Variant report

Variant	rs4416625
Chromosome Location	chr5:95405538-95405539
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr5:95192803..95195845-chr5:95402156..95405628,4	K562	blood:
2	chr5:95403553..95405838-chr5:95406923..95410499,3	K562	blood:
3	chr5:95401831..95405579-chr5:95411274..95417557,7	K562	blood:

Variant related genes	Relation type
ENSG00000207578	Chromatin interaction

Extended variants
information (count: 61 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:52)

rs_ID	r²[population]
rs10056771	0.81[CEU][hapmap];0.95[JPT][hapmap];0.87[MEX][hapmap];1.00[TSI][hapmap];0.87[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs10079268	0.89[AMR][1000 genomes];0.92[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs10085034	0.81[CEU][hapmap];0.95[JPT][hapmap];0.87[MEX][hapmap];1.00[TSI][hapmap];0.87[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs11740207	0.86[EUR][1000 genomes]
rs11949461	0.86[EUR][1000 genomes]
rs11951463	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];0.96[GIH][hapmap];0.95[JPT][hapmap];1.00[TSI][hapmap];0.85[AMR][1000 genomes];0.91[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs11956456	0.86[EUR][1000 genomes]
rs11960219	0.86[EUR][1000 genomes]
rs13155375	0.81[CEU][hapmap];0.95[JPT][hapmap];0.87[MEX][hapmap];1.00[TSI][hapmap];0.87[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs13172783	0.81[CEU][hapmap];0.95[JPT][hapmap];0.87[MEX][hapmap];1.00[TSI][hapmap];0.87[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs13186419	0.87[EUR][1000 genomes]
rs1389827	0.87[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs1870270	0.88[EUR][1000 genomes]
rs2067498	0.85[AMR][1000 genomes];0.85[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4077350	0.83[EUR][1000 genomes]
rs4128178	0.81[ASW][hapmap];1.00[CEU][hapmap];0.98[GIH][hapmap];1.00[MEX][hapmap];0.93[MKK][hapmap];1.00[TSI][hapmap];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs4270717	0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4367316	0.82[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs4479864	0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4513721	0.86[EUR][1000 genomes]
rs4869256	1.00[CEU][hapmap];0.80[MEX][hapmap];1.00[TSI][hapmap];0.95[EUR][1000 genomes]
rs4869258	0.92[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs4869259	0.86[EUR][1000 genomes]
rs4869260	0.86[EUR][1000 genomes]
rs4869264	0.82[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs4869266	0.84[EUR][1000 genomes]
rs4998057	0.94[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs6556899	0.96[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs6556900	0.86[EUR][1000 genomes]
rs66683317	0.96[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs6866723	1.00[CEU][hapmap];0.92[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs6873504	0.86[EUR][1000 genomes]
rs6879658	0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6879847	0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6884999	0.96[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs6886983	0.84[EUR][1000 genomes]
rs6889697	0.86[EUR][1000 genomes]
rs6894768	0.86[EUR][1000 genomes]
rs6895121	0.94[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs6895146	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7341111	0.95[JPT][hapmap];0.86[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs7700425	0.99[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs7702346	0.85[AMR][1000 genomes];0.85[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7702646	0.86[AMR][1000 genomes];0.85[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7710337	0.89[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs7715650	0.82[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs7717351	0.88[AMR][1000 genomes];0.84[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7734224	0.81[CEU][hapmap];0.95[JPT][hapmap];0.86[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs7734985	0.85[CEU][hapmap];1.00[JPT][hapmap];0.86[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs9314163	0.89[EUR][1000 genomes]
rs9314164	0.91[AMR][1000 genomes];0.92[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9314165	0.86[EUR][1000 genomes]

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	esv2758003	chr5:95231706-95540433	Flanking Active TSS Weak transcription Enhancers Strong transcription Active TSS Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA	20 gene(s)	inside rSNPs	diseases
2	esv2759355	chr5:95231706-95540433	Weak transcription Flanking Active TSS Enhancers Bivalent/Poised TSS Active TSS Strong transcription Genic enhancers 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	20 gene(s)	inside rSNPs	diseases
3	nsv823146	chr5:95300912-95453557	Enhancers Weak transcription Flanking Active TSS Active TSS ZNF genes & repeats Genic enhancers Bivalent Enhancer Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA miRNA	9 gene(s)	inside rSNPs	diseases
4	esv2757121	chr5:95304236-95539536	Enhancers Weak transcription Flanking Active TSS Genic enhancers Active TSS Strong transcription Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA	8 gene(s)	inside rSNPs	diseases
5	esv34203	chr5:95310985-95452324	Enhancers ZNF genes & repeats Weak transcription Flanking Active TSS Active TSS Strong transcription Bivalent Enhancer Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA	8 gene(s)	inside rSNPs	diseases
6	nsv522097	chr5:95347786-95425199	Flanking Active TSS Weak transcription Enhancers ZNF genes & repeats Bivalent Enhancer Genic enhancers Active TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA	6 gene(s)	inside rSNPs	diseases
7	nsv522465	chr5:95347786-95425199	Enhancers Weak transcription Genic enhancers Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Active TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA	6 gene(s)	inside rSNPs	diseases
8	nsv1030444	chr5:95353620-95995619	Weak transcription Enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Active TSS Bivalent Enhancer Bivalent/Poised TSS Strong transcription Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	16 gene(s)	inside rSNPs	diseases
9	nsv537810	chr5:95353620-95995619	Enhancers Weak transcription Flanking Active TSS Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Strong transcription Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	16 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs4416625	RRAGD	trans	lymphoblastoid	seeQTL

Chromatin state (count:36 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:95401600-95416400	Weak transcription	Psoas Muscle	Psoas
2	chr5:95402000-95406800	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
3	chr5:95402000-95410600	Weak transcription	Stomach Mucosa	stomach
4	chr5:95402200-95406200	Weak transcription	Colonic Mucosa	Colon
5	chr5:95402200-95406200	Weak transcription	HepG2	liver
6	chr5:95402200-95406800	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
7	chr5:95402600-95410600	Weak transcription	Sigmoid Colon	Sigmoid Colon
8	chr5:95402600-95423800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
9	chr5:95404000-95406200	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
10	chr5:95404200-95405600	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
11	chr5:95404200-95405600	Weak transcription	Primary hematopoietic stem cells short term culture	blood
12	chr5:95404200-95406000	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
13	chr5:95404200-95406200	Weak transcription	Placenta	Placenta
14	chr5:95404200-95406400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
15	chr5:95404200-95410200	Weak transcription	Pancreas	Pancrea
16	chr5:95404200-95410200	Weak transcription	Small Intestine	intestine
17	chr5:95404400-95406000	Weak transcription	A549	lung
18	chr5:95404400-95406200	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
19	chr5:95404400-95408400	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
20	chr5:95404400-95410200	Weak transcription	HSMM	muscle
21	chr5:95404400-95416800	Weak transcription	Aorta	Aorta
22	chr5:95404600-95410200	Weak transcription	Osteobl	bone
23	chr5:95404800-95405800	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
24	chr5:95404800-95406000	Weak transcription	Muscle Satellite Cultured Cells	--
25	chr5:95404800-95406000	Weak transcription	HMEC	breast
26	chr5:95404800-95406200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
27	chr5:95404800-95406400	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
28	chr5:95404800-95406400	Weak transcription	NHEK	skin
29	chr5:95404800-95410200	Weak transcription	HUVEC	blood vessel
30	chr5:95404800-95411600	Weak transcription	NHDF-Ad	bronchial
31	chr5:95405000-95406600	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
32	chr5:95405200-95408200	Weak transcription	Breast Myoepithelial Primary Cells	Breast
33	chr5:95405400-95406800	Enhancers	NHLF	lung
34	chr5:95405400-95407000	Enhancers	Dnd41	blood
35	chr5:95405400-95407200	Enhancers	Primary monocytes fromperipheralblood	blood
36	chr5:95405400-95407200	Enhancers	Hela-S3	cervix

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links