colon
45	chr17:60111400-60123000	Weak transcription	Skeletal Muscle Female	skeletal muscle
46	chr17:60111400-60123800	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
47	chr17:60111400-60123800	Weak transcription	Brain Substantia Nigra	brain
48	chr17:60111400-60124600	Weak transcription	NHLF	lung
49	chr17:60111400-60128200	Weak transcription	NHEK	skin
50	chr17:60111400-60138400	Weak transcription	Fetal Brain Male	brain

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