Variant report

Variant	rs6859296
Chromosome Location	chr5:179983602-179983603
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr5:179982621..179985082-chr5:179986194..179988848,3	K562	blood:
2	chr5:179977718..179980387-chr5:179982082..179983928,2	MCF-7	breast:
3	chr5:179982448..179984121-chr5:179987078..179988868,3	K562	blood:

Extended variants
information (count: 93 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:84)

rs_ID	r²[population]
rs10464103	0.87[ASW][hapmap];0.81[CEU][hapmap];0.88[CHB][hapmap];0.88[CHD][hapmap];0.81[GIH][hapmap];0.83[JPT][hapmap];0.85[MEX][hapmap];0.86[TSI][hapmap];0.90[YRI][hapmap];0.82[EUR][1000 genomes]
rs10516143	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];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10516144	0.87[ASW][hapmap];0.81[CEU][hapmap];0.88[CHB][hapmap];0.89[CHD][hapmap];0.81[GIH][hapmap];0.92[JPT][hapmap];0.85[MEX][hapmap];0.86[TSI][hapmap];0.86[YRI][hapmap];0.83[AMR][1000 genomes];0.86[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs10516145	0.94[ASW][hapmap];0.81[CEU][hapmap];0.88[CHB][hapmap];0.89[CHD][hapmap];0.81[GIH][hapmap];0.92[JPT][hapmap];0.94[LWK][hapmap];0.85[MEX][hapmap];0.86[TSI][hapmap];1.00[YRI][hapmap];0.86[EUR][1000 genomes]
rs10903256	0.88[CHB][hapmap];0.83[JPT][hapmap];0.81[YRI][hapmap];0.82[EUR][1000 genomes]
rs10903257	0.83[EUR][1000 genomes]
rs10903261	0.87[CEU][hapmap];0.86[CHB][hapmap];0.85[JPT][hapmap];0.83[AMR][1000 genomes];0.87[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs1105972	0.87[ASW][hapmap];0.81[CEU][hapmap];0.88[CHB][hapmap];0.88[CHD][hapmap];0.81[GIH][hapmap];0.83[JPT][hapmap];0.85[MEX][hapmap];0.86[TSI][hapmap];0.95[YRI][hapmap];0.82[EUR][1000 genomes]
rs11249716	0.81[CEU][hapmap];0.88[CHB][hapmap];0.92[JPT][hapmap];1.00[YRI][hapmap];0.80[AFR][1000 genomes];0.84[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs11249717	0.87[ASW][hapmap];0.81[CEU][hapmap];0.88[CHB][hapmap];0.86[CHD][hapmap];0.81[GIH][hapmap];0.92[JPT][hapmap];0.85[MEX][hapmap];0.86[TSI][hapmap];0.82[YRI][hapmap];0.83[AMR][1000 genomes];0.86[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs11249719	0.87[ASW][hapmap];0.81[CEU][hapmap];0.88[CHB][hapmap];0.89[CHD][hapmap];0.81[GIH][hapmap];0.92[JPT][hapmap];0.85[MEX][hapmap];0.86[TSI][hapmap];0.86[YRI][hapmap];0.83[AMR][1000 genomes];0.86[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs11249720	0.81[AMR][1000 genomes];0.85[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs11249722	0.82[AMR][1000 genomes];0.87[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs11249723	0.81[AMR][1000 genomes];0.87[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs11249725	0.83[AMR][1000 genomes];0.87[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs11249726	0.89[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11249728	0.88[AMR][1000 genomes];0.89[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11249729	1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[AFR][1000 genomes];0.85[AMR][1000 genomes];0.89[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11249731	0.83[AMR][1000 genomes];0.89[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11249732	0.81[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[YRI][hapmap];0.89[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11738044	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];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11738129	0.94[ASW][hapmap];0.81[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];0.83[GIH][hapmap];1.00[JPT][hapmap];0.90[MEX][hapmap];0.84[MKK][hapmap];0.86[TSI][hapmap];0.86[YRI][hapmap];0.83[AFR][1000 genomes];0.88[AMR][1000 genomes];0.89[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11738199	0.87[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[YRI][hapmap];0.83[AFR][1000 genomes];0.88[AMR][1000 genomes];0.89[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11740950	0.83[AMR][1000 genomes];0.86[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs11743298	0.82[AMR][1000 genomes];0.86[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs11748611	0.82[EUR][1000 genomes]
rs11748880	0.83[AMR][1000 genomes];0.87[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs11750412	0.81[CEU][hapmap];0.88[CHB][hapmap];0.92[JPT][hapmap];0.86[YRI][hapmap];0.81[AMR][1000 genomes];0.86[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs11750506	0.84[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11949971	0.81[CEU][hapmap];0.81[CHB][hapmap];0.92[JPT][hapmap];1.00[YRI][hapmap];0.84[AFR][1000 genomes];0.81[AMR][1000 genomes];0.84[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs11956294	0.90[AFR][1000 genomes];0.83[AMR][1000 genomes];0.87[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs12054820	0.80[ASW][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[JPT][hapmap];0.85[MEX][hapmap];0.82[TSI][hapmap];0.82[YRI][hapmap];0.81[AFR][1000 genomes];0.85[AMR][1000 genomes];0.89[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12187407	0.83[EUR][1000 genomes]
rs12188182	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12188688	0.84[JPT][hapmap]
rs13152935	0.98[ASN][1000 genomes]
rs13154251	0.83[EUR][1000 genomes]
rs13164926	0.86[AFR][1000 genomes];0.83[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs13165676	0.85[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs13166941	0.81[ASN][1000 genomes]
rs13168301	0.81[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs13168976	0.83[AMR][1000 genomes];0.86[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs13169807	0.81[CEU][hapmap];0.88[CHB][hapmap];0.83[JPT][hapmap];0.95[YRI][hapmap];0.82[EUR][1000 genomes]
rs13171802	0.81[EUR][1000 genomes]
rs13172721	0.81[EUR][1000 genomes]
rs13174261	0.81[AMR][1000 genomes];0.86[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs13181218	0.82[EUR][1000 genomes]
rs13182715	0.81[CEU][hapmap];0.88[CHB][hapmap];0.83[JPT][hapmap];0.95[YRI][hapmap]
rs13185444	0.82[EUR][1000 genomes]
rs13190607	0.84[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[YRI][hapmap];0.81[AFR][1000 genomes];0.85[AMR][1000 genomes];0.89[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs13361838	0.83[CHB][hapmap];0.82[JPT][hapmap]
rs1478360	0.87[ASW][hapmap];0.81[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[TSI][hapmap];0.86[YRI][hapmap];0.88[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1994912	0.82[AFR][1000 genomes];0.88[AMR][1000 genomes];0.89[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2131811	0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2387283	0.81[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[YRI][hapmap];0.81[AFR][1000 genomes];0.88[AMR][1000 genomes];0.89[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2387284	0.98[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2387287	0.83[EUR][1000 genomes]
rs2387288	0.81[CEU][hapmap];0.94[CHB][hapmap];0.83[JPT][hapmap];0.95[YRI][hapmap];0.83[EUR][1000 genomes]
rs2617262	0.82[ASN][1000 genomes]
rs34294053	0.84[EUR][1000 genomes]
rs4002641	0.82[EUR][1000 genomes]
rs57665202	0.89[ASN][1000 genomes]
rs62405497	0.81[EUR][1000 genomes]
rs62405523	0.82[EUR][1000 genomes]
rs62405524	0.83[EUR][1000 genomes]
rs62405545	0.84[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs6601127	0.83[AMR][1000 genomes];0.87[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6601129	0.87[ASW][hapmap];0.81[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];0.83[GIH][hapmap];1.00[JPT][hapmap];0.89[MEX][hapmap];0.84[MKK][hapmap];0.86[TSI][hapmap];0.86[YRI][hapmap];0.83[AMR][1000 genomes];0.89[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs67607816	0.83[AMR][1000 genomes];0.87[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs6864038	0.81[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];0.86[YRI][hapmap];0.88[AMR][1000 genomes];0.89[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6874985	0.87[ASW][hapmap];0.81[CEU][hapmap];0.94[CHB][hapmap];0.97[CHD][hapmap];0.83[GIH][hapmap];1.00[JPT][hapmap];0.90[MEX][hapmap];0.86[TSI][hapmap];0.86[YRI][hapmap];0.81[AFR][1000 genomes];0.87[AMR][1000 genomes];0.89[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6879011	0.88[CHB][hapmap];0.92[JPT][hapmap];0.81[YRI][hapmap];0.84[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs6888064	0.81[CEU][hapmap];0.88[CHB][hapmap];0.83[JPT][hapmap];0.95[YRI][hapmap];0.83[EUR][1000 genomes]
rs6888805	0.83[AFR][1000 genomes];0.88[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6894846	0.81[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[YRI][hapmap];0.81[AFR][1000 genomes];0.85[AMR][1000 genomes];0.89[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6897365	0.81[CEU][hapmap];0.88[CHB][hapmap];0.92[JPT][hapmap];0.90[YRI][hapmap];0.84[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs7704287	0.81[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7705358	0.86[AMR][1000 genomes];0.85[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7705421	0.87[ASW][hapmap];0.81[CEU][hapmap];0.88[CHB][hapmap];0.89[CHD][hapmap];0.81[GIH][hapmap];0.83[JPT][hapmap];0.90[MEX][hapmap];0.86[TSI][hapmap];0.95[YRI][hapmap];0.83[EUR][1000 genomes]
rs7705521	0.82[AMR][1000 genomes];0.86[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7722020	0.81[CEU][hapmap];0.88[CHB][hapmap];0.83[JPT][hapmap];0.81[YRI][hapmap];0.83[EUR][1000 genomes]
rs7724243	0.86[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7727679	0.81[CEU][hapmap];0.88[CHB][hapmap];0.92[JPT][hapmap];0.86[YRI][hapmap];0.83[AMR][1000 genomes];0.87[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs937919	0.88[CHB][hapmap];0.88[CHD][hapmap];0.83[JPT][hapmap]

Variant overlapped rSNPs/rCNVs (count:9 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1023914	chr5:179649883-180040672	Weak transcription Enhancers Strong transcription Bivalent/Poised TSS ZNF genes & repeats Flanking Active TSS Active TSS Transcr. at gene 5' and 3' Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	31 gene(s)	inside rSNPs	diseases
2	nsv537983	chr5:179649883-180040672	Strong transcription ZNF genes & repeats Weak transcription Enhancers Flanking Active TSS Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	31 gene(s)	inside rSNPs	diseases
3	nsv1030697	chr5:179710469-180686563	ZNF genes & repeats Enhancers Transcr. at gene 5' and 3' Genic enhancers Strong transcription Weak transcription Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	184 gene(s)	inside rSNPs	diseases
4	nsv1026417	chr5:179721376-180291360	Enhancers Weak transcription Transcr. at gene 5' and 3' Flanking Active TSS Strong transcription Flanking Bivalent TSS/Enh Active TSS ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	90 gene(s)	inside rSNPs	diseases
5	nsv1031836	chr5:179742033-180676122	Strong transcription Flanking Active TSS Transcr. at gene 5' and 3' Active TSS Bivalent Enhancer Enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Weak transcription Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	177 gene(s)	inside rSNPs	diseases
6	nsv537984	chr5:179742033-180676122	Active TSS Bivalent Enhancer Flanking Active TSS Genic enhancers Weak transcription Flanking Bivalent TSS/Enh Enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Strong transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	177 gene(s)	inside rSNPs	diseases
7	nsv949199	chr5:179743553-180696889	Weak transcription Transcr. at gene 5' and 3' Enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Strong transcription Flanking Active TSS Genic enhancers Bivalent/Poised TSS Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	182 gene(s)	inside rSNPs	diseases
8	nsv830564	chr5:179867394-180010096	Enhancers Weak transcription Strong transcription Flanking Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Active TSS Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	20 gene(s)	inside rSNPs	diseases
9	esv1810959	chr5:179945112-179997861	Weak transcription Strong transcription Enhancers Genic enhancers ZNF genes & repeats Active TSS Transcr. at gene 5' and 3' Flanking Active TSS	TF binding region CpG island Chromatin interactive region	4 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs6859296	RGS14	cis	parietal	SCAN
rs6859296	GRK6	cis	cerebellum	SCAN
rs6859296	RAB24	cis	cerebellum	SCAN

Chromatin state (count:124 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:179950200-179984400	Weak transcription	NHDF-Ad	bronchial
2	chr5:179950200-179992000	Weak transcription	Right Ventricle	heart
3	chr5:179950400-179992400	Weak transcription	Skeletal Muscle Male	skeletal muscle
4	chr5:179950600-180004000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
5	chr5:179951000-179991800	Weak transcription	Small Intestine	intestine
6	chr5:179959800-179991600	Weak transcription	HMEC	breast
7	chr5:179960000-180000600	Weak transcription	iPS-15b Cell Line	embryonic stem cell
8	chr5:179960200-179991600	Weak transcription	Esophagus	oesophagus
9	chr5:179960200-179998200	Weak transcription	Spleen	Spleen
10	chr5:179960400-179991600	Weak transcription	Gastric	stomach
11	chr5:179961200-179992600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
12	chr5:179961400-179991800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
13	chr5:179961600-179991800	Weak transcription	Colon Smooth Muscle	Colon
14	chr5:179962200-179991800	Weak transcription	Brain Hippocampus Middle	brain
15	chr5:179964000-179992600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
16	chr5:179966800-179987400	Strong transcription	Dnd41	blood
17	chr5:179967600-179991800	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
18	chr5:179969200-179985000	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
19	chr5:179969600-179991600	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
20	chr5:179970000-179992200	Weak transcription	HSMM	muscle
21	chr5:179970800-180006600	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
22	chr5:179971600-179992000	Weak transcription	HUVEC	blood vessel
23	chr5:179972000-179988600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
24	chr5:179973800-180005200	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
25	chr5:179974400-180005800	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
26	chr5:179975000-180005800	Strong transcription	Monocytes-CD14+_RO01746	blood
27	chr5:179975200-179983800	Strong transcription	HUES6 Cell Line	embryonic stem cell
28	chr5:179975200-179983800	Strong transcription	iPS-20b Cell Line	embryonic stem cell
29	chr5:179975600-179985200	Strong transcription	HUES64 Cell Line	embryonic stem cell
30	chr5:179975600-179992000	Weak transcription	Psoas Muscle	Psoas
31	chr5:179975600-180004600	Weak transcription	Pancreatic Islets	Pancreatic Islet
32	chr5:179976200-179998200	Weak transcription	Fetal Heart	heart
33	chr5:179976200-180007200	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
34	chr5:179976600-179988600	Weak transcription	Pancreas	Pancrea
35	chr5:179976800-179983800	Strong transcription	Primary T helper cells fromperipheralblood	blood
36	chr5:179976800-179984600	Strong transcription	Primary monocytes fromperipheralblood	blood
37	chr5:179976800-179985400	Strong transcription	Fetal Thymus	thymus
38	chr5:179977000-179983800	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
39	chr5:179977000-179983800	Strong transcription	Thymus	Thymus
40	chr5:179977000-179986800	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
41	chr5:179978000-179984800	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
42	chr5:179978000-179992000	Weak transcription	Colonic Mucosa	Colon
43	chr5:179978000-179992400	Weak transcription	NHEK	skin
44	chr5:179978200-179990600	Weak transcription	Brain Cingulate Gyrus	brain
45	chr5:179978200-179991000	Weak transcription	Brain Inferior Temporal Lobe	brain
46	chr5:179978200-179991800	Weak transcription	Rectal Smooth Muscle	rectum
47	chr5:179978400-179985000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
48	chr5:179978400-179985200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
49	chr5:179978400-179990600	Weak transcription	Brain Substantia Nigra	brain
50	chr5:179978400-179992400	Weak transcription	H9 Cell Line	embryonic stem cell

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