Variant report

Variant	rs7754947
Chromosome Location	chr6:74208171-74208172
allele	C/T
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:10)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:10 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	6:74062967-74076046..6:74208016-74225478	GM12878	blood:
2	chr6:74207712..74210147-chr6:74213274..74215713,2	K562	blood:
3	chr6:74205310..74209199-chr6:74229303..74231458,3	K562	blood:
4	chr6:74203362..74206596-chr6:74207328..74210282,3	K562	blood:
5	6:74078047-74099067..6:74208016-74225478	GM12878	blood:
6	chr6:74207206..74209084-chr6:74351350..74353881,2	K562	blood:
7	6:74160392-74184826..6:74208016-74225478	GM12878	blood:
8	chr6:74207699..74210892-chr6:74229260..74231458,3	K562	blood:
9	chr6:74207658..74210612-chr6:74224071..74227518,3	K562	blood:
10	6:74099986-74112890..6:74208016-74225478	Hela-S3	cervix:

No data

Variant related genes	Relation type
ENSG00000203908	Chromatin interaction
ENSG00000207023	Chromatin interaction
ENSG00000135297	Chromatin interaction
ENSG00000203909	Chromatin interaction
ENSG00000224221	Chromatin interaction
ENSG00000231332	Chromatin interaction
ENSG00000156508	Chromatin interaction
ENSG00000080007	Chromatin interaction
ENSG00000203907	Chromatin interaction
ENSG00000164430	Chromatin interaction
ENSG00000238464	Chromatin interaction
ENSG00000235174	Chromatin interaction

Extended variants
information (count: 58 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:49)

rs_ID	r²[population]
rs10943096	0.98[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11754630	0.89[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs11755449	0.86[CHB][hapmap];0.86[JPT][hapmap];0.80[ASN][1000 genomes]
rs11756187	0.89[AMR][1000 genomes];0.98[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs11756242	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[YRI][hapmap];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11756668	0.91[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs11757033	0.87[EUR][1000 genomes]
rs11760131	0.92[CEU][hapmap];1.00[CHB][hapmap];0.90[JPT][hapmap];0.94[EUR][1000 genomes]
rs12524204	0.88[AFR][1000 genomes];0.91[AMR][1000 genomes];0.93[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs12524548	0.83[EUR][1000 genomes]
rs12525146	0.85[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12526457	0.92[EUR][1000 genomes]
rs12526483	0.95[EUR][1000 genomes]
rs12526844	1.00[CEU][hapmap];1.00[CHB][hapmap];0.85[CHD][hapmap];1.00[GIH][hapmap];0.86[JPT][hapmap];1.00[MEX][hapmap];0.93[TSI][hapmap];0.89[AMR][1000 genomes];0.98[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs12527011	0.89[AMR][1000 genomes];0.98[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs12527340	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12529857	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];0.98[AFR][1000 genomes];0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs17757139	0.84[CEU][hapmap];0.93[CHB][hapmap];1.00[JPT][hapmap];0.89[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2036039	0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2073465	0.81[CEU][hapmap];0.86[CHB][hapmap];0.88[CHD][hapmap];1.00[JPT][hapmap];0.89[TSI][hapmap];0.89[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs3173188	0.83[YRI][hapmap]
rs3806981	0.92[EUR][1000 genomes]
rs4340968	0.91[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4440422	0.89[AMR][1000 genomes];0.98[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs4706541	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4708055	0.81[CHB][hapmap]
rs4708056	0.81[AMR][1000 genomes];0.93[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs4708059	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.93[MKK][hapmap];1.00[TSI][hapmap];0.85[YRI][hapmap];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs58462079	0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs62438380	0.95[AFR][1000 genomes];0.91[AMR][1000 genomes];0.93[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs62438381	0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs62438385	0.91[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62438400	0.90[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs62438403	0.89[EUR][1000 genomes]
rs62438405	0.86[EUR][1000 genomes]
rs62438406	0.85[EUR][1000 genomes]
rs6453676	0.98[AFR][1000 genomes];0.91[AMR][1000 genomes];0.93[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs6908789	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];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6920811	0.80[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs6923919	0.85[YRI][hapmap]
rs6925541	0.80[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs72961994	0.81[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs73450672	0.89[AFR][1000 genomes]
rs73450674	0.89[AFR][1000 genomes]
rs73450677	0.89[AFR][1000 genomes]
rs73452507	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7453831	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.93[MKK][hapmap];1.00[TSI][hapmap];0.90[YRI][hapmap];0.85[AMR][1000 genomes];0.93[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7765670	0.84[AMR][1000 genomes];0.97[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs9800809	0.89[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	esv3410973	chr6:73716033-74419545	Active TSS Bivalent Enhancer Flanking Active TSS Weak transcription Enhancers Strong transcription Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	191 gene(s)	inside rSNPs	diseases
2	nsv830693	chr6:74049342-74216080	Flanking Active TSS Strong transcription Weak transcription Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Enhancers Flanking Bivalent TSS/Enh Genic enhancers ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	27 gene(s)	inside rSNPs	diseases
3	nsv886158	chr6:74126084-74436825	Weak transcription Active TSS Strong transcription Enhancers Genic enhancers Flanking Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	179 gene(s)	inside rSNPs	diseases
4	nsv1027968	chr6:74155378-74521923	Active TSS Flanking Active TSS Strong transcription Bivalent Enhancer Weak transcription Enhancers Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	178 gene(s)	inside rSNPs	diseases
5	nsv538305	chr6:74155378-74521923	Flanking Active TSS Weak transcription Enhancers Strong transcription Active TSS Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	178 gene(s)	inside rSNPs	diseases
6	nsv1017716	chr6:74173173-74401162	Weak transcription Strong transcription Enhancers Genic enhancers Active TSS Flanking Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	170 gene(s)	inside rSNPs	diseases
7	nsv1023250	chr6:74189642-74605976	Strong transcription Weak transcription Genic enhancers Active TSS Flanking Active TSS Enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	172 gene(s)	inside rSNPs	diseases
8	nsv538306	chr6:74189642-74605976	Strong transcription Enhancers Active TSS Bivalent Enhancer Weak transcription Flanking Active TSS Genic enhancers ZNF genes & repeats 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	172 gene(s)	inside rSNPs	diseases
9	esv2763576	chr6:74197638-74277249	Strong transcription Flanking Active TSS Enhancers Active TSS Weak transcription Bivalent/Poised TSS Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	160 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs7754947	C6orf221	cis	cerebellum	SCAN
rs7754947	EEF1A1	cis	cerebellum	SCAN
rs7754947	MTO1	cis	Whole Blood	GTEx
rs7754947	EEF1A1	cis	parietal	SCAN

Chromatin state (count:125 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:74172200-74229200	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
2	chr6:74181800-74214800	Strong transcription	Primary T helper cells fromperipheralblood	blood
3	chr6:74184000-74212000	Strong transcription	Monocytes-CD14+_RO01746	blood
4	chr6:74187600-74228400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
5	chr6:74192000-74214200	Weak transcription	Pancreatic Islets	Pancreatic Islet
6	chr6:74192000-74225000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
7	chr6:74192200-74226000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
8	chr6:74192400-74225000	Weak transcription	Stomach Mucosa	stomach
9	chr6:74197800-74213200	Weak transcription	Fetal Heart	heart
10	chr6:74197800-74225200	Weak transcription	Colonic Mucosa	Colon
11	chr6:74198200-74211200	Weak transcription	H9 Cell Line	embryonic stem cell
12	chr6:74198600-74209600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
13	chr6:74198600-74213800	Weak transcription	Gastric	stomach
14	chr6:74198800-74211200	Weak transcription	Aorta	Aorta
15	chr6:74198800-74213000	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
16	chr6:74198800-74225000	Weak transcription	Fetal Brain Male	brain
17	chr6:74199000-74224200	Weak transcription	A549	lung
18	chr6:74200000-74212000	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
19	chr6:74200000-74215000	Strong transcription	Primary T cells fromperipheralblood	blood
20	chr6:74200000-74215200	Strong transcription	Liver	Liver
21	chr6:74200200-74212800	Strong transcription	Primary T helper cells PMA-I stimulated	--
22	chr6:74200400-74211800	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
23	chr6:74200400-74211800	Strong transcription	Dnd41	blood
24	chr6:74200400-74212000	Strong transcription	Primary hematopoietic stem cells short term culture	blood
25	chr6:74200400-74212200	Strong transcription	Primary monocytes fromperipheralblood	blood
26	chr6:74200400-74214000	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
27	chr6:74200400-74214000	Strong transcription	Fetal Intestine Large	intestine
28	chr6:74200400-74214600	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
29	chr6:74200600-74208200	Strong transcription	Rectal Mucosa Donor 31	rectum
30	chr6:74200600-74211800	Strong transcription	HUES48 Cell Line	embryonic stem cell
31	chr6:74200600-74211800	Strong transcription	Left Ventricle	heart
32	chr6:74200600-74212000	Strong transcription	Sigmoid Colon	Sigmoid Colon
33	chr6:74200600-74214600	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
34	chr6:74200600-74214800	Strong transcription	Fetal Thymus	thymus
35	chr6:74200800-74214400	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
36	chr6:74200800-74214800	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
37	chr6:74201000-74212000	Strong transcription	Primary neutrophils fromperipheralblood	blood
38	chr6:74201000-74215400	Strong transcription	Fetal Intestine Small	intestine
39	chr6:74201200-74211600	Strong transcription	Skeletal Muscle Male	skeletal muscle
40	chr6:74201400-74214600	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
41	chr6:74201800-74213200	Strong transcription	Primary T helper naive cells fromperipheralblood	blood
42	chr6:74202000-74208600	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
43	chr6:74202200-74209400	Weak transcription	K562	blood
44	chr6:74202600-74209200	Weak transcription	NHLF	lung
45	chr6:74203600-74214000	Strong transcription	Fetal Lung	lung
46	chr6:74203600-74214600	Strong transcription	Fetal Muscle Trunk	muscle
47	chr6:74203600-74215000	Strong transcription	Breast Myoepithelial Primary Cells	Breast
48	chr6:74203800-74212600	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
49	chr6:74204000-74211800	Strong transcription	Skeletal Muscle Female	skeletal muscle
50	chr6:74204400-74212000	Strong transcription	Fetal Brain Female	brain

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