Variant report

Variant	rs577372
Chromosome Location	chr6:74200726-74200727
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:1)
CpG islands
(count:0)
Chromatin interactive
region (count:7)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

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

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr6:74200575-74200909	K562	blood:	n/a	n/a

No data

(count:7 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr6:74200414..74202246-chr6:74223331..74226250,3	K562	blood:
2	6:74160392-74184826..6:74198757-74202228	Hela-S3	cervix:
3	6:74099986-74112890..6:74198757-74202228	GM12878	blood:
4	6:74062967-74076046..6:74198757-74202228	GM12878	blood:
5	6:74078047-74099067..6:74198757-74202228	GM12878	blood:
6	chr6:74198950..74200761-chr6:74222278..74223851,2	MCF-7	breast:
7	chr6:74197243..74199833-chr6:74200536..74205034,4	K562	blood:

No data

Variant related genes	Relation type
ENSG00000271986	TF binding region
ENSG00000203909	Chromatin interaction
ENSG00000235174	Chromatin interaction
ENSG00000231332	Chromatin interaction
ENSG00000224221	Chromatin interaction
ENSG00000207023	Chromatin interaction
ENSG00000080007	Chromatin interaction
ENSG00000238464	Chromatin interaction
ENSG00000271986	Chromatin interaction
ENSG00000203907	Chromatin interaction
ENSG00000135297	Chromatin interaction
ENSG00000203908	Chromatin interaction
ENSG00000164430	Chromatin interaction

Extended variants
information (count: 33 )
Associated
traits (count: 6 )

rSNPs within LD-proxies of this variant (count:24)

rs_ID	r²[population]
rs1128073	0.92[AFR][1000 genomes];0.92[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs12661226	0.86[ASN][1000 genomes]
rs1874229	0.83[TSI][hapmap]
rs1874230	0.94[ASW][hapmap];0.91[CEU][hapmap];0.86[GIH][hapmap];0.86[LWK][hapmap];1.00[MEX][hapmap];0.86[MKK][hapmap];0.97[TSI][hapmap];0.92[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs2073466	1.00[ASW][hapmap];0.91[CEU][hapmap];0.83[GIH][hapmap];0.80[JPT][hapmap];0.87[LWK][hapmap];1.00[MEX][hapmap];0.90[MKK][hapmap];0.97[TSI][hapmap];0.96[YRI][hapmap];0.90[AFR][1000 genomes];0.90[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs2882584	0.87[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs3822960	1.00[ASW][hapmap];0.91[CEU][hapmap];0.84[GIH][hapmap];0.86[LWK][hapmap];0.91[MEX][hapmap];0.90[MKK][hapmap];0.97[TSI][hapmap];0.96[YRI][hapmap];0.90[AFR][1000 genomes];0.89[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs4257823	0.81[EUR][1000 genomes]
rs514582	0.82[AFR][1000 genomes];0.84[EUR][1000 genomes]
rs569652	0.82[AFR][1000 genomes];0.90[EUR][1000 genomes]
rs610913	0.87[CHD][hapmap];0.82[JPT][hapmap]
rs613787	0.83[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs617464	0.81[TSI][hapmap]
rs673265	0.98[AFR][1000 genomes];0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs693434	0.92[EUR][1000 genomes]
rs7741376	0.82[AFR][1000 genomes];0.92[EUR][1000 genomes]
rs7751342	0.81[ASW][hapmap];0.91[CEU][hapmap];0.86[GIH][hapmap];1.00[MEX][hapmap];0.97[TSI][hapmap];0.88[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs7773147	0.83[AMR][1000 genomes]
rs9341425	0.85[ASN][1000 genomes]
rs9352001	0.91[CEU][hapmap];0.96[YRI][hapmap];0.92[AFR][1000 genomes];0.91[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs9352003	0.87[AFR][1000 genomes];0.90[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs9352004	0.91[CEU][hapmap];0.85[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs9352006	0.85[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs9360681	0.81[AFR][1000 genomes];0.83[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:6)

SNP	Gene	Cis/trans	Tissue	Source
rs577372	SMAP1	cis	parietal	SCAN
rs577372	EEF1A1	Cis_1M	lymphoblastoid	RTeQTL
rs577372	EEF1A1	cis	parietal	SCAN
rs577372	MTO1	Cis_1M	lymphoblastoid	RTeQTL
rs577372	EEF1A1	cis	cerebellum	SCAN
rs577372	MTO1	cis	lymphoblastoid	seeQTL

Chromatin state (count:126 , 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	chr6:74173800-74206200	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
3	chr6:74175800-74201000	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
4	chr6:74181800-74214800	Strong transcription	Primary T helper cells fromperipheralblood	blood
5	chr6:74182400-74206200	Strong transcription	Primary B cells from peripheral blood	blood
6	chr6:74184000-74212000	Strong transcription	Monocytes-CD14+_RO01746	blood
7	chr6:74187600-74228400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
8	chr6:74189200-74202600	Strong transcription	Primary B cells from cord blood	blood
9	chr6:74192000-74207800	Weak transcription	Psoas Muscle	Psoas
10	chr6:74192000-74214200	Weak transcription	Pancreatic Islets	Pancreatic Islet
11	chr6:74192000-74225000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
12	chr6:74192200-74226000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
13	chr6:74192400-74225000	Weak transcription	Stomach Mucosa	stomach
14	chr6:74192600-74201400	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
15	chr6:74193400-74201000	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
16	chr6:74194400-74200800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
17	chr6:74196200-74201600	Weak transcription	HSMMtube	muscle
18	chr6:74196400-74200800	Weak transcription	HUVEC	blood vessel
19	chr6:74197400-74201200	Strong transcription	Fetal Kidney	kidney
20	chr6:74197600-74204400	Weak transcription	Esophagus	oesophagus
21	chr6:74197600-74207000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
22	chr6:74197800-74213200	Weak transcription	Fetal Heart	heart
23	chr6:74197800-74225200	Weak transcription	Colonic Mucosa	Colon
24	chr6:74198000-74205600	Weak transcription	Rectal Smooth Muscle	rectum
25	chr6:74198200-74207400	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
26	chr6:74198200-74211200	Weak transcription	H9 Cell Line	embryonic stem cell
27	chr6:74198600-74200800	Weak transcription	Brain Angular Gyrus	brain
28	chr6:74198600-74207600	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
29	chr6:74198600-74209600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
30	chr6:74198600-74213800	Weak transcription	Gastric	stomach
31	chr6:74198800-74200800	Weak transcription	HUES6 Cell Line	embryonic stem cell
32	chr6:74198800-74200800	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
33	chr6:74198800-74200800	Weak transcription	Fetal Stomach	stomach
34	chr6:74198800-74200800	Weak transcription	Ovary	ovary
35	chr6:74198800-74201000	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
36	chr6:74198800-74201000	Weak transcription	Fetal Intestine Small	intestine
37	chr6:74198800-74201200	Weak transcription	Skeletal Muscle Male	skeletal muscle
38	chr6:74198800-74201800	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
39	chr6:74198800-74202000	Weak transcription	H1 Cell Line	embryonic stem cell
40	chr6:74198800-74202000	Weak transcription	Brain Hippocampus Middle	brain
41	chr6:74198800-74202000	Weak transcription	Brain Substantia Nigra	brain
42	chr6:74198800-74202200	Weak transcription	Lung	lung
43	chr6:74198800-74202200	Weak transcription	Spleen	Spleen
44	chr6:74198800-74203400	Weak transcription	iPS-15b Cell Line	embryonic stem cell
45	chr6:74198800-74203600	Weak transcription	Primary T helper naive cells from peripheral blood	blood
46	chr6:74198800-74204600	Weak transcription	Pancreas	Pancrea
47	chr6:74198800-74205600	Weak transcription	Right Ventricle	heart
48	chr6:74198800-74207000	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
49	chr6:74198800-74207200	Weak transcription	Brain Cingulate Gyrus	brain
50	chr6:74198800-74207200	Weak transcription	HMEC	breast

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