Variant report

Variant	rs4968467
Chromosome Location	chr17:60129875-60129876
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr17:60125809..60127843-chr17:60128789..60132797,3	MCF-7	breast:
2	chr17:60121545..60124034-chr17:60127922..60130507,2	MCF-7	breast:
3	chr17:60128527..60131258-chr3:15246063..15247729,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000131375	Chromatin interaction
ENSG00000230524	Chromatin interaction

Extended variants
information (count: 56 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:52)

rs_ID	r²[population]
rs10512492	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[AMR][1000 genomes];0.90[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12450560	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12451910	0.90[CEU][hapmap];0.83[JPT][hapmap]
rs12452094	1.00[CEU][hapmap];0.83[JPT][hapmap];0.81[EUR][1000 genomes]
rs12452742	1.00[CEU][hapmap];0.83[JPT][hapmap];1.00[YRI][hapmap]
rs12600620	0.84[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs12600909	0.91[CEU][hapmap];0.83[JPT][hapmap]
rs12604037	1.00[CEU][hapmap];0.91[CHB][hapmap];0.95[JPT][hapmap];0.86[EUR][1000 genomes]
rs16945692	0.90[CEU][hapmap];0.82[JPT][hapmap]
rs16945753	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.92[AFR][1000 genomes];0.88[AMR][1000 genomes];0.90[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs16945756	0.92[AFR][1000 genomes];0.85[AMR][1000 genomes];0.90[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs16945759	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.92[AFR][1000 genomes];0.85[AMR][1000 genomes];0.88[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs16945801	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]
rs2271576	0.90[CEU][hapmap];1.00[YRI][hapmap]
rs2278812	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs28654524	0.92[AFR][1000 genomes];0.93[AMR][1000 genomes];0.93[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs3744434	0.90[CEU][hapmap];0.83[JPT][hapmap]
rs3809753	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs3826419	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];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4422036	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap]
rs4968408	0.90[CEU][hapmap];0.83[JPT][hapmap]
rs4968455	0.91[CEU][hapmap];0.83[JPT][hapmap]
rs4968456	0.91[CEU][hapmap];0.83[JPT][hapmap]
rs4968457	0.91[CEU][hapmap];0.82[JPT][hapmap]
rs4968460	0.90[CEU][hapmap];0.83[JPT][hapmap];1.00[YRI][hapmap]
rs4968461	1.00[CEU][hapmap];0.87[JPT][hapmap];1.00[YRI][hapmap];0.81[EUR][1000 genomes]
rs4968462	0.82[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap]
rs4968463	0.82[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs4968464	0.80[AFR][1000 genomes]
rs4968468	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];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4968470	0.92[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4968476	0.91[CEU][hapmap]
rs57137451	0.92[AFR][1000 genomes];0.85[AMR][1000 genomes];0.88[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs57746689	0.88[AFR][1000 genomes];0.93[AMR][1000 genomes];0.93[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs57918684	0.81[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs58241345	0.92[AFR][1000 genomes];0.90[AMR][1000 genomes];0.93[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs58335059	0.92[ASN][1000 genomes]
rs60053512	0.92[AFR][1000 genomes];0.93[AMR][1000 genomes];0.93[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs61469058	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61658218	0.82[EUR][1000 genomes]
rs6504084	0.90[CEU][hapmap]
rs7218724	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];0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7221089	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];0.93[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs72843781	0.81[AFR][1000 genomes];0.85[ASN][1000 genomes]
rs73334621	0.81[EUR][1000 genomes]
rs73336436	0.87[AMR][1000 genomes];0.92[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs8065778	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.92[AFR][1000 genomes];0.85[AMR][1000 genomes];0.92[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs8066964	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.92[AFR][1000 genomes];0.85[AMR][1000 genomes];0.89[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs8074890	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.92[AFR][1000 genomes];0.83[AMR][1000 genomes];0.87[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs8080599	0.90[CEU][hapmap];0.82[JPT][hapmap]
rs8081917	0.90[CEU][hapmap];0.83[JPT][hapmap]
rs9630736	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.86[AFR][1000 genomes];0.88[AMR][1000 genomes];0.90[EUR][1000 genomes];0.90[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	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
2	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
3	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
4	esv3415630	chr17:60124819-60401635	Enhancers Genic enhancers Weak transcription Active TSS Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Strong transcription ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	34 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	chr17:60077200-60136800	Strong transcription	Fetal Thymus	thymus
2	chr17:60098600-60139200	Strong transcription	Monocytes-CD14+_RO01746	blood
3	chr17:60098800-60135000	Strong transcription	Dnd41	blood
4	chr17:60099000-60134200	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
5	chr17:60099400-60131000	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
6	chr17:60099400-60139000	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
7	chr17:60108000-60141400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
8	chr17:60108800-60139000	Weak transcription	Placenta Amnion	Placenta Amnion
9	chr17:60109000-60141200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
10	chr17:60110600-60135200	Weak transcription	Aorta	Aorta
11	chr17:60110600-60139800	Weak transcription	Spleen	Spleen
12	chr17:60111000-60130600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
13	chr17:60111000-60133800	Weak transcription	Pancreas	Pancrea
14	chr17:60111200-60140200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
15	chr17:60111400-60138400	Weak transcription	Fetal Brain Male	brain
16	chr17:60111400-60140400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
17	chr17:60111400-60141400	Weak transcription	H9 Cell Line	embryonic stem cell
18	chr17:60115000-60140000	Weak transcription	Gastric	stomach
19	chr17:60115400-60131400	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
20	chr17:60115400-60135000	Strong transcription	Rectal Mucosa Donor 29	rectum
21	chr17:60116000-60131000	Strong transcription	HUES6 Cell Line	embryonic stem cell
22	chr17:60116000-60139800	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
23	chr17:60116200-60139800	Strong transcription	Primary monocytes fromperipheralblood	blood
24	chr17:60116400-60130600	Strong transcription	Primary hematopoietic stem cells short term culture	blood
25	chr17:60116400-60133800	Strong transcription	iPS-20b Cell Line	embryonic stem cell
26	chr17:60116600-60131000	Strong transcription	iPS-18 Cell Line	embryonic stem cell
27	chr17:60116600-60139000	Strong transcription	HUES48 Cell Line	embryonic stem cell
28	chr17:60117000-60130800	Strong transcription	Primary neutrophils fromperipheralblood	blood
29	chr17:60117200-60130200	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
30	chr17:60117200-60130600	Strong transcription	Rectal Mucosa Donor 31	rectum
31	chr17:60117200-60133800	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
32	chr17:60117200-60136800	Strong transcription	Primary B cells from peripheral blood	blood
33	chr17:60117400-60139200	Strong transcription	HUES64 Cell Line	embryonic stem cell
34	chr17:60118000-60130800	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
35	chr17:60118000-60135000	Strong transcription	Placenta	Placenta
36	chr17:60118200-60131200	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
37	chr17:60119800-60136800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
38	chr17:60120000-60133600	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
39	chr17:60120600-60136800	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
40	chr17:60121000-60133600	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
41	chr17:60121600-60136800	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
42	chr17:60122000-60130600	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
43	chr17:60122400-60130200	Strong transcription	Fetal Lung	lung
44	chr17:60122400-60130400	Strong transcription	Duodenum Mucosa	Duodenum
45	chr17:60123400-60133800	Weak transcription	HSMMtube	muscle
46	chr17:60124000-60134000	Weak transcription	Brain Hippocampus Middle	brain
47	chr17:60124000-60136800	Weak transcription	Fetal Heart	heart
48	chr17:60124200-60130400	Weak transcription	Brain Substantia Nigra	brain
49	chr17:60124200-60130400	Weak transcription	Skeletal Muscle Male	skeletal muscle
50	chr17:60124200-60133000	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin

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