Variant report

Variant	rs17164380
Chromosome Location	chr4:1159889-1159890
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:3)
CpG islands
(count:0)
Chromatin interactive
region (count:9)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:3 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	SIN3AK20	chr4:1159401-1161758	PFSK-1	brain:	n/a	n/a
2	POLR2A	chr4:1159180-1166648	PFSK-1	brain:	n/a	n/a
3	POLR2A	chr4:1159517-1165015	PFSK-1	brain:	n/a	n/a

No data

(count:9 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr4:1148836..1150656-chr4:1158742..1161485,3	K562	blood:
2	chr4:1157936..1161506-chr4:1282339..1285236,6	K562	blood:
3	chr4:1159229..1162099-chr4:1242725..1245069,2	K562	blood:
4	chr4:1159882..1162594-chr4:1225934..1228487,2	MCF-7	breast:
5	chr4:1158166..1163360-chr4:1238498..1245354,13	MCF-7	breast:
6	chr4:1157568..1159327-chr4:1159533..1161126,2	MCF-7	breast:
7	chr4:1159479..1162008-chr4:1166717..1168665,3	MCF-7	breast:
8	chr4:1159747..1163015-chr4:1240558..1244483,3	K562	blood:
9	chr4:1159320..1162756-chr4:1282339..1286135,5	K562	blood:

No data

Variant related genes	Relation type
ENSG00000273179	TF binding region
ENSG00000159674	Chromatin interaction
ENSG00000159692	Chromatin interaction
ENSG00000090316	Chromatin interaction
ENSG00000196810	Chromatin interaction

Extended variants
information (count: 73 )
Associated
traits (count: 7 )

rSNPs within LD-proxies of this variant (count:53)

rs_ID	r²[population]
rs10084890	0.83[CHD][hapmap];0.90[JPT][hapmap]
rs1010342	0.86[CHD][hapmap];0.90[JPT][hapmap]
rs10902752	0.86[CHD][hapmap];0.90[JPT][hapmap];1.00[YRI][hapmap]
rs11247973	0.95[JPT][hapmap]
rs11732520	0.90[JPT][hapmap]
rs11939380	0.86[CHD][hapmap];0.90[JPT][hapmap]
rs1250125	0.87[MEX][hapmap];0.88[TSI][hapmap]
rs1250126	0.86[TSI][hapmap]
rs12645644	0.86[CHD][hapmap];0.90[JPT][hapmap]
rs12647929	0.90[JPT][hapmap]
rs13107058	0.86[CHD][hapmap];0.90[JPT][hapmap];1.00[YRI][hapmap]
rs13118508	0.83[EUR][1000 genomes]
rs13135215	0.86[CHD][hapmap];0.90[JPT][hapmap];1.00[YRI][hapmap]
rs1466214	0.84[JPT][hapmap]
rs1466215	0.80[JPT][hapmap]
rs1670533	0.86[CHD][hapmap];0.90[JPT][hapmap];1.00[YRI][hapmap]
rs1670534	0.86[CHD][hapmap];0.90[JPT][hapmap];1.00[YRI][hapmap]
rs2014318	0.85[CHD][hapmap];0.90[JPT][hapmap];1.00[YRI][hapmap]
rs2045065	0.84[CHD][hapmap];0.80[JPT][hapmap];1.00[YRI][hapmap]
rs2045066	0.86[CHD][hapmap];0.90[JPT][hapmap]
rs2100411	0.90[JPT][hapmap];1.00[YRI][hapmap]
rs2242278	0.86[CEU][hapmap];0.93[TSI][hapmap];0.91[EUR][1000 genomes]
rs2242279	0.91[EUR][1000 genomes]
rs2290408	0.86[CHD][hapmap];0.90[JPT][hapmap];1.00[LWK][hapmap];1.00[YRI][hapmap]
rs3796619	0.86[CHD][hapmap];0.81[JPT][hapmap]
rs3796620	0.90[JPT][hapmap];1.00[YRI][hapmap]
rs4045481	0.86[CHD][hapmap];0.90[JPT][hapmap]
rs4690212	0.86[CHD][hapmap];0.90[JPT][hapmap];1.00[YRI][hapmap]
rs4690213	0.86[CHD][hapmap];0.90[JPT][hapmap]
rs4690214	0.86[CHD][hapmap];0.90[JPT][hapmap];1.00[YRI][hapmap]
rs4974601	0.85[CHD][hapmap];0.81[JPT][hapmap]
rs4974633	0.94[CHB][hapmap];1.00[YRI][hapmap];0.90[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs4974638	0.95[JPT][hapmap]
rs610218	0.90[JPT][hapmap];1.00[YRI][hapmap]
rs62293562	0.82[EUR][1000 genomes]
rs629260	0.94[JPT][hapmap];1.00[YRI][hapmap]
rs651017	0.86[CHD][hapmap];0.90[JPT][hapmap]
rs652063	0.88[JPT][hapmap];1.00[YRI][hapmap]
rs6599276	0.90[JPT][hapmap];1.00[YRI][hapmap]
rs6812586	0.86[CHD][hapmap];0.90[JPT][hapmap];1.00[YRI][hapmap]
rs6812596	0.90[JPT][hapmap];1.00[YRI][hapmap]
rs6822863	0.86[CHD][hapmap];0.90[JPT][hapmap]
rs6836350	0.90[JPT][hapmap]
rs6837145	0.89[JPT][hapmap]
rs6839931	0.86[CHD][hapmap];0.90[JPT][hapmap];1.00[YRI][hapmap]
rs6852850	0.90[JPT][hapmap];1.00[YRI][hapmap]
rs6854793	0.90[JPT][hapmap]
rs6857085	0.90[JPT][hapmap];1.00[YRI][hapmap]
rs7673898	0.86[CHD][hapmap];0.90[JPT][hapmap];1.00[YRI][hapmap]
rs7700083	0.98[AMR][1000 genomes];0.90[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs935970	1.00[YRI][hapmap]
rs935971	1.00[YRI][hapmap]
rs935972	1.00[YRI][hapmap]

Variant overlapped rSNPs/rCNVs (count:20 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv822425	chr4:540105-1413799	Weak transcription Flanking Bivalent TSS/Enh Active TSS Flanking Active TSS Enhancers ZNF genes & repeats Strong transcription Bivalent Enhancer Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	108 gene(s)	inside rSNPs	diseases
2	nsv530490	chr4:614355-1399150	Bivalent Enhancer Enhancers Flanking Active TSS Weak transcription Genic enhancers ZNF genes & repeats Strong transcription Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	104 gene(s)	inside rSNPs	diseases
3	nsv536980	chr4:827866-1167377	Active TSS Weak transcription Flanking Bivalent TSS/Enh Strong transcription Genic enhancers Enhancers Bivalent Enhancer Flanking Active TSS Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	40 gene(s)	inside rSNPs	diseases
4	nsv1009619	chr4:901897-1215657	Strong transcription Weak transcription ZNF genes & repeats Flanking Active TSS Enhancers Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	43 gene(s)	inside rSNPs	diseases
5	nsv1003876	chr4:927509-1191316	Weak transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Enhancers Flanking Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' Strong transcription Active TSS Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	37 gene(s)	inside rSNPs	diseases
6	nsv1000381	chr4:927509-1198766	Weak transcription Enhancers Genic enhancers Flanking Bivalent TSS/Enh Strong transcription Active TSS Flanking Active TSS Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	38 gene(s)	inside rSNPs	diseases
7	esv3339080	chr4:970630-1546223	Active TSS Flanking Active TSS Bivalent/Poised TSS Enhancers Bivalent Enhancer Weak transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Strong transcription Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	82 gene(s)	inside rSNPs	diseases
8	nsv1005990	chr4:1015652-1167619	Flanking Bivalent TSS/Enh Bivalent Enhancer Strong transcription Enhancers Weak transcription Flanking Active TSS Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	22 gene(s)	inside rSNPs	diseases
9	nsv1012892	chr4:1086871-1176630	Enhancers Bivalent Enhancer Weak transcription Transcr. at gene 5' and 3' Active TSS Flanking Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Genic enhancers Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases
10	nsv829835	chr4:1097586-1304239	Enhancers Genic enhancers Flanking Active TSS Active TSS Bivalent Enhancer Weak transcription ZNF genes & repeats Strong transcription Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	59 gene(s)	inside rSNPs	diseases
11	nsv878328	chr4:1141573-1990425	Weak transcription Flanking Active TSS Enhancers Strong transcription Genic enhancers Active TSS Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	121 gene(s)	inside rSNPs	diseases
12	nsv878329	chr4:1147407-1254930	Genic enhancers Bivalent/Poised TSS Flanking Active TSS Bivalent Enhancer Weak transcription Active TSS Strong transcription Enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	49 gene(s)	inside rSNPs	diseases
13	nsv878330	chr4:1147407-1523930	Strong transcription Bivalent Enhancer Weak transcription Enhancers Flanking Active TSS Active TSS Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	71 gene(s)	inside rSNPs	diseases
14	nsv519106	chr4:1158991-1174861	Enhancers Bivalent Enhancer Flanking Active TSS Active TSS Weak transcription Flanking Bivalent TSS/Enh Genic enhancers Strong transcription Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
15	nsv593276	chr4:1159680-1227469	Flanking Active TSS Genic enhancers Weak transcription Strong transcription Enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Active TSS Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	14 gene(s)	inside rSNPs	diseases
16	nsv461151	chr4:1159680-1236840	Enhancers Flanking Bivalent TSS/Enh Strong transcription Weak transcription Flanking Active TSS Active TSS Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	16 gene(s)	inside rSNPs	diseases
17	nsv593277	chr4:1159680-1236840	Flanking Active TSS Weak transcription Flanking Bivalent TSS/Enh Enhancers Strong transcription ZNF genes & repeats Bivalent Enhancer Genic enhancers Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	16 gene(s)	inside rSNPs	diseases
18	nsv878331	chr4:1159680-1254930	Weak transcription Bivalent Enhancer Enhancers Flanking Active TSS Active TSS Transcr. at gene 5' and 3' Strong transcription Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	49 gene(s)	inside rSNPs	diseases
19	nsv461152	chr4:1159680-1415698	Enhancers Active TSS Flanking Active TSS Strong transcription Bivalent Enhancer Genic enhancers Weak transcription Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	70 gene(s)	inside rSNPs	diseases
20	nsv593278	chr4:1159680-1415698	Enhancers Flanking Bivalent TSS/Enh Genic enhancers Strong transcription Weak transcription Flanking Active TSS Active TSS ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	70 gene(s)	inside rSNPs	diseases

mRNA abundance (count:7)

SNP	Gene	Cis/trans	Tissue	Source
rs17164380	GAK	cis	cerebellum	SCAN
rs17164380	IDUA	cis	cerebellum	SCAN
rs17164380	CTBP1	Cis_1M	lymphoblastoid	RTeQTL
rs17164380	RNF212	cis	Muscle Skeletal	GTEx
rs17164380	RNF212	cis	cerebellum	SCAN
rs17164380	CRIPAK	cis	lymphoblastoid	seeQTL
rs17164380	UVSSA	cis	Skin Sun Exposed Lower leg	GTEx

Chromatin state (count:25 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:1146600-1160800	Weak transcription	Ovary	ovary
2	chr4:1149200-1161000	Weak transcription	Right Atrium	heart
3	chr4:1149600-1160800	Weak transcription	Colon Smooth Muscle	Colon
4	chr4:1149600-1161000	Weak transcription	Gastric	stomach
5	chr4:1155600-1160400	Weak transcription	Colonic Mucosa	Colon
6	chr4:1156600-1160400	Weak transcription	Liver	Liver
7	chr4:1156600-1160800	Weak transcription	Duodenum Mucosa	Duodenum
8	chr4:1157200-1160800	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
9	chr4:1157600-1160800	Weak transcription	Stomach Mucosa	stomach
10	chr4:1158000-1160400	Weak transcription	Fetal Muscle Leg	muscle
11	chr4:1158000-1160400	Weak transcription	K562	blood
12	chr4:1158000-1160600	Weak transcription	Primary B cells from cord blood	blood
13	chr4:1158000-1160800	Weak transcription	Skeletal Muscle Female	skeletal muscle
14	chr4:1158200-1160000	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
15	chr4:1158400-1160600	Weak transcription	Primary monocytes fromperipheralblood	blood
16	chr4:1158400-1160600	Strong transcription	Fetal Stomach	stomach
17	chr4:1158600-1160000	Weak transcription	NHLF	lung
18	chr4:1158600-1160200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
19	chr4:1158600-1160400	Weak transcription	Pancreas	Pancrea
20	chr4:1158600-1160600	Weak transcription	Monocytes-CD14+_RO01746	blood
21	chr4:1158800-1160400	Weak transcription	Primary B cells from peripheral blood	blood
22	chr4:1158800-1160800	Weak transcription	Spleen	Spleen
23	chr4:1159400-1160400	Strong transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
24	chr4:1159600-1160000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
25	chr4:1159800-1160400	Strong transcription	Foreskin Fibroblast Primary Cells skin01	Skin

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links