Variant report

Variant	rs4660862
Chromosome Location	chr1:45955056-45955057
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr1:45954972..45958180-chr1:45986651..45988959,5	K562	blood:
2	chr1:45293211..45295000-chr1:45954094..45956498,2	K562	blood:
3	chr1:45954905..45960579-chr1:45960652..45966878,10	K562	blood:
4	chr1:45951915..45956979-chr1:46048471..46052743,8	K562	blood:
5	chr1:45451104..45453643-chr1:45953899..45956205,2	K562	blood:
6	chr1:45285250..45286919-chr1:45954512..45956558,2	K562	blood:
7	chr1:45934784..45936489-chr1:45953495..45956365,2	K562	blood:

Variant related genes	Relation type
ENSG00000132780	Chromatin interaction
ENSG00000202444	Chromatin interaction
ENSG00000117450	Chromatin interaction
ENSG00000132763	Chromatin interaction
ENSG00000236624	Chromatin interaction
ENSG00000070785	Chromatin interaction

Extended variants
information (count: 79 )
Associated
traits (count: 20 )

rSNPs within LD-proxies of this variant (count:69)

rs_ID	r²[population]
rs10157597	0.83[AFR][1000 genomes];0.90[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs1044717	0.92[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs10493120	0.86[GIH][hapmap];1.00[MEX][hapmap]
rs10736426	0.96[CEU][hapmap];0.92[CHD][hapmap];0.96[GIH][hapmap];0.89[MEX][hapmap];0.97[TSI][hapmap];0.90[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs10789466	0.81[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs1088099	0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs11211110	0.86[GIH][hapmap];1.00[MEX][hapmap]
rs11211113	0.84[CHD][hapmap];0.86[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap]
rs11211132	1.00[ASW][hapmap];0.96[CEU][hapmap];0.96[GIH][hapmap];0.84[LWK][hapmap];1.00[MEX][hapmap];0.90[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.89[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs11211134	0.91[EUR][1000 genomes]
rs12038608	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs12042481	0.85[CHB][hapmap];0.84[CHD][hapmap];0.85[ASN][1000 genomes]
rs12047498	0.85[ASN][1000 genomes]
rs12048936	0.84[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs12082256	0.80[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs12145526	0.95[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12729974	0.83[AFR][1000 genomes];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs12749658	0.91[EUR][1000 genomes]
rs1337902	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];1.00[ASN][1000 genomes]
rs1494813	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1691217	0.86[GIH][hapmap];0.89[MEX][hapmap]
rs1765711	1.00[JPT][hapmap]
rs1974271	0.87[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs2065708	0.85[CHB][hapmap];0.84[CHD][hapmap]
rs2077808	0.86[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs2152077	0.95[CEU][hapmap];0.90[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs2356555	0.90[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs2356559	1.00[ASW][hapmap];0.96[CEU][hapmap];0.81[CHD][hapmap];0.96[GIH][hapmap];0.84[LWK][hapmap];1.00[MEX][hapmap];0.89[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap]
rs2356560	0.90[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs2356561	0.90[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs2991966	0.92[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs2993257	0.80[AFR][1000 genomes];0.84[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs2993259	0.86[AFR][1000 genomes];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs34315657	0.81[EUR][1000 genomes]
rs3748643	1.00[CEU][hapmap];0.85[CHB][hapmap];1.00[YRI][hapmap];0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs4233498	0.89[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs4660306	1.00[ASW][hapmap];0.96[CEU][hapmap];0.96[GIH][hapmap];0.84[LWK][hapmap];1.00[MEX][hapmap];0.90[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.89[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs4660309	0.86[EUR][1000 genomes]
rs4660860	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4660864	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.92[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4660866	0.86[EUR][1000 genomes]
rs4660867	0.80[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs4660868	0.80[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs4660871	0.82[EUR][1000 genomes]
rs4660872	0.88[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs6429566	0.82[CHD][hapmap];0.86[GIH][hapmap];1.00[JPT][hapmap];0.89[MEX][hapmap]
rs6429567	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6429569	0.96[CEU][hapmap];0.96[GIH][hapmap];0.92[TSI][hapmap];0.90[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs6667191	0.87[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs6673477	0.82[EUR][1000 genomes]
rs6688424	0.81[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs6688516	0.90[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs7516006	0.87[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs7522705	0.96[CEU][hapmap];0.92[CHD][hapmap];0.96[GIH][hapmap];0.89[MEX][hapmap];0.95[TSI][hapmap];0.90[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs7534467	0.89[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs7536557	0.96[CEU][hapmap];0.92[CHD][hapmap];0.96[GIH][hapmap];0.89[MEX][hapmap];0.95[TSI][hapmap];0.90[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs7539253	1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7543076	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs7546268	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs7549093	0.86[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs781059	0.83[CHD][hapmap];0.84[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap]
rs781060	0.83[CHD][hapmap];0.86[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap]
rs781061	1.00[JPT][hapmap]
rs781066	0.95[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs882803	0.96[CEU][hapmap];0.92[CHD][hapmap];0.96[GIH][hapmap];0.88[MEX][hapmap];0.97[TSI][hapmap];0.90[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs937290	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs945179	1.00[ASW][hapmap];1.00[CEU][hapmap];0.85[CHB][hapmap];0.84[CHD][hapmap];1.00[GIH][hapmap];0.88[LWK][hapmap];1.00[MEX][hapmap];0.97[MKK][hapmap];0.97[TSI][hapmap];0.90[YRI][hapmap];0.90[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs9725380	0.88[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs9803979	0.90[AMR][1000 genomes];0.93[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:10 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv498036	chr1:45428030-46050934	Active TSS Enhancers Flanking Active TSS Genic enhancers Weak transcription Strong transcription Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	191 gene(s)	inside rSNPs	diseases
2	nsv997548	chr1:45733596-45955845	Genic enhancers Enhancers Active TSS Weak transcription Flanking Active TSS Strong transcription Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	56 gene(s)	inside rSNPs	diseases
3	nsv534942	chr1:45733596-45955845	Weak transcription Enhancers Active TSS Genic enhancers Bivalent Enhancer Strong transcription Flanking Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	56 gene(s)	inside rSNPs	diseases
4	esv1795802	chr1:45819489-46009818	Enhancers Weak transcription Active TSS Genic enhancers Flanking Active TSS Strong transcription Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	126 gene(s)	inside rSNPs	diseases
5	esv1831217	chr1:45819489-46009818	Strong transcription Enhancers Genic enhancers Active TSS Weak transcription Flanking Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	126 gene(s)	inside rSNPs	diseases
6	nsv530016	chr1:45868543-46069020	Flanking Active TSS Genic enhancers Weak transcription Active TSS Enhancers Transcr. at gene 5' and 3' Strong transcription Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	149 gene(s)	inside rSNPs	diseases
7	nsv829726	chr1:45897581-46103186	Weak transcription Enhancers Flanking Active TSS Strong transcription Active TSS Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	148 gene(s)	inside rSNPs	diseases
8	nsv529631	chr1:45905936-46335246	Enhancers Flanking Active TSS Transcr. at gene 5' and 3' Strong transcription Weak transcription Active TSS Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	207 gene(s)	inside rSNPs	diseases
9	nsv932680	chr1:45935520-46686477	Strong transcription Weak transcription Flanking Active TSS Active TSS Enhancers Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	232 gene(s)	inside rSNPs	diseases
10	nsv868828	chr1:45953923-46686477	Active TSS Weak transcription Enhancers Flanking Active TSS Strong transcription Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	232 gene(s)	inside rSNPs	diseases

mRNA abundance (count:20)

SNP	Gene	Cis/trans	Tissue	Source
rs4660862	CCDC163P	cis	Artery Aorta	GTEx
rs4660862	CCDC163P	cis	Heart Left Ventricle	GTEx
rs4660862	CCDC163P	cis	Muscle Skeletal	GTEx
rs4660862	CCDC163P	cis	lymphoblastoid	seeQTL
rs4660862	CCDC163P	cis	Artery Tibial	GTEx
rs4660862	CCDC163P	cis	Stomach	GTEx
rs4660862	LOC126661	Cis_1M	lymphoblastoid	RTeQTL
rs4660862	CCDC163P	cis	Nerve Tibial	GTEx
rs4660862	CCDC163P	cis	Skin Sun Exposed Lower leg	GTEx
rs4660862	ST3GAL3	cis	parietal	SCAN
rs4660862	CCDC163P	cis	Whole Blood	GTEx
rs4660862	CYP4A11	cis	parietal	SCAN
rs4660862	CCDC163P	cis	Esophagus Mucosa	GTEx
rs4660862	CYP4Z2P	cis	parietal	SCAN
rs4660862	BEND5	cis	cerebellum	SCAN
rs4660862	CCDC163P	cis	lung	GTEx
rs4660862	CCDC163P	cis	Esophagus Muscularis	GTEx
rs4660862	CCDC163P	cis	Thyroid	GTEx
rs4660862	TESK2	cis	lymphoblastoid	seeQTL
rs4660862	CCDC163P	cis	Adipose Subcutaneous	GTEx

Chromatin state (count:58 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:45944400-45955600	Weak transcription	Small Intestine	intestine
2	chr1:45945200-45955400	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
3	chr1:45945200-45955800	Weak transcription	Sigmoid Colon	Sigmoid Colon
4	chr1:45945600-45955800	Weak transcription	Left Ventricle	heart
5	chr1:45950000-45955600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
6	chr1:45952000-45955400	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
7	chr1:45954000-45955200	Enhancers	Fetal Intestine Small	intestine
8	chr1:45954000-45955400	Enhancers	Liver	Liver
9	chr1:45954000-45955600	Enhancers	Brain Substantia Nigra	brain
10	chr1:45954000-45955600	Weak transcription	Right Atrium	heart
11	chr1:45954000-45955600	Enhancers	K562	blood
12	chr1:45954200-45955200	Weak transcription	Primary monocytes fromperipheralblood	blood
13	chr1:45954200-45955200	Enhancers	Brain Cingulate Gyrus	brain
14	chr1:45954200-45955200	Enhancers	HepG2	liver
15	chr1:45954200-45955400	Enhancers	Primary neutrophils fromperipheralblood	blood
16	chr1:45954200-45955600	Enhancers	Skeletal Muscle Male	skeletal muscle
17	chr1:45954400-45955200	Enhancers	Breast Myoepithelial Primary Cells	Breast
18	chr1:45954400-45955200	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
19	chr1:45954400-45955200	Enhancers	Placenta	Placenta
20	chr1:45954400-45955600	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
21	chr1:45954600-45955400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
22	chr1:45954600-45955400	Enhancers	Spleen	Spleen
23	chr1:45954600-45955600	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
24	chr1:45954800-45955200	Flanking Active TSS	HUES48 Cell Line	embryonic stem cell
25	chr1:45954800-45955200	Flanking Active TSS	HUES6 Cell Line	embryonic stem cell
26	chr1:45954800-45955200	Flanking Active TSS	iPS-15b Cell Line	embryonic stem cell
27	chr1:45954800-45955200	Flanking Bivalent TSS/Enh	iPS-20b Cell Line	embryonic stem cell
28	chr1:45954800-45955200	Weak transcription	Primary hematopoietic stem cells	blood
29	chr1:45954800-45955200	Enhancers	NHEK	skin
30	chr1:45954800-45955400	Weak transcription	Primary hematopoietic stem cells short term culture	blood
31	chr1:45954800-45955400	Enhancers	Primary T helper cells PMA-I stimulated	--
32	chr1:45954800-45955400	Weak transcription	Brain Angular Gyrus	brain
33	chr1:45954800-45955400	Flanking Active TSS	Duodenum Mucosa	Duodenum
34	chr1:45954800-45955400	Flanking Active TSS	GM12878-XiMat	blood
35	chr1:45954800-45955400	Enhancers	Monocytes-CD14+_RO01746	blood
36	chr1:45954800-45955600	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
37	chr1:45954800-45956400	Bivalent/Poised TSS	HUES64 Cell Line	embryonic stem cell
38	chr1:45955000-45955200	Flanking Bivalent TSS/Enh	ES-I3 Cell Line	embryonic stem cell
39	chr1:45955000-45955200	Active TSS	H1 Cell Line	embryonic stem cell
40	chr1:45955000-45955200	Enhancers	Primary B cells from peripheral blood	blood
41	chr1:45955000-45955200	Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
42	chr1:45955000-45955200	Active TSS	Rectal Mucosa Donor 29	rectum
43	chr1:45955000-45955400	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
44	chr1:45955000-45955400	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
45	chr1:45955000-45955400	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
46	chr1:45955000-45955400	Enhancers	Brain Anterior Caudate	brain
47	chr1:45955000-45955400	Flanking Active TSS	Fetal Intestine Large	intestine
48	chr1:45955000-45955400	Flanking Active TSS	Skeletal Muscle Female	skeletal muscle
49	chr1:45955000-45955600	Enhancers	Primary T helper naive cells fromperipheralblood	blood
50	chr1:45955000-45955600	Enhancers	Primary T helper 17 cells PMA-I stimulated	--

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links