Variant report

Variant	rs7555476
Chromosome Location	chr1:92310666-92310667
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr1:92309780..92313855-chr1:92314421..92317529,4	K562	blood:
2	chr1:92088173..92091117-chr1:92308700..92311610,2	MCF-7	breast:
3	chr1:92306378..92308491-chr1:92309526..92312029,2	K562	blood:

Extended variants
information (count: 56 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:33)

rs_ID	r²[population]
rs10493857	0.82[CEU][hapmap]
rs10875030	0.82[CEU][hapmap]
rs11165556	0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11165595	0.93[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.96[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11165637	0.84[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11165679	0.82[CEU][hapmap]
rs11590254	0.87[CEU][hapmap];0.83[CHB][hapmap];0.89[CHD][hapmap]
rs1192524	0.82[CEU][hapmap]
rs1192528	0.93[ASW][hapmap];0.91[CEU][hapmap];0.94[CHB][hapmap];0.83[CHD][hapmap];0.81[GIH][hapmap];1.00[JPT][hapmap];0.81[LWK][hapmap];1.00[MEX][hapmap];0.93[TSI][hapmap];0.83[AMR][1000 genomes];0.86[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs1192529	1.00[ASW][hapmap];0.91[CEU][hapmap];0.94[CHB][hapmap];0.83[CHD][hapmap];0.81[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.93[TSI][hapmap];0.86[YRI][hapmap];0.83[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs12043241	1.00[CEU][hapmap];0.94[YRI][hapmap];0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12127774	0.82[CEU][hapmap]
rs12569180	0.82[CEU][hapmap]
rs12726500	0.93[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.92[GIH][hapmap];1.00[JPT][hapmap];0.91[LWK][hapmap];1.00[MEX][hapmap];0.89[MKK][hapmap];1.00[TSI][hapmap];0.88[AFR][1000 genomes];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17516329	0.87[CEU][hapmap];0.83[CHB][hapmap];0.86[CHD][hapmap]
rs17881430	0.83[CHB][hapmap];0.83[CHD][hapmap]
rs2489188	0.82[MEX][hapmap]
rs2810904	0.83[AMR][1000 genomes];0.86[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs284139	0.83[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs284140	0.82[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs284142	0.93[ASW][hapmap];0.91[CEU][hapmap];0.94[CHB][hapmap];0.83[CHD][hapmap];0.81[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];0.93[TSI][hapmap];0.84[AMR][1000 genomes];0.86[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs284143	0.82[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];0.81[ASN][1000 genomes]
rs284144	0.88[AMR][1000 genomes];0.90[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs284147	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs284149	0.93[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.89[CHD][hapmap];0.87[GIH][hapmap];1.00[JPT][hapmap];0.84[LWK][hapmap];0.95[MEX][hapmap];0.80[MKK][hapmap];0.93[TSI][hapmap];0.91[YRI][hapmap];0.94[AMR][1000 genomes];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs284152	0.89[CHB][hapmap];0.84[JPT][hapmap]
rs284153	0.82[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.89[CHD][hapmap];0.87[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];0.93[TSI][hapmap];0.94[AMR][1000 genomes];0.93[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs284154	0.92[AMR][1000 genomes];0.93[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs284159	0.91[CEU][hapmap];1.00[CHB][hapmap];0.91[JPT][hapmap];1.00[YRI][hapmap];0.82[AFR][1000 genomes];0.95[AMR][1000 genomes];0.91[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs416624	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.81[AFR][1000 genomes];0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6656018	0.82[CEU][hapmap]
rs7555548	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.95[LWK][hapmap];1.00[MEX][hapmap];0.81[MKK][hapmap];0.97[TSI][hapmap];1.00[YRI][hapmap];0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9661103	0.82[CEU][hapmap]

Variant overlapped rSNPs/rCNVs (count:23 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1012864	chr1:92067100-92827761	Flanking Active TSS Strong transcription Enhancers Active TSS Weak transcription Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	33 gene(s)	inside rSNPs	diseases
2	nsv535029	chr1:92067100-92827761	Strong transcription Weak transcription Enhancers Active TSS Genic enhancers Flanking Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	33 gene(s)	inside rSNPs	diseases
3	nsv530438	chr1:92091957-92827760	Weak transcription Active TSS Strong transcription Flanking Bivalent TSS/Enh Enhancers Flanking Active TSS Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	33 gene(s)	inside rSNPs	diseases
4	nsv1010179	chr1:92140209-92655952	Weak transcription Genic enhancers Flanking Active TSS Enhancers Strong transcription Active TSS ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	19 gene(s)	inside rSNPs	diseases
5	nsv535030	chr1:92140209-92655952	Enhancers Weak transcription Flanking Bivalent TSS/Enh Active TSS Flanking Active TSS Strong transcription ZNF genes & repeats Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	19 gene(s)	inside rSNPs	diseases
6	nsv1005917	chr1:92189945-92378683	Flanking Active TSS Enhancers Weak transcription Genic enhancers Strong transcription Active TSS Bivalent Enhancer 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	4 gene(s)	inside rSNPs	diseases
7	nsv949449	chr1:92211020-92585831	Strong transcription Enhancers Genic enhancers Weak transcription Active TSS Flanking Bivalent TSS/Enh Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases
8	nsv524845	chr1:92215725-92598705	Enhancers Weak transcription Flanking Active TSS Active TSS Strong transcription Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	15 gene(s)	inside rSNPs	diseases
9	nsv462517	chr1:92215725-92598705	Weak transcription Bivalent Enhancer Enhancers Active TSS Genic enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Strong transcription Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	15 gene(s)	inside rSNPs	diseases
10	nsv546810	chr1:92215725-92598705	Flanking Active TSS Enhancers Weak transcription Active TSS Genic enhancers Strong transcription Bivalent Enhancer 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	15 gene(s)	inside rSNPs	diseases
11	nsv1006318	chr1:92216408-92608324	Flanking Active TSS Enhancers Active TSS Transcr. at gene 5' and 3' Weak transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh Genic enhancers Strong transcription ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	15 gene(s)	inside rSNPs	diseases
12	nsv432498	chr1:92218245-92618323	Weak transcription Strong transcription Genic enhancers Flanking Active TSS Enhancers Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	15 gene(s)	inside rSNPs	diseases
13	nsv1004570	chr1:92220544-92622129	Weak transcription Enhancers Active TSS Flanking Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Strong transcription Transcr. at gene 5' and 3' Bivalent Enhancer Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	15 gene(s)	inside rSNPs	diseases
14	nsv1007661	chr1:92220544-92655952	Weak transcription Enhancers Active TSS Bivalent Enhancer Flanking Active TSS ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Genic enhancers Strong transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	19 gene(s)	inside rSNPs	diseases
15	nsv1014837	chr1:92233905-92618839	Enhancers Active TSS Weak transcription Flanking Active TSS Bivalent/Poised TSS Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	15 gene(s)	inside rSNPs	diseases
16	nsv535031	chr1:92233905-92618839	Bivalent/Poised TSS Enhancers Weak transcription Bivalent Enhancer Genic enhancers Strong transcription Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	15 gene(s)	inside rSNPs	diseases
17	nsv1012134	chr1:92235485-92598800	Weak transcription Genic enhancers Flanking Active TSS Active TSS Enhancers Strong transcription Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	15 gene(s)	inside rSNPs	diseases
18	nsv546818	chr1:92236048-92579206	Enhancers Flanking Active TSS Weak transcription Bivalent Enhancer Active TSS Strong transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases
19	nsv546819	chr1:92256626-92558583	Strong transcription Enhancers Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Weak transcription Bivalent/Poised TSS Genic enhancers ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases
20	nsv546820	chr1:92273644-92558583	Weak transcription Enhancers Bivalent Enhancer Flanking Active TSS Active TSS Genic enhancers Strong transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases
21	nsv530046	chr1:92277460-92799794	Enhancers Flanking Active TSS ZNF genes & repeats Strong transcription Weak transcription Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	32 gene(s)	inside rSNPs	diseases
22	nsv1007270	chr1:92289298-92598800	Active TSS Enhancers Weak transcription Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Genic enhancers Strong transcription Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	15 gene(s)	inside rSNPs	diseases
23	nsv1002730	chr1:92302541-92565229	Active TSS Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Strong transcription Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs7555476	GBP7	cis	parietal	SCAN
rs7555476	GFI1	cis	parietal	SCAN

Chromatin state (count:68 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:92294800-92311600	Weak transcription	Gastric	stomach
2	chr1:92296400-92335800	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
3	chr1:92296800-92311400	Weak transcription	Stomach Mucosa	stomach
4	chr1:92297000-92311000	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
5	chr1:92297200-92311800	Weak transcription	Fetal Intestine Large	intestine
6	chr1:92297200-92313600	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
7	chr1:92298200-92314600	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
8	chr1:92300800-92329600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
9	chr1:92301000-92311000	Weak transcription	Rectal Smooth Muscle	rectum
10	chr1:92302600-92310800	Weak transcription	Stomach Smooth Muscle	stomach
11	chr1:92304800-92311600	Weak transcription	Right Atrium	heart
12	chr1:92306000-92314800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
13	chr1:92307000-92311000	Weak transcription	Skeletal Muscle Female	skeletal muscle
14	chr1:92307000-92311200	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
15	chr1:92308000-92313600	Enhancers	Fetal Adrenal Gland	Adrenal Gland
16	chr1:92308200-92311200	Weak transcription	K562	blood
17	chr1:92308200-92311400	Weak transcription	Rectal Mucosa Donor 29	rectum
18	chr1:92308200-92317400	Weak transcription	Lung	lung
19	chr1:92308400-92311000	Weak transcription	Rectal Mucosa Donor 31	rectum
20	chr1:92308400-92311600	Enhancers	Hela-S3	cervix
21	chr1:92308600-92311000	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
22	chr1:92308600-92311000	Weak transcription	Small Intestine	intestine
23	chr1:92308600-92311400	Weak transcription	Primary T helper naive cells from peripheral blood	blood
24	chr1:92308600-92316400	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
25	chr1:92308800-92311000	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
26	chr1:92309200-92312800	Enhancers	NHLF	lung
27	chr1:92309400-92313200	Weak transcription	Right Ventricle	heart
28	chr1:92309600-92311000	Enhancers	Muscle Satellite Cultured Cells	--
29	chr1:92309600-92311600	Weak transcription	Primary T cells fromperipheralblood	blood
30	chr1:92309600-92312200	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
31	chr1:92309800-92311600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
32	chr1:92309800-92311600	Weak transcription	Left Ventricle	heart
33	chr1:92309800-92313400	Weak transcription	Esophagus	oesophagus
34	chr1:92310000-92312200	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
35	chr1:92310000-92312400	Enhancers	Osteobl	bone
36	chr1:92310000-92315000	Enhancers	Breast Myoepithelial Primary Cells	Breast
37	chr1:92310200-92312000	Enhancers	HSMM	muscle
38	chr1:92310200-92312000	Enhancers	HSMMtube	muscle
39	chr1:92310200-92312200	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
40	chr1:92310200-92312200	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
41	chr1:92310200-92312200	Enhancers	HMEC	breast
42	chr1:92310200-92312800	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
43	chr1:92310200-92312800	Enhancers	Fetal Lung	lung
44	chr1:92310200-92313600	Enhancers	NHDF-Ad	bronchial
45	chr1:92310200-92316000	Weak transcription	Fetal Muscle Trunk	muscle
46	chr1:92310400-92310800	Active TSS	A549	lung
47	chr1:92310400-92310800	Flanking Active TSS	NHEK	skin
48	chr1:92310400-92311000	Enhancers	Duodenum Smooth Muscle	Duodenum
49	chr1:92310400-92311000	Enhancers	Fetal Heart	heart
50	chr1:92310400-92311000	Flanking Active TSS	HepG2	liver

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links