Variant report

Variant	rs11972491
Chromosome Location	chr7:100751106-100751107
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:13)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:13 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr7:100749240..100751319-chr7:100753473..100755309,2	K562	blood:
2	chr7:100748557..100751885-chr7:100761807..100763776,3	MCF-7	breast:
3	chr7:100494214..100497155-chr7:100747765..100751191,3	K562	blood:
4	chr7:100749234..100751319-chr7:100752722..100755802,5	K562	blood:
5	chr7:100731272..100734037-chr7:100750691..100752349,2	K562	blood:
6	chr7:100750163..100751939-chr7:100756081..100757683,2	MCF-7	breast:
7	chr7:100749902..100752214-chr7:100764849..100766479,2	MCF-7	breast:
8	chr7:100737701..100741221-chr7:100750993..100753482,3	MCF-7	breast:
9	chr7:100750619..100754326-chr7:100769826..100772467,4	MCF-7	breast:
10	chr7:100750302..100752925-chr7:100778093..100782237,4	MCF-7	breast:
11	chr7:100748249..100751163-chr7:100779870..100782174,3	K562	blood:
12	chr7:100747760..100750554-chr7:100750656..100752898,2	K562	blood:
13	chr7:100741837..100746865-chr7:100749791..100753773,5	MCF-7	breast:

No data

Variant related genes	Relation type
ENSG00000106366	Chromatin interaction
ENSG00000169871	Chromatin interaction
ENSG00000087085	Chromatin interaction

Extended variants
information (count: 33 )
Associated
traits (count: 1 )

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

rs_ID	r²[population]
rs10231438	0.91[JPT][hapmap]
rs10231529	0.91[JPT][hapmap]
rs10953318	0.91[JPT][hapmap]
rs10953321	0.86[CEU][hapmap];1.00[CHB][hapmap];0.90[CHD][hapmap];1.00[GIH][hapmap];0.91[JPT][hapmap];1.00[MEX][hapmap];0.96[TSI][hapmap];0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs10953322	0.86[CEU][hapmap];1.00[CHB][hapmap];0.90[CHD][hapmap];0.93[GIH][hapmap];0.91[JPT][hapmap];0.89[LWK][hapmap];1.00[MEX][hapmap];0.81[MKK][hapmap];1.00[TSI][hapmap];0.84[AFR][1000 genomes];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11760747	0.91[EUR][1000 genomes]
rs11761555	0.85[AFR][1000 genomes];0.88[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs11973843	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11980635	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12667943	0.82[YRI][hapmap]
rs12668231	1.00[CEU][hapmap];0.88[CHB][hapmap];0.86[YRI][hapmap];0.98[EUR][1000 genomes]
rs12669411	0.85[ASW][hapmap];1.00[CEU][hapmap];0.94[CHB][hapmap];0.87[GIH][hapmap];0.88[MEX][hapmap];0.81[MKK][hapmap];0.92[TSI][hapmap];0.95[YRI][hapmap];0.83[AFR][1000 genomes];0.81[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs12673732	0.93[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs13228919	0.80[TSI][hapmap]
rs4571672	0.80[TSI][hapmap]
rs57569772	0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs66492618	0.90[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs67321422	0.83[AFR][1000 genomes];0.82[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs67520893	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs67568738	0.90[AFR][1000 genomes];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs67947224	0.93[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs73178519	0.87[EUR][1000 genomes]
rs73404898	0.90[AMR][1000 genomes];0.93[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9792109	0.83[TSI][hapmap]

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	nsv1031942	chr7:100606734-100788660	Strong transcription Enhancers Active TSS Weak transcription Flanking Active TSS Bivalent Enhancer 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 miRNA target site	36 gene(s)	inside rSNPs	diseases
2	esv1833777	chr7:100632790-100800131	Flanking Active TSS Weak transcription Active TSS Enhancers Bivalent Enhancer Strong transcription Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	39 gene(s)	inside rSNPs	diseases
3	nsv1033081	chr7:100669629-100771824	Weak transcription Enhancers Genic enhancers Active TSS Flanking Active TSS Bivalent Enhancer Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	32 gene(s)	inside rSNPs	diseases
4	nsv831075	chr7:100692297-100917018	Bivalent/Poised TSS Weak transcription Enhancers Active TSS Transcr. at gene 5' and 3' Genic enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Strong transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	61 gene(s)	inside rSNPs	diseases
5	nsv933653	chr7:100701931-101515782	Active TSS ZNF genes & repeats Bivalent Enhancer Enhancers Genic enhancers Weak transcription Flanking Active TSS Flanking Bivalent TSS/Enh Strong transcription Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	107 gene(s)	inside rSNPs	diseases
6	nsv1030604	chr7:100717732-101223465	Weak transcription Flanking Active TSS Active TSS Transcr. at gene 5' and 3' Enhancers Strong transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	76 gene(s)	inside rSNPs	diseases
7	nsv464649	chr7:100739682-100810983	Flanking Active TSS Active TSS Weak transcription Bivalent Enhancer Enhancers Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Strong transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	39 gene(s)	inside rSNPs	diseases
8	nsv607972	chr7:100739682-100810983	Enhancers Weak transcription Strong transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Genic enhancers Active TSS Bivalent/Poised TSS Flanking Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	39 gene(s)	inside rSNPs	diseases
9	esv2422376	chr7:100743485-101016471	Weak transcription Enhancers Strong transcription Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	63 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs11972491	GATS	cis	parietal	SCAN

Chromatin state (count:53 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:100733600-100755400	Weak transcription	Aorta	Aorta
2	chr7:100744000-100751800	Weak transcription	Left Ventricle	heart
3	chr7:100744400-100751200	Weak transcription	Psoas Muscle	Psoas
4	chr7:100744400-100751600	Weak transcription	Ovary	ovary
5	chr7:100745200-100751600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
6	chr7:100745400-100751600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
7	chr7:100745600-100751800	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
8	chr7:100745600-100752200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
9	chr7:100747000-100752000	Weak transcription	Placenta Amnion	Placenta Amnion
10	chr7:100747200-100751600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
11	chr7:100747600-100751600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
12	chr7:100747600-100751600	Weak transcription	HSMMtube	muscle
13	chr7:100747600-100755400	Weak transcription	NHLF	lung
14	chr7:100747600-100760400	Weak transcription	HUES6 Cell Line	embryonic stem cell
15	chr7:100747800-100751200	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
16	chr7:100747800-100751600	Weak transcription	Cortex derived primary cultured neurospheres	brain
17	chr7:100747800-100752200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
18	chr7:100747800-100760600	Weak transcription	H1 Cell Line	embryonic stem cell
19	chr7:100748400-100751600	Weak transcription	HMEC	breast
20	chr7:100748600-100751600	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
21	chr7:100748600-100751600	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
22	chr7:100748600-100751600	Weak transcription	NHEK	skin
23	chr7:100748600-100751800	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
24	chr7:100748600-100751800	Weak transcription	Lung	lung
25	chr7:100748600-100751800	Weak transcription	Osteobl	bone
26	chr7:100748600-100752200	Weak transcription	Right Atrium	heart
27	chr7:100749400-100752200	Enhancers	Primary neutrophils fromperipheralblood	blood
28	chr7:100750000-100751600	Weak transcription	K562	blood
29	chr7:100750000-100760200	Weak transcription	Hela-S3	cervix
30	chr7:100750400-100752600	Enhancers	Spleen	Spleen
31	chr7:100750600-100752200	Enhancers	Monocytes-CD14+_RO01746	blood
32	chr7:100750800-100752000	Genic enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
33	chr7:100750800-100752400	Enhancers	Primary monocytes fromperipheralblood	blood
34	chr7:100750800-100752600	Enhancers	Adipose Nuclei	Adipose
35	chr7:100750800-100752800	Enhancers	GM12878-XiMat	blood
36	chr7:100750800-100753000	Genic enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
37	chr7:100750800-100753400	Enhancers	NHDF-Ad	bronchial
38	chr7:100750800-100753600	Enhancers	Muscle Satellite Cultured Cells	--
39	chr7:100750800-100753600	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
40	chr7:100750800-100756600	Enhancers	HUVEC	blood vessel
41	chr7:100751000-100751200	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
42	chr7:100751000-100751200	Enhancers	Right Ventricle	heart
43	chr7:100751000-100751600	Weak transcription	Skeletal Muscle Female	skeletal muscle
44	chr7:100751000-100751800	Enhancers	Liver	Liver
45	chr7:100751000-100751800	Enhancers	A549	lung
46	chr7:100751000-100752400	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
47	chr7:100751000-100752400	Enhancers	Brain Hippocampus Middle	brain
48	chr7:100751000-100752600	Enhancers	NH-A	brain
49	chr7:100751000-100752800	Enhancers	Esophagus	oesophagus
50	chr7:100751000-100752800	Enhancers	Fetal Muscle Trunk	muscle

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links