Variant report

Variant	rs3862894
Chromosome Location	chr1:77837106-77837107
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 19 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:12)

rs_ID	r²[population]
rs10782647	0.82[CHD][hapmap]
rs11162331	0.80[JPT][hapmap]
rs11162333	0.88[JPT][hapmap]
rs17100308	0.85[JPT][hapmap]
rs17100475	1.00[ASW][hapmap];0.94[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];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17100521	0.80[JPT][hapmap]
rs3896706	0.80[JPT][hapmap]
rs3911801	0.80[JPT][hapmap]
rs60053175	0.95[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72641177	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72641178	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7518696	0.89[JPT][hapmap]

Variant overlapped rSNPs/rCNVs (count:7 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1005183	chr1:77728990-77949309	Weak transcription Flanking Active TSS Enhancers Strong transcription Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
2	nsv535010	chr1:77728990-77949309	Bivalent Enhancer Weak transcription Enhancers ZNF genes & repeats Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh Strong transcription Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
3	nsv932557	chr1:77730247-77958687	Flanking Active TSS Enhancers Strong transcription Weak transcription ZNF genes & repeats Bivalent Enhancer Genic enhancers Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
4	nsv1003714	chr1:77756861-77949309	Weak transcription Strong transcription Enhancers Flanking Active TSS Genic enhancers Bivalent Enhancer Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
5	nsv470719	chr1:77774413-78269207	Weak transcription Enhancers Flanking Active TSS Strong transcription Active TSS Genic enhancers ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	34 gene(s)	inside rSNPs	diseases
6	nsv546591	chr1:77774413-78269207	Active TSS Weak transcription Flanking Active TSS Enhancers Genic enhancers Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	34 gene(s)	inside rSNPs	diseases
7	esv2764210	chr1:77825478-77838400	Flanking Active TSS Weak transcription Enhancers Active TSS Genic enhancers Strong transcription Bivalent Enhancer	TF binding region CpG island Chromatin interactive region	1 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs3862894	LHX8	cis	parietal	SCAN
rs3862894	CRYZ	cis	parietal	SCAN
rs3862894	MSH4	cis	parietal	SCAN

Chromatin state (count:42 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:77803400-77839200	Weak transcription	Breast Myoepithelial Primary Cells	Breast
2	chr1:77834000-77839800	Enhancers	NHDF-Ad	bronchial
3	chr1:77834200-77839000	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
4	chr1:77835200-77837200	Enhancers	Brain Cingulate Gyrus	brain
5	chr1:77835200-77838000	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
6	chr1:77835600-77837200	Enhancers	Foreskin Melanocyte Primary Cells skin01	Skin
7	chr1:77835600-77837400	Enhancers	Primary hematopoietic stem cells short term culture	blood
8	chr1:77835600-77837400	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
9	chr1:77835600-77837400	Enhancers	NH-A	brain
10	chr1:77835600-77838000	Enhancers	Primary T helper naive cells fromperipheralblood	blood
11	chr1:77835800-77837200	Flanking Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
12	chr1:77835800-77837200	Enhancers	Fetal Stomach	stomach
13	chr1:77835800-77837400	Enhancers	HMEC	breast
14	chr1:77835800-77846400	Weak transcription	Aorta	Aorta
15	chr1:77836000-77837400	Enhancers	Brain Hippocampus Middle	brain
16	chr1:77836000-77837800	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
17	chr1:77836000-77837800	Enhancers	Osteobl	bone
18	chr1:77836400-77837200	Enhancers	ES-I3 Cell Line	embryonic stem cell
19	chr1:77836400-77837200	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
20	chr1:77836400-77837400	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
21	chr1:77836400-77837400	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
22	chr1:77836400-77837800	Enhancers	Primary T helper naive cells from peripheral blood	blood
23	chr1:77836400-77838000	Enhancers	Primary T cells from cord blood	blood
24	chr1:77836400-77838000	Enhancers	Primary T helper cells fromperipheralblood	blood
25	chr1:77836400-77838400	Enhancers	Primary T helper cells PMA-I stimulated	--
26	chr1:77836600-77837200	Flanking Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
27	chr1:77836600-77837200	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
28	chr1:77836600-77837400	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
29	chr1:77836600-77837400	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
30	chr1:77836600-77837400	Enhancers	NHEK	skin
31	chr1:77836600-77840800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
32	chr1:77836600-77844000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
33	chr1:77836600-77844400	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
34	chr1:77837000-77837200	Bivalent Enhancer	Foreskin Keratinocyte Primary Cells skin02	Skin
35	chr1:77837000-77837400	Flanking Active TSS	Muscle Satellite Cultured Cells	--
36	chr1:77837000-77837400	Enhancers	Brain Angular Gyrus	brain
37	chr1:77837000-77837400	Flanking Active TSS	HSMM	muscle
38	chr1:77837000-77837400	Flanking Active TSS	HSMMtube	muscle
39	chr1:77837000-77837600	Flanking Active TSS	NHLF	lung
40	chr1:77837000-77840600	Weak transcription	Brain Anterior Caudate	brain
41	chr1:77837000-77840800	Weak transcription	Brain Substantia Nigra	brain
42	chr1:77837000-77844400	Weak transcription	Brain Inferior Temporal Lobe	brain

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links