Variant report

Variant	rs7546157
Chromosome Location	chr1:180983057-180983058
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr1:180982550..180985295-chr1:181057964..181060051,2	K562	blood:
2	chr1:180981578..180983592-chr1:181056387..181059227,2	MCF-7	breast:
3	chr1:180976308..180980103-chr1:180980772..180983671,4	K562	blood:
4	chr1:180982909..180985432-chr1:181080154..181081871,2	MCF-7	breast:
5	chr1:180982571..180984251-chr1:181018903..181020478,2	K562	blood:

Variant related genes	Relation type
ENSG00000162783	Chromatin interaction

Extended variants
information (count: 20 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:16)

rs_ID	r²[population]
rs10494536	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];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10797662	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10797663	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11584852	0.82[EUR][1000 genomes]
rs12752307	1.00[CEU][hapmap];0.94[CHB][hapmap];0.93[JPT][hapmap];0.81[YRI][hapmap];0.84[EUR][1000 genomes]
rs1411479	0.83[ASW][hapmap];0.96[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];0.96[GIH][hapmap];0.94[JPT][hapmap];1.00[MEX][hapmap];0.97[TSI][hapmap];0.81[YRI][hapmap];0.85[EUR][1000 genomes]
rs2225332	0.86[EUR][1000 genomes]
rs3789361	0.83[AMR][1000 genomes];0.88[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs3827708	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]
rs6425659	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.87[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6665134	0.81[JPT][hapmap]
rs71516924	0.87[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs7528255	0.93[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs7528526	0.81[JPT][hapmap]
rs7556005	1.00[CEU][hapmap];0.92[CHD][hapmap];0.91[GIH][hapmap];0.88[MEX][hapmap];0.97[TSI][hapmap];0.93[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs883859	0.96[CEU][hapmap];0.85[CHB][hapmap];0.85[AMR][1000 genomes];0.88[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 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
4	nsv1011081	chr1:180973159-181135953	Weak transcription Strong transcription Flanking Active TSS Enhancers Active TSS Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	95 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs7546157	STX6	cis	parietal	SCAN
rs7546157	PAPPA2	cis	cerebellum	SCAN
rs7546157	RGS8	cis	parietal	SCAN

Chromatin state (count:124 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:180940400-180988400	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
2	chr1:180959200-180990800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
3	chr1:180960600-180985200	Weak transcription	Stomach Mucosa	stomach
4	chr1:180973800-180988200	Weak transcription	Fetal Brain Male	brain
5	chr1:180973800-180989600	Weak transcription	iPS-15b Cell Line	embryonic stem cell
6	chr1:180973800-180990600	Weak transcription	Colonic Mucosa	Colon
7	chr1:180973800-180990800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
8	chr1:180974000-180990800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
9	chr1:180974400-180990000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
10	chr1:180974600-180984000	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
11	chr1:180974600-180984200	Weak transcription	HUVEC	blood vessel
12	chr1:180974600-180986600	Weak transcription	Fetal Intestine Large	intestine
13	chr1:180974600-180988200	Weak transcription	Gastric	stomach
14	chr1:180974600-180990000	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
15	chr1:180974600-180990600	Weak transcription	Liver	Liver
16	chr1:180974600-180990600	Weak transcription	Fetal Muscle Trunk	muscle
17	chr1:180974600-180990600	Weak transcription	Fetal Muscle Leg	muscle
18	chr1:180974800-180983800	Weak transcription	Rectal Mucosa Donor 29	rectum
19	chr1:180974800-180989800	Weak transcription	H1 Cell Line	embryonic stem cell
20	chr1:180974800-180990800	Weak transcription	Rectal Mucosa Donor 31	rectum
21	chr1:180975000-180983600	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
22	chr1:180975000-180989600	Weak transcription	iPS-20b Cell Line	embryonic stem cell
23	chr1:180975000-180990000	Weak transcription	iPS-18 Cell Line	embryonic stem cell
24	chr1:180975200-180990200	Weak transcription	HUES6 Cell Line	embryonic stem cell
25	chr1:180975600-180983400	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
26	chr1:180976400-180987000	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
27	chr1:180978600-180983200	Enhancers	Breast Myoepithelial Primary Cells	Breast
28	chr1:180978800-180986200	Enhancers	Primary monocytes fromperipheralblood	blood
29	chr1:180979800-180983200	Enhancers	HSMM	muscle
30	chr1:180979800-180986000	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
31	chr1:180980000-180986000	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
32	chr1:180980000-180991000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
33	chr1:180980200-180983800	Weak transcription	Ovary	ovary
34	chr1:180980400-180985800	Enhancers	Primary T helper cells PMA-I stimulated	--
35	chr1:180980400-180990600	Weak transcription	Fetal Stomach	stomach
36	chr1:180980600-180989600	Weak transcription	HUES64 Cell Line	embryonic stem cell
37	chr1:180980800-180983600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
38	chr1:180980800-180985000	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
39	chr1:180980800-180986600	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
40	chr1:180980800-180988200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
41	chr1:180980800-180988600	Weak transcription	Fetal Brain Female	brain
42	chr1:180980800-180989400	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
43	chr1:180980800-180989600	Weak transcription	Pancreatic Islets	Pancreatic Islet
44	chr1:180980800-180989800	Weak transcription	HUES48 Cell Line	embryonic stem cell
45	chr1:180980800-180990000	Weak transcription	Colon Smooth Muscle	Colon
46	chr1:180981000-180984200	Weak transcription	NHEK	skin
47	chr1:180981000-180984600	Enhancers	Primary T cells from cord blood	blood
48	chr1:180981000-180986800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
49	chr1:180981000-180987200	Weak transcription	Skeletal Muscle Male	skeletal muscle
50	chr1:180981000-180988000	Weak transcription	Brain Germinal Matrix	brain

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