Variant report

Variant	rs10228495
Chromosome Location	chr7:102440184-102440185
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 65 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:55)

rs_ID	r²[population]
rs10227402	0.84[ASN][1000 genomes]
rs10241865	0.86[CHB][hapmap];0.91[JPT][hapmap]
rs10242028	0.86[CHB][hapmap];0.91[JPT][hapmap]
rs10257317	0.95[ASN][1000 genomes]
rs10271184	0.86[ASW][hapmap];0.86[CHB][hapmap];0.95[CHD][hapmap];0.90[JPT][hapmap];0.89[LWK][hapmap];0.94[YRI][hapmap];0.83[ASN][1000 genomes]
rs10273725	0.93[CHD][hapmap];0.85[JPT][hapmap]
rs10279449	0.86[ASW][hapmap];0.86[CHB][hapmap];0.95[CHD][hapmap];0.95[JPT][hapmap];0.87[LWK][hapmap];0.94[YRI][hapmap];0.91[AFR][1000 genomes];0.90[ASN][1000 genomes]
rs10953374	0.91[AFR][1000 genomes];0.94[ASN][1000 genomes]
rs11514917	0.86[CHB][hapmap];0.90[CHD][hapmap];0.86[JPT][hapmap]
rs11978799	0.95[CHD][hapmap];0.91[JPT][hapmap]
rs11981980	0.93[CHD][hapmap];0.95[JPT][hapmap];0.86[ASN][1000 genomes]
rs12537977	0.86[CHB][hapmap];0.93[CHD][hapmap];0.86[JPT][hapmap]
rs12668434	0.95[CHD][hapmap];0.95[JPT][hapmap];0.82[ASN][1000 genomes]
rs13233521	0.86[CHB][hapmap];0.93[CHD][hapmap];0.86[JPT][hapmap]
rs13242493	0.93[CHD][hapmap];0.86[JPT][hapmap]
rs1541519	0.86[ASW][hapmap];0.81[CHB][hapmap];0.95[CHD][hapmap];1.00[JPT][hapmap];0.89[LWK][hapmap];0.94[YRI][hapmap];0.89[AFR][1000 genomes];0.90[ASN][1000 genomes]
rs1608651	0.81[CHB][hapmap];0.88[CHD][hapmap]
rs17136090	0.95[CHD][hapmap];0.95[JPT][hapmap];0.82[ASN][1000 genomes]
rs2411046	1.00[YRI][hapmap];0.80[ASN][1000 genomes]
rs2411056	0.80[ASN][1000 genomes]
rs2430070	0.88[YRI][hapmap]
rs41501847	0.95[CHD][hapmap];0.91[JPT][hapmap]
rs4620204	0.86[CHB][hapmap];0.93[CHD][hapmap];0.86[JPT][hapmap]
rs4729860	0.80[CHB][hapmap];0.81[JPT][hapmap]
rs56269620	0.84[ASN][1000 genomes]
rs57253646	0.88[ASN][1000 genomes]
rs59544295	0.81[ASN][1000 genomes]
rs59709436	0.81[ASN][1000 genomes]
rs6465873	0.87[ASN][1000 genomes]
rs6465876	0.86[CHB][hapmap];0.95[CHD][hapmap];0.91[JPT][hapmap];0.83[ASN][1000 genomes]
rs6465878	0.90[JPT][hapmap]
rs6946773	0.95[CHD][hapmap];0.95[JPT][hapmap];0.88[ASN][1000 genomes]
rs6947403	0.93[CHD][hapmap];0.86[JPT][hapmap]
rs6949391	0.95[ASN][1000 genomes]
rs6953980	0.95[CHD][hapmap];0.91[JPT][hapmap]
rs6960428	0.83[CHB][hapmap];0.90[JPT][hapmap]
rs6969054	0.90[CHB][hapmap];0.86[JPT][hapmap];0.90[YRI][hapmap];0.95[ASN][1000 genomes]
rs6975388	0.90[ASN][1000 genomes]
rs6979964	0.80[AFR][1000 genomes]
rs7778418	0.90[CHB][hapmap];0.98[CHD][hapmap];0.95[JPT][hapmap]
rs7779145	0.93[CHD][hapmap];0.95[JPT][hapmap];0.81[ASN][1000 genomes]
rs7780981	0.95[CHD][hapmap];0.95[JPT][hapmap];0.88[ASN][1000 genomes]
rs7782908	1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[YRI][hapmap];0.89[ASN][1000 genomes]
rs7789252	0.81[CHB][hapmap]
rs7794668	0.86[CHB][hapmap];0.95[CHD][hapmap];0.91[JPT][hapmap];0.82[ASN][1000 genomes]
rs7800548	0.86[ASW][hapmap];0.86[CHB][hapmap];0.93[CHD][hapmap];0.95[JPT][hapmap];0.81[LWK][hapmap];0.95[YRI][hapmap];0.84[ASN][1000 genomes]
rs7804322	0.81[ASN][1000 genomes]
rs847646	0.86[JPT][hapmap]
rs847647	0.93[CHD][hapmap];0.86[JPT][hapmap]
rs847648	0.86[CHB][hapmap];0.93[CHD][hapmap];0.91[JPT][hapmap]
rs847649	0.86[CHB][hapmap];0.93[CHD][hapmap];0.86[JPT][hapmap]
rs847656	0.93[CHD][hapmap];0.86[JPT][hapmap]
rs847658	0.86[JPT][hapmap]
rs869332	0.81[CHB][hapmap];0.88[CHD][hapmap]
rs9718453	0.86[CHB][hapmap];0.93[CHD][hapmap];0.82[JPT][hapmap]

Variant overlapped rSNPs/rCNVs (count:10 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1016563	chr7:101912320-102695860	Weak transcription Genic enhancers Flanking Active TSS Enhancers Strong transcription Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	76 gene(s)	inside rSNPs	diseases
2	nsv1028438	chr7:101912320-102704135	Strong transcription Weak transcription Enhancers Active TSS Flanking Active TSS Genic enhancers ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	76 gene(s)	inside rSNPs	diseases
3	nsv1025363	chr7:102072448-102471485	Flanking Active TSS Enhancers Weak transcription Strong transcription Genic enhancers Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	42 gene(s)	inside rSNPs	diseases
4	nsv469620	chr7:102296392-102454063	Enhancers Weak transcription Active TSS Flanking Active TSS Strong transcription Bivalent Enhancer ZNF genes & repeats Genic enhancers Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
5	nsv482714	chr7:102296392-102454063	Active TSS Enhancers Strong transcription Weak transcription ZNF genes & repeats Flanking Active TSS Bivalent/Poised TSS Genic enhancers Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
6	nsv868996	chr7:102332827-102991361	ZNF genes & repeats Strong transcription Weak transcription Enhancers Flanking Active TSS Active TSS Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	46 gene(s)	inside rSNPs	diseases
7	esv2761100	chr7:102335787-102481978	Enhancers Weak transcription Strong transcription Active TSS Flanking Active TSS ZNF genes & repeats Genic enhancers Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
8	esv2752138	chr7:102358320-102787135	Enhancers Weak transcription Strong transcription Active TSS Flanking Active TSS ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	33 gene(s)	inside rSNPs	diseases
9	nsv470382	chr7:102375663-102538515	Enhancers Weak transcription ZNF genes & repeats Flanking Active TSS Strong transcription Active TSS Bivalent Enhancer Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
10	nsv608057	chr7:102440184-102538515	Enhancers Strong transcription Weak transcription Flanking Active TSS Active TSS ZNF genes & repeats Genic enhancers Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs10228495	POLR2J3	cis	Muscle Skeletal	GTEx
rs10228495	DPY19L2P2	cis	parietal	SCAN
rs10228495	POLR2J3	cis	Adipose Subcutaneous	GTEx
rs10228495	CUX1	cis	cerebellum	SCAN

Chromatin state (count:23 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:102390800-102448800	Weak transcription	Breast Myoepithelial Primary Cells	Breast
2	chr7:102391600-102448600	Weak transcription	Adipose Nuclei	Adipose
3	chr7:102416400-102467600	Weak transcription	Brain Anterior Caudate	brain
4	chr7:102419600-102454200	Weak transcription	Osteobl	bone
5	chr7:102419600-102456000	Weak transcription	Brain Inferior Temporal Lobe	brain
6	chr7:102419800-102454000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
7	chr7:102420400-102448600	Weak transcription	K562	blood
8	chr7:102420800-102449000	Weak transcription	Rectal Mucosa Donor 29	rectum
9	chr7:102421600-102449000	Weak transcription	Liver	Liver
10	chr7:102421600-102452000	Weak transcription	Monocytes-CD14+_RO01746	blood
11	chr7:102421600-102475600	Weak transcription	Fetal Thymus	thymus
12	chr7:102422000-102448800	Weak transcription	Primary hematopoietic stem cells short term culture	blood
13	chr7:102422000-102474800	Weak transcription	Duodenum Mucosa	Duodenum
14	chr7:102422000-102476000	Weak transcription	Fetal Muscle Trunk	muscle
15	chr7:102436000-102454000	Weak transcription	NH-A	brain
16	chr7:102437200-102448800	Weak transcription	Fetal Stomach	stomach
17	chr7:102437400-102452000	Weak transcription	HUVEC	blood vessel
18	chr7:102437600-102449200	Weak transcription	Fetal Lung	lung
19	chr7:102439000-102459600	Weak transcription	Brain Hippocampus Middle	brain
20	chr7:102439600-102467400	Weak transcription	Thymus	Thymus
21	chr7:102439800-102463800	Weak transcription	Placenta Amnion	Placenta Amnion
22	chr7:102440000-102440200	Weak transcription	Primary T cells from cord blood	blood
23	chr7:102440000-102440400	ZNF genes & repeats	Primary hematopoietic stem cells G-CSF-mobilized Male	--

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links