Variant report

Variant	rs3827708
Chromosome Location	chr1:180972363-180972364
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr1:180971335..180974394-chr1:180989293..180992610,3	K562	blood:
2	chr1:180970472..180977735-chr1:180989614..180993655,8	MCF-7	breast:
3	chr1:180970620..180972519-chr1:180973045..180976019,2	K562	blood:
4	chr1:180970943..180973873-chr1:181056129..181057947,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000162783	Chromatin interaction
ENSG00000135823	Chromatin interaction

Extended variants
information (count: 17 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:14)

rs_ID	r²[population]
rs10494536	1.00[ASW][hapmap];1.00[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];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10797662	0.85[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10797663	0.82[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11584852	0.82[EUR][1000 genomes]
rs12752307	1.00[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];0.83[EUR][1000 genomes]
rs1411479	0.92[ASW][hapmap];0.96[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];0.96[GIH][hapmap];1.00[JPT][hapmap];0.94[MEX][hapmap];0.97[TSI][hapmap];0.83[EUR][1000 genomes]
rs2225332	0.85[EUR][1000 genomes]
rs3789361	0.87[AMR][1000 genomes];0.89[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6425659	1.00[CEU][hapmap];0.95[CHB][hapmap];0.94[JPT][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs71516924	0.83[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs7528255	0.89[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs7546157	0.91[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.94[JPT][hapmap];0.92[LWK][hapmap];0.94[MEX][hapmap];0.96[MKK][hapmap];1.00[TSI][hapmap];0.84[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7556005	1.00[CEU][hapmap];0.92[CHD][hapmap];0.91[GIH][hapmap];0.81[JPT][hapmap];0.81[MEX][hapmap];0.97[TSI][hapmap];0.89[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs883859	0.96[CEU][hapmap];0.85[CHB][hapmap];0.81[JPT][hapmap];0.81[AMR][1000 genomes];0.89[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1014404	chr1:180770155-181090200	Weak transcription Active TSS Enhancers Genic enhancers Strong transcription Flanking Active TSS ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	97 gene(s)	inside rSNPs	diseases
2	esv3342865	chr1:180933678-181018012	Flanking Active TSS Strong transcription Weak transcription Enhancers Active TSS Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	27 gene(s)	inside rSNPs	diseases
3	esv3383831	chr1:180937224-181029755	Strong transcription Active TSS Weak transcription Genic enhancers Flanking Active TSS Enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	27 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs3827708	RGS8	cis	parietal	SCAN
rs3827708	STX6	cis	parietal	SCAN
rs3827708	PAPPA2	cis	cerebellum	SCAN

Chromatin state (count:126 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:180933400-180974600	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
2	chr1:180940400-180988400	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
3	chr1:180943600-180979800	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
4	chr1:180945400-180975000	Strong transcription	Monocytes-CD14+_RO01746	blood
5	chr1:180945600-180974800	Strong transcription	Primary monocytes fromperipheralblood	blood
6	chr1:180952200-180974800	Strong transcription	HUES64 Cell Line	embryonic stem cell
7	chr1:180956600-180973200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
8	chr1:180958000-180973600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
9	chr1:180959000-180975000	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
10	chr1:180959200-180972800	Weak transcription	iPS-15b Cell Line	embryonic stem cell
11	chr1:180959200-180990800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
12	chr1:180959400-180973200	Weak transcription	Aorta	Aorta
13	chr1:180959600-180973000	Weak transcription	Small Intestine	intestine
14	chr1:180959800-180979800	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
15	chr1:180960600-180973400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
16	chr1:180960600-180985200	Weak transcription	Stomach Mucosa	stomach
17	chr1:180960800-180973200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
18	chr1:180960800-180979800	Weak transcription	Rectal Smooth Muscle	rectum
19	chr1:180961000-180973000	Weak transcription	Spleen	Spleen
20	chr1:180961000-180973400	Weak transcription	Colonic Mucosa	Colon
21	chr1:180961400-180979800	Weak transcription	NH-A	brain
22	chr1:180961600-180973000	Weak transcription	Primary T killer memory cells from peripheral blood	blood
23	chr1:180963800-180972600	Weak transcription	Left Ventricle	heart
24	chr1:180963800-180973200	Weak transcription	Gastric	stomach
25	chr1:180963800-180973200	Weak transcription	Pancreas	Pancrea
26	chr1:180964000-180980400	Weak transcription	Fetal Heart	heart
27	chr1:180964400-180975200	Strong transcription	Cortex derived primary cultured neurospheres	brain
28	chr1:180965000-180974800	Strong transcription	HUES48 Cell Line	embryonic stem cell
29	chr1:180965200-180973200	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
30	chr1:180965600-180974600	Strong transcription	Primary T cells from cord blood	blood
31	chr1:180965600-180975000	Strong transcription	iPS-20b Cell Line	embryonic stem cell
32	chr1:180966400-180974600	Strong transcription	GM12878-XiMat	blood
33	chr1:180967000-180975000	Strong transcription	Primary T helper cells PMA-I stimulated	--
34	chr1:180967000-180975200	Strong transcription	Primary T helper cells fromperipheralblood	blood
35	chr1:180967400-180975000	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
36	chr1:180967400-180975000	Strong transcription	Dnd41	blood
37	chr1:180967400-180975600	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
38	chr1:180967800-180974600	Strong transcription	Primary neutrophils fromperipheralblood	blood
39	chr1:180967800-180974800	Strong transcription	Primary T cells fromperipheralblood	blood
40	chr1:180967800-180974800	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
41	chr1:180968000-180974600	Strong transcription	Primary B cells from peripheral blood	blood
42	chr1:180968000-180974800	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
43	chr1:180968000-180975000	Strong transcription	Hela-S3	cervix
44	chr1:180968200-180972800	Weak transcription	NHDF-Ad	bronchial
45	chr1:180968200-180974600	Strong transcription	Foreskin Fibroblast Primary Cells skin01	Skin
46	chr1:180968800-180975000	Strong transcription	iPS-18 Cell Line	embryonic stem cell
47	chr1:180968800-180976800	Strong transcription	Primary B cells from cord blood	blood
48	chr1:180969000-180972800	Weak transcription	HUVEC	blood vessel
49	chr1:180969200-180974400	Strong transcription	Breast Myoepithelial Primary Cells	Breast
50	chr1:180969200-180974600	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast

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