Variant report

Variant	rs7177699
Chromosome Location	chr15:79089734-79089735
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr15:79086760..79090463-chr15:79101047..79102921,3	K562	blood:

Variant related genes	Relation type
ENSG00000185787	Chromatin interaction

Extended variants
information (count: 31 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:27)

rs_ID	r²[population]
rs11072803	0.90[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs11072804	0.93[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs11072806	0.94[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs11631955	0.92[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs11632102	0.92[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs11634042	0.96[CEU][hapmap];1.00[CHB][hapmap];0.89[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.94[MEX][hapmap];0.93[TSI][hapmap];0.91[AMR][1000 genomes];0.91[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs11634450	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11638321	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11639044	0.96[CEU][hapmap];0.93[TSI][hapmap];0.89[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs11856536	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11858210	0.92[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs12050525	0.89[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs12592721	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12592762	0.85[JPT][hapmap];0.81[ASN][1000 genomes]
rs12899147	0.82[ASW][hapmap];1.00[CEU][hapmap];0.88[CHB][hapmap];0.89[MEX][hapmap];0.93[TSI][hapmap];0.94[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs12903203	1.00[CEU][hapmap];0.86[CHB][hapmap];0.82[AFR][1000 genomes];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs1809420	0.84[MEX][hapmap]
rs1825087	0.93[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs1994016	0.89[CEU][hapmap];0.88[CHB][hapmap];0.89[MEX][hapmap];0.90[MKK][hapmap];0.80[TSI][hapmap];0.82[YRI][hapmap];0.83[AFR][1000 genomes];0.92[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs2277545	1.00[CEU][hapmap];0.88[CHB][hapmap];0.82[YRI][hapmap];0.84[AFR][1000 genomes];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs2277546	0.83[AFR][1000 genomes];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs28610385	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2904220	0.94[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs3825807	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4886592	0.81[AFR][1000 genomes];0.95[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs4887113	0.94[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs7173267	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][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	nsv917303	chr15:78491050-79205255	Enhancers Genic enhancers Weak transcription Flanking Active TSS Strong transcription Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	122 gene(s)	inside rSNPs	diseases
2	nsv904431	chr15:79006442-79155088	Bivalent/Poised TSS Enhancers Active TSS Flanking Bivalent TSS/Enh Strong transcription Weak transcription Genic enhancers Bivalent Enhancer Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
3	esv33573	chr15:79053484-79293881	Weak transcription Strong transcription Enhancers Flanking Active TSS Active TSS ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	20 gene(s)	inside rSNPs	diseases
4	nsv904432	chr15:79066932-79175813	Active TSS Enhancers Weak transcription Bivalent/Poised TSS Bivalent Enhancer Flanking Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Genic enhancers Strong transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs7177699	CHRNA5	cis	parietal	SCAN
rs7177699	BCL2A1	cis	parietal	SCAN
rs7177699	CLK3	cis	parietal	SCAN

Chromatin state (count:68 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:79058000-79090000	Weak transcription	Breast Myoepithelial Primary Cells	Breast
2	chr15:79069200-79090200	Weak transcription	NHDF-Ad	bronchial
3	chr15:79072000-79096600	Weak transcription	Brain Substantia Nigra	brain
4	chr15:79072000-79096800	Weak transcription	Colon Smooth Muscle	Colon
5	chr15:79072800-79089800	Weak transcription	Skeletal Muscle Male	skeletal muscle
6	chr15:79072800-79102400	Weak transcription	Fetal Kidney	kidney
7	chr15:79076400-79090400	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
8	chr15:79076400-79090400	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
9	chr15:79076400-79090800	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
10	chr15:79077200-79089800	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
11	chr15:79077200-79096600	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
12	chr15:79077800-79090600	Strong transcription	Brain Germinal Matrix	brain
13	chr15:79078200-79093200	Strong transcription	Fetal Stomach	stomach
14	chr15:79078400-79091800	Weak transcription	Gastric	stomach
15	chr15:79078600-79089800	Weak transcription	HMEC	breast
16	chr15:79078600-79090600	Strong transcription	Fetal Brain Female	brain
17	chr15:79079400-79091000	Weak transcription	HUVEC	blood vessel
18	chr15:79079600-79090600	Weak transcription	NH-A	brain
19	chr15:79080400-79096200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
20	chr15:79080800-79095200	Weak transcription	Fetal Intestine Large	intestine
21	chr15:79082600-79089800	Weak transcription	Stomach Smooth Muscle	stomach
22	chr15:79082800-79096200	Weak transcription	iPS-15b Cell Line	embryonic stem cell
23	chr15:79082800-79102200	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
24	chr15:79083200-79102000	Weak transcription	Fetal Heart	heart
25	chr15:79083800-79102400	Weak transcription	Aorta	Aorta
26	chr15:79084200-79090000	Weak transcription	Right Atrium	heart
27	chr15:79085800-79090200	Strong transcription	Fetal Muscle Trunk	muscle
28	chr15:79085800-79090800	Strong transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
29	chr15:79086000-79090400	Strong transcription	iPS-18 Cell Line	embryonic stem cell
30	chr15:79086000-79091000	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
31	chr15:79086200-79090200	Strong transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
32	chr15:79086200-79091400	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
33	chr15:79086600-79089800	Strong transcription	Muscle Satellite Cultured Cells	--
34	chr15:79086600-79090200	Strong transcription	Fetal Muscle Leg	muscle
35	chr15:79087000-79090600	Strong transcription	HUES64 Cell Line	embryonic stem cell
36	chr15:79087400-79090000	Strong transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
37	chr15:79087400-79090200	Strong transcription	H9 Cell Line	embryonic stem cell
38	chr15:79087400-79090200	Strong transcription	Adipose Nuclei	Adipose
39	chr15:79087400-79090400	Strong transcription	HUES48 Cell Line	embryonic stem cell
40	chr15:79087400-79090400	Strong transcription	Cortex derived primary cultured neurospheres	brain
41	chr15:79087600-79090400	Strong transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
42	chr15:79087600-79090600	Strong transcription	H1 Cell Line	embryonic stem cell
43	chr15:79087600-79090600	Strong transcription	HUES6 Cell Line	embryonic stem cell
44	chr15:79087800-79090400	Strong transcription	Fetal Intestine Small	intestine
45	chr15:79088200-79090200	Strong transcription	Fetal Lung	lung
46	chr15:79088200-79094000	Weak transcription	Lung	lung
47	chr15:79088200-79096800	Weak transcription	Brain Angular Gyrus	brain
48	chr15:79088600-79090400	Weak transcription	Osteobl	bone
49	chr15:79088600-79090800	Genic enhancers	Foreskin Melanocyte Primary Cells skin01	Skin
50	chr15:79088600-79093400	Weak transcription	Spleen	Spleen

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