Variant report

Variant	rs8180337
Chromosome Location	chr4:6946860-6946861
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:0)
CpG islands
(count:0)
Chromatin interactive
region (count:6)
LncRNA
region (count:1)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:6 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr4:6910492..6915918-chr4:6946437..6950272,7	K562	blood:
2	chr4:6944446..6947031-chr4:6951567..6953686,2	K562	blood:
3	chr4:6918951..6920987-chr4:6946551..6948090,2	K562	blood:
4	chr4:6917668..6920987-chr4:6945472..6948090,3	K562	blood:
5	chr4:6909142..6912159-chr4:6946034..6948699,3	K562	blood:
6	chr4:6945003..6947109-chr4:6955850..6957643,2	K562	blood:

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

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-KIAA0232-3	chr4:6945338-6947476	NONHSAT095027

No data

Variant related genes	Relation type
ENSG00000132405	Chromatin interaction

Extended variants
information (count: 42 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:40)

rs_ID	r²[population]
rs10012590	0.85[CHD][hapmap]
rs1048009	0.81[LWK][hapmap]
rs10516181	0.82[AFR][1000 genomes]
rs10937772	0.83[AFR][1000 genomes];0.95[AMR][1000 genomes];0.89[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs10937774	0.95[CEU][hapmap];0.82[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs10937776	0.82[AFR][1000 genomes]
rs11732898	1.00[CEU][hapmap];0.85[CHD][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];0.82[MKK][hapmap];0.94[TSI][hapmap];0.86[YRI][hapmap];0.82[AFR][1000 genomes];0.84[AMR][1000 genomes];0.97[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs11934364	1.00[CHB][hapmap]
rs12510715	1.00[CHB][hapmap];0.85[CHD][hapmap]
rs12642852	0.83[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs13108082	0.83[ASN][1000 genomes]
rs13111887	0.83[ASN][1000 genomes]
rs13135912	0.83[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs2301818	1.00[CHB][hapmap];0.85[CHD][hapmap]
rs2301819	1.00[CHB][hapmap];0.85[CHD][hapmap]
rs2359194	0.82[AFR][1000 genomes];0.81[AMR][1000 genomes]
rs3188939	0.85[CHD][hapmap]
rs34219101	0.83[ASN][1000 genomes]
rs3857171	0.82[AFR][1000 genomes]
rs3892490	0.83[ASW][hapmap];0.95[CEU][hapmap];0.85[CHD][hapmap];0.96[GIH][hapmap];0.93[LWK][hapmap];1.00[MEX][hapmap];0.91[TSI][hapmap];0.86[YRI][hapmap];0.84[AMR][1000 genomes];0.87[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs4234788	0.83[ASN][1000 genomes]
rs4296677	0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4428285	1.00[CEU][hapmap];1.00[CHB][hapmap];0.87[AMR][1000 genomes];0.98[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs4458452	0.84[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4645214	1.00[CEU][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4689059	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.85[CHD][hapmap];1.00[GIH][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.99[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs4689060	0.86[AFR][1000 genomes];0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs4689568	0.85[CEU][hapmap];0.85[CHD][hapmap];0.85[GIH][hapmap];0.94[MEX][hapmap];0.81[TSI][hapmap];0.86[YRI][hapmap];0.82[AMR][1000 genomes];0.88[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs4689573	0.81[AMR][1000 genomes]
rs55822670	0.82[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs6816660	0.83[ASN][1000 genomes]
rs6816882	0.82[AMR][1000 genomes];0.87[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs6831129	0.81[AMR][1000 genomes];0.80[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs6854776	0.85[CHD][hapmap]
rs7655563	0.85[CEU][hapmap];0.82[EUR][1000 genomes]
rs7658198	0.95[CEU][hapmap];0.86[YRI][hapmap];0.84[AMR][1000 genomes];0.88[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs7661462	0.95[CEU][hapmap];0.83[YRI][hapmap];0.82[AMR][1000 genomes];0.80[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs7675524	0.85[CHD][hapmap]
rs7693321	0.82[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs9291126	1.00[CHB][hapmap];1.00[CHD][hapmap]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv878529	chr4:6883012-6983677	Enhancers Flanking Active TSS Weak transcription Active TSS Strong transcription Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	30 gene(s)	inside rSNPs	diseases
2	nsv878530	chr4:6888932-7058473	Strong transcription Enhancers Weak transcription Genic enhancers Bivalent Enhancer Flanking Active TSS Transcr. at gene 5' and 3' Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	39 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs8180337	GRPEL1	cis	lymphoblastoid	seeQTL
rs8180337	HMX1	cis	parietal	SCAN

Chromatin state (count:96 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:6928000-6969600	Weak transcription	Aorta	Aorta
2	chr4:6939200-6947000	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
3	chr4:6939200-6947200	Enhancers	HUES6 Cell Line	embryonic stem cell
4	chr4:6939200-6948000	Enhancers	H1 Cell Line	embryonic stem cell
5	chr4:6939600-6947000	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
6	chr4:6941400-6947200	Enhancers	Fetal Adrenal Gland	Adrenal Gland
7	chr4:6941600-6947000	Enhancers	Placenta Amnion	Placenta Amnion
8	chr4:6941800-6947000	Enhancers	HUES48 Cell Line	embryonic stem cell
9	chr4:6941800-6947000	Enhancers	iPS-15b Cell Line	embryonic stem cell
10	chr4:6941800-6947800	Enhancers	HUES64 Cell Line	embryonic stem cell
11	chr4:6942000-6948000	Enhancers	iPS-18 Cell Line	embryonic stem cell
12	chr4:6942200-6947400	Enhancers	Fetal Intestine Large	intestine
13	chr4:6942400-6947000	Enhancers	Small Intestine	intestine
14	chr4:6942600-6947000	Enhancers	Brain Anterior Caudate	brain
15	chr4:6943200-6947000	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
16	chr4:6943200-6947200	Enhancers	Skeletal Muscle Male	skeletal muscle
17	chr4:6943800-6955400	Weak transcription	Brain Substantia Nigra	brain
18	chr4:6944200-6947200	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
19	chr4:6944400-6947000	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
20	chr4:6944400-6949800	Weak transcription	Fetal Lung	lung
21	chr4:6944600-6947000	Enhancers	A549	lung
22	chr4:6944600-6947200	Enhancers	Primary T helper naive cells from peripheral blood	blood
23	chr4:6944600-6947800	Enhancers	Primary T helper cells PMA-I stimulated	--
24	chr4:6944800-6947400	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
25	chr4:6944800-6955400	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
26	chr4:6945000-6947200	Enhancers	Primary T killer naive cells fromperipheralblood	blood
27	chr4:6945000-6949000	Genic enhancers	Fetal Intestine Small	intestine
28	chr4:6945000-6949600	Weak transcription	Fetal Kidney	kidney
29	chr4:6945000-6955400	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
30	chr4:6945000-6970200	Weak transcription	Hela-S3	cervix
31	chr4:6945200-6947000	Enhancers	ES-I3 Cell Line	embryonic stem cell
32	chr4:6945200-6955600	Weak transcription	Fetal Brain Female	brain
33	chr4:6945400-6947000	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
34	chr4:6945400-6947000	Enhancers	Primary T helper cells fromperipheralblood	blood
35	chr4:6945400-6953600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
36	chr4:6945400-6955400	Weak transcription	Fetal Stomach	stomach
37	chr4:6945600-6947000	Enhancers	Colonic Mucosa	Colon
38	chr4:6945600-6949800	Weak transcription	Sigmoid Colon	Sigmoid Colon
39	chr4:6945600-6952800	Weak transcription	Esophagus	oesophagus
40	chr4:6945600-6952800	Weak transcription	K562	blood
41	chr4:6945600-6953000	Weak transcription	Primary B cells from peripheral blood	blood
42	chr4:6945600-6953600	Weak transcription	GM12878-XiMat	blood
43	chr4:6945600-6955600	Weak transcription	Left Ventricle	heart
44	chr4:6945800-6953600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
45	chr4:6945800-6965800	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
46	chr4:6946000-6947000	Enhancers	Skeletal Muscle Female	skeletal muscle
47	chr4:6946000-6947000	Genic enhancers	Thymus	Thymus
48	chr4:6946000-6947000	Genic enhancers	Monocytes-CD14+_RO01746	blood
49	chr4:6946000-6947200	Strong transcription	HepG2	liver
50	chr4:6946000-6949800	Weak transcription	Rectal Smooth Muscle	rectum

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