Variant report

Variant	rs17416706
Chromosome Location	chr4:129936036-129936037
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 64 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:57)

rs_ID	r²[population]
rs1030830	1.00[ASW][hapmap];0.96[CEU][hapmap];1.00[CHB][hapmap];0.81[CHD][hapmap];0.95[GIH][hapmap];0.95[JPT][hapmap];0.84[LWK][hapmap];1.00[MEX][hapmap];0.85[MKK][hapmap];1.00[TSI][hapmap];0.92[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs10494317	0.85[JPT][hapmap]
rs10518539	0.92[CEU][hapmap];0.90[JPT][hapmap]
rs12500341	0.96[CEU][hapmap];0.95[CHB][hapmap];0.95[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];0.87[MEX][hapmap];0.97[TSI][hapmap];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12500557	0.81[CEU][hapmap];0.90[CHB][hapmap];0.81[CHD][hapmap];0.87[GIH][hapmap];0.90[JPT][hapmap];0.91[MEX][hapmap];0.81[TSI][hapmap]
rs12503465	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[YRI][hapmap];1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12504200	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.96[LWK][hapmap];1.00[MEX][hapmap];0.93[MKK][hapmap];1.00[TSI][hapmap];0.81[YRI][hapmap];0.90[AFR][1000 genomes];0.87[AMR][1000 genomes];0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12512345	1.00[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap];0.81[YRI][hapmap];0.89[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1376202	0.81[YRI][hapmap]
rs17185550	0.81[CEU][hapmap];0.90[CHB][hapmap];0.95[JPT][hapmap]
rs172168	1.00[YRI][hapmap]
rs17349255	0.90[JPT][hapmap]
rs17416188	1.00[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap];0.81[YRI][hapmap];0.89[AMR][1000 genomes];0.99[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1757938	0.82[LWK][hapmap];1.00[YRI][hapmap];0.81[AFR][1000 genomes]
rs1757942	0.81[AFR][1000 genomes]
rs1877836	0.81[CHB][hapmap];0.81[CHD][hapmap];0.83[GIH][hapmap];0.85[JPT][hapmap]
rs1900397	1.00[ASW][hapmap];1.00[CEU][hapmap];0.95[CHB][hapmap];0.95[CHD][hapmap];0.98[GIH][hapmap];0.95[JPT][hapmap];0.96[LWK][hapmap];0.95[MEX][hapmap];0.87[MKK][hapmap];1.00[TSI][hapmap];0.81[YRI][hapmap];0.87[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1993035	0.92[CEU][hapmap];0.90[JPT][hapmap]
rs2044523	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.96[LWK][hapmap];1.00[MEX][hapmap];0.96[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2592948	0.82[LWK][hapmap];1.00[YRI][hapmap];0.81[AFR][1000 genomes]
rs2597837	0.81[YRI][hapmap]
rs2655311	1.00[YRI][hapmap];0.81[AFR][1000 genomes]
rs2777823	0.81[AFR][1000 genomes]
rs280601	0.81[YRI][hapmap]
rs3099902	1.00[YRI][hapmap];0.81[AFR][1000 genomes]
rs36195612	0.91[AFR][1000 genomes];0.83[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs3980331	1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4423892	0.92[CEU][hapmap];0.89[JPT][hapmap]
rs4975191	1.00[CEU][hapmap];0.95[CHB][hapmap];0.92[CHD][hapmap];0.98[GIH][hapmap];0.95[JPT][hapmap];0.97[TSI][hapmap];0.80[AMR][1000 genomes];0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4975293	0.84[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4975294	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[YRI][hapmap];0.90[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs55925207	0.85[AFR][1000 genomes];0.85[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs59540486	0.89[AMR][1000 genomes];0.99[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6825433	0.92[CEU][hapmap];0.90[JPT][hapmap]
rs6830023	0.81[AFR][1000 genomes];0.89[AMR][1000 genomes];0.99[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6832138	0.91[CEU][hapmap];0.88[JPT][hapmap]
rs6835359	0.88[CEU][hapmap];0.90[JPT][hapmap]
rs6840353	0.92[CEU][hapmap];0.90[JPT][hapmap]
rs6845314	1.00[AFR][1000 genomes];0.87[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6847784	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.87[AMR][1000 genomes];0.94[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs72683669	0.98[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs72683673	0.82[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs72683684	0.81[AFR][1000 genomes];0.89[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs72683693	0.84[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs72685321	1.00[AFR][1000 genomes];0.86[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72685324	0.90[AFR][1000 genomes];0.84[AMR][1000 genomes];0.93[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs72685328	0.90[AFR][1000 genomes];0.85[AMR][1000 genomes];0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs72685351	0.97[ASN][1000 genomes]
rs72685352	0.90[AFR][1000 genomes];0.80[AMR][1000 genomes];0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs72685353	0.97[AFR][1000 genomes];0.82[AMR][1000 genomes];0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs72685365	0.88[AFR][1000 genomes];0.92[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs7654405	0.81[AFR][1000 genomes]
rs7675408	0.81[AFR][1000 genomes];0.90[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs796886	0.81[AFR][1000 genomes]
rs921375	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.85[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs921376	0.81[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs921377	0.96[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.85[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:7 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv869258	chr4:129191619-130138148	Weak transcription Enhancers Flanking Active TSS Strong transcription Active TSS ZNF genes & repeats Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	79 gene(s)	inside rSNPs	diseases
2	nsv1026938	chr4:129770961-129936205	Weak transcription Strong transcription Enhancers Flanking Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Active TSS	TF binding region CpG island Chromatin interactive region miRNA target site	4 gene(s)	inside rSNPs	diseases
3	nsv1030513	chr4:129770961-129965026	Strong transcription Genic enhancers Weak transcription Enhancers ZNF genes & repeats Flanking Active TSS Transcr. at gene 5' and 3' Active TSS	TF binding region CpG island Chromatin interactive region miRNA target site	4 gene(s)	inside rSNPs	diseases
4	nsv870175	chr4:129771718-129937945	Genic enhancers Weak transcription Strong transcription Enhancers ZNF genes & repeats Flanking Active TSS Transcr. at gene 5' and 3' Active TSS	TF binding region CpG island Chromatin interactive region miRNA target site	4 gene(s)	inside rSNPs	diseases
5	nsv1026772	chr4:129773881-129936205	ZNF genes & repeats Flanking Active TSS Weak transcription Strong transcription Genic enhancers Enhancers Transcr. at gene 5' and 3' Active TSS	TF binding region CpG island Chromatin interactive region miRNA target site	4 gene(s)	inside rSNPs	diseases
6	nsv534538	chr4:129799138-130431688	Enhancers Weak transcription Strong transcription Active TSS ZNF genes & repeats Flanking 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	12 gene(s)	inside rSNPs	diseases
7	nsv522694	chr4:129862073-129994690	Weak transcription Strong transcription ZNF genes & repeats Genic enhancers Enhancers Active TSS Flanking Active TSS	TF binding region Chromatin interactive region	2 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs17416706	LOC132321	cis	multi-tissue	Pritchard
rs17416706	FLJ30655	cis	multi-tissue	Pritchard
rs17416706	SCLT1	Cis_1M	lymphoblastoid	RTeQTL
rs17416706	PHF17	cis	multi-tissue	Pritchard

Chromatin state (count:74 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:129911400-129936800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
2	chr4:129917400-129936200	Weak transcription	Left Ventricle	heart
3	chr4:129917400-129942400	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
4	chr4:129930800-129936200	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
5	chr4:129932000-129944000	Weak transcription	Muscle Satellite Cultured Cells	--
6	chr4:129932200-129947000	Weak transcription	Rectal Smooth Muscle	rectum
7	chr4:129933200-129942200	Weak transcription	Rectal Mucosa Donor 29	rectum
8	chr4:129933400-129942000	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
9	chr4:129933400-129942000	Weak transcription	Primary B cells from peripheral blood	blood
10	chr4:129933800-129937400	Weak transcription	NHEK	skin
11	chr4:129934000-129942400	Weak transcription	Brain Hippocampus Middle	brain
12	chr4:129934200-129942600	Weak transcription	Primary T helper cells fromperipheralblood	blood
13	chr4:129934200-129944200	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
14	chr4:129934400-129936400	Weak transcription	Duodenum Smooth Muscle	Duodenum
15	chr4:129934600-129944200	Weak transcription	Primary T cells fromperipheralblood	blood
16	chr4:129934600-129944200	Weak transcription	Pancreatic Islets	Pancreatic Islet
17	chr4:129935000-129942200	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
18	chr4:129935400-129937000	ZNF genes & repeats	Primary hematopoietic stem cells short term culture	blood
19	chr4:129935400-129937000	ZNF genes & repeats	Fetal Muscle Trunk	muscle
20	chr4:129935400-129937200	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
21	chr4:129935400-129937200	ZNF genes & repeats	Monocytes-CD14+_RO01746	blood
22	chr4:129935400-129937800	ZNF genes & repeats	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
23	chr4:129935400-129937800	ZNF genes & repeats	Primary hematopoietic stem cells G-CSF-mobilized Male	--
24	chr4:129935600-129936400	Enhancers	HSMM	muscle
25	chr4:129935600-129936800	Weak transcription	Brain Angular Gyrus	brain
26	chr4:129935600-129936800	Genic enhancers	Dnd41	blood
27	chr4:129935600-129937000	ZNF genes & repeats	ES-UCSF4 Cell Line	embryonic stem cell
28	chr4:129935600-129937000	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
29	chr4:129935600-129937000	ZNF genes & repeats	Foreskin Melanocyte Primary Cells skin01	Skin
30	chr4:129935600-129937000	ZNF genes & repeats	Foreskin Melanocyte Primary Cells skin03	Skin
31	chr4:129935600-129943400	Weak transcription	Rectal Mucosa Donor 31	rectum
32	chr4:129935800-129936200	ZNF genes & repeats	Primary T cells from cord blood	blood
33	chr4:129935800-129936200	ZNF genes & repeats	Duodenum Mucosa	Duodenum
34	chr4:129935800-129936400	ZNF genes & repeats	iPS DF 6.9 Cell Line	embryonic stem cell
35	chr4:129935800-129936600	Genic enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
36	chr4:129935800-129936800	Strong transcription	Stomach Smooth Muscle	stomach
37	chr4:129935800-129936800	Strong transcription	Thymus	Thymus
38	chr4:129935800-129936800	Strong transcription	A549	lung
39	chr4:129935800-129937000	ZNF genes & repeats	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
40	chr4:129935800-129937000	Strong transcription	Cortex derived primary cultured neurospheres	brain
41	chr4:129935800-129937000	ZNF genes & repeats	Foreskin Keratinocyte Primary Cells skin02	Skin
42	chr4:129935800-129937000	ZNF genes & repeats	Fetal Intestine Small	intestine
43	chr4:129935800-129937000	ZNF genes & repeats	Lung	lung
44	chr4:129935800-129937000	ZNF genes & repeats	Ovary	ovary
45	chr4:129935800-129937000	ZNF genes & repeats	Pancreas	Pancrea
46	chr4:129935800-129937200	Strong transcription	Foreskin Fibroblast Primary Cells skin02	Skin
47	chr4:129935800-129937200	Strong transcription	Fetal Lung	lung
48	chr4:129935800-129937200	ZNF genes & repeats	Fetal Stomach	stomach
49	chr4:129935800-129937600	Strong transcription	Primary neutrophils fromperipheralblood	blood
50	chr4:129935800-129937600	ZNF genes & repeats	Fetal Muscle Leg	muscle

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