Variant report

Variant	rs4968470
Chromosome Location	chr17:60139500-60139501
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr17:60078768..60080759-chr17:60137398..60140129,2	MCF-7	breast:
2	chr17:60109100..60115940-chr17:60139087..60144589,10	MCF-7	breast:
3	chr17:60080572..60082564-chr17:60139030..60141974,2	K562	blood:
4	chr17:60117240..60120020-chr17:60137315..60140366,3	MCF-7	breast:
5	chr17:60138388..60140363-chr17:60151078..60153588,2	K562	blood:

Variant related genes	Relation type
ENSG00000200842	Chromatin interaction
ENSG00000108510	Chromatin interaction

Extended variants
information (count: 48 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:44)

rs_ID	r²[population]
rs10512492	1.00[CEU][hapmap];0.85[AMR][1000 genomes];0.92[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs12450560	1.00[CEU][hapmap];0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12451910	0.82[CEU][hapmap]
rs12452094	0.81[EUR][1000 genomes]
rs12600620	0.84[EUR][1000 genomes]
rs12604037	0.82[CEU][hapmap];0.86[EUR][1000 genomes]
rs16945692	0.82[CEU][hapmap]
rs16945753	0.84[AFR][1000 genomes];0.86[AMR][1000 genomes];0.90[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs16945756	0.84[AFR][1000 genomes];0.83[AMR][1000 genomes];0.90[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs16945759	1.00[CEU][hapmap];0.84[AFR][1000 genomes];0.83[AMR][1000 genomes];0.88[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs16945801	1.00[CEU][hapmap];0.88[AFR][1000 genomes];0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2271576	0.82[CEU][hapmap]
rs28654524	0.84[AFR][1000 genomes];0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs3744434	0.82[CEU][hapmap]
rs3809753	1.00[CEU][hapmap];0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs3826419	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4410139	0.80[EUR][1000 genomes]
rs4422036	1.00[CEU][hapmap]
rs4968408	0.82[CEU][hapmap]
rs4968460	0.82[CEU][hapmap]
rs4968461	0.81[EUR][1000 genomes]
rs4968463	0.84[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs4968467	0.92[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4968468	1.00[CEU][hapmap];0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs57137451	0.84[AFR][1000 genomes];0.83[AMR][1000 genomes];0.88[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs57746689	0.80[AFR][1000 genomes];0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs57918684	0.83[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs58241345	0.84[AFR][1000 genomes];0.88[AMR][1000 genomes];0.93[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs58335059	0.90[ASN][1000 genomes]
rs60053512	0.84[AFR][1000 genomes];0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs61469058	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs61658218	0.82[EUR][1000 genomes]
rs6504084	0.82[CEU][hapmap]
rs7218724	1.00[CEU][hapmap];0.88[AFR][1000 genomes];0.91[AMR][1000 genomes];0.93[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7221089	1.00[CEU][hapmap];0.84[AFR][1000 genomes];0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs72843781	0.83[ASN][1000 genomes]
rs73334621	0.81[EUR][1000 genomes]
rs73336436	0.85[AMR][1000 genomes];0.90[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs8065778	0.84[AFR][1000 genomes];0.83[AMR][1000 genomes];0.92[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs8066964	1.00[CEU][hapmap];0.84[AFR][1000 genomes];0.83[AMR][1000 genomes];0.91[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs8074890	0.84[AFR][1000 genomes];0.82[AMR][1000 genomes];0.89[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs8080599	0.82[CEU][hapmap]
rs8081917	0.82[CEU][hapmap]
rs9630736	1.00[CEU][hapmap];0.86[AMR][1000 genomes];0.92[EUR][1000 genomes];0.89[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:127 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr17:60108000-60141400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
2	chr17:60109000-60141200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
3	chr17:60110600-60139800	Weak transcription	Spleen	Spleen
4	chr17:60111200-60140200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
5	chr17:60111400-60140400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
6	chr17:60111400-60141400	Weak transcription	H9 Cell Line	embryonic stem cell
7	chr17:60115000-60140000	Weak transcription	Gastric	stomach
8	chr17:60116000-60139800	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
9	chr17:60116200-60139800	Strong transcription	Primary monocytes fromperipheralblood	blood
10	chr17:60126200-60141600	Weak transcription	Esophagus	oesophagus
11	chr17:60133600-60140200	Genic enhancers	Primary T regulatory cells fromperipheralblood	blood
12	chr17:60133800-60140000	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
13	chr17:60133800-60140000	Enhancers	Primary T killer naive cells fromperipheralblood	blood
14	chr17:60134000-60140000	Weak transcription	Small Intestine	intestine
15	chr17:60134200-60139600	Genic enhancers	HepG2	liver
16	chr17:60134200-60141000	Weak transcription	Fetal Muscle Trunk	muscle
17	chr17:60134600-60140800	Genic enhancers	Primary T helper cells fromperipheralblood	blood
18	chr17:60134800-60140000	Weak transcription	iPS-15b Cell Line	embryonic stem cell
19	chr17:60135200-60139600	Weak transcription	Stomach Mucosa	stomach
20	chr17:60135200-60139800	Weak transcription	Brain Cingulate Gyrus	brain
21	chr17:60135600-60140000	Weak transcription	HSMMtube	muscle
22	chr17:60135800-60139800	Weak transcription	Aorta	Aorta
23	chr17:60137000-60140800	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
24	chr17:60137200-60139600	Weak transcription	Primary hematopoietic stem cells	blood
25	chr17:60137200-60139600	Weak transcription	HMEC	breast
26	chr17:60137200-60139800	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
27	chr17:60137200-60139800	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
28	chr17:60137200-60139800	Weak transcription	Brain Germinal Matrix	brain
29	chr17:60137200-60139800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
30	chr17:60137200-60139800	Weak transcription	Colonic Mucosa	Colon
31	chr17:60137200-60140000	Weak transcription	Right Atrium	heart
32	chr17:60137200-60140200	Weak transcription	H1 Cell Line	embryonic stem cell
33	chr17:60137400-60139600	Weak transcription	Brain Substantia Nigra	brain
34	chr17:60137400-60139800	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
35	chr17:60137600-60139800	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
36	chr17:60137800-60139800	Genic enhancers	HUES6 Cell Line	embryonic stem cell
37	chr17:60137800-60140000	Weak transcription	Ovary	ovary
38	chr17:60138000-60139600	Enhancers	Skeletal Muscle Male	skeletal muscle
39	chr17:60138000-60140200	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
40	chr17:60138000-60141000	Weak transcription	Sigmoid Colon	Sigmoid Colon
41	chr17:60138200-60139800	Genic enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
42	chr17:60138200-60140400	Enhancers	Colon Smooth Muscle	Colon
43	chr17:60138200-60140800	Transcr. at gene 5' and 3'	Dnd41	blood
44	chr17:60138400-60139800	Enhancers	Fetal Brain Male	brain
45	chr17:60138400-60139800	Weak transcription	Left Ventricle	heart
46	chr17:60138400-60139800	Weak transcription	Psoas Muscle	Psoas
47	chr17:60138400-60139800	Weak transcription	Thymus	Thymus
48	chr17:60138400-60140000	Genic enhancers	ES-I3 Cell Line	embryonic stem cell
49	chr17:60138400-60140000	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
50	chr17:60138400-60140000	Weak transcription	Fetal Intestine Small	intestine

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