Variant report

Variant	rs41323648
Chromosome Location	chr7:83673516-83673517
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 55 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:47)

rs_ID	r²[population]
rs13437857	0.85[TSI][hapmap]
rs1534075	0.87[CEU][hapmap];0.90[CHB][hapmap];0.92[CHD][hapmap];0.92[GIH][hapmap];0.94[JPT][hapmap];0.92[TSI][hapmap];0.85[AMR][1000 genomes];0.82[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs16887610	0.87[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[ASN][1000 genomes]
rs16887642	0.85[TSI][hapmap]
rs17158521	0.86[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs17158529	0.80[CHB][hapmap];0.92[CHD][hapmap];0.92[GIH][hapmap];0.82[JPT][hapmap];0.92[TSI][hapmap];0.86[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs17158532	0.87[CEU][hapmap];0.90[CHB][hapmap];0.92[CHD][hapmap];0.92[GIH][hapmap];0.94[JPT][hapmap];0.92[TSI][hapmap];0.91[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs17158583	0.87[CEU][hapmap];0.96[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[TSI][hapmap];0.88[ASN][1000 genomes]
rs17158686	0.85[TSI][hapmap]
rs2372020	0.85[CEU][hapmap];0.90[CHB][hapmap];0.92[CHD][hapmap];0.92[GIH][hapmap];0.93[JPT][hapmap];0.92[TSI][hapmap];0.85[AMR][1000 genomes];0.91[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs3735516	0.82[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs3779441	0.82[CEU][hapmap];0.89[CHB][hapmap];0.93[JPT][hapmap];0.85[AMR][1000 genomes];0.82[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs3801604	0.85[AMR][1000 genomes];0.82[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs59023591	0.85[AMR][1000 genomes];0.91[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs60359427	0.88[ASN][1000 genomes]
rs61482260	0.88[ASN][1000 genomes]
rs66493308	0.94[ASN][1000 genomes]
rs67536627	0.82[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs68158025	0.87[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs73181988	0.85[AMR][1000 genomes];0.82[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs73183709	0.82[EUR][1000 genomes]
rs73185435	0.85[AMR][1000 genomes];0.82[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs73185447	0.85[AMR][1000 genomes];0.86[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs73185458	0.85[AMR][1000 genomes];0.91[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs73185463	0.85[AMR][1000 genomes];0.91[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs73185469	0.91[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs73185480	0.85[AMR][1000 genomes];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs73187439	0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs73187440	0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs73187443	0.85[AMR][1000 genomes];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs73187445	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs73187447	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs73187448	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs73187451	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs73187453	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs73187455	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs73187457	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs73187458	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs73187460	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs73187462	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs73187464	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs73187466	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs73187470	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs73187479	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs73187480	0.92[ASN][1000 genomes]
rs73189355	0.88[ASN][1000 genomes]
rs73189358	0.88[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:8 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1020784	chr7:83577402-83687108	Weak transcription Enhancers Flanking Active TSS Strong transcription Genic enhancers ZNF genes & repeats Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer	Chromatin interactive region	n/a	inside rSNPs	diseases
2	nsv888623	chr7:83596683-83687622	Weak transcription Enhancers Strong transcription Flanking Active TSS ZNF genes & repeats Genic enhancers Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer	Chromatin interactive region	n/a	inside rSNPs	diseases
3	nsv888624	chr7:83596683-83698177	Weak transcription Flanking Active TSS Enhancers Strong transcription Active TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer	Chromatin interactive region	n/a	inside rSNPs	diseases
4	nsv888625	chr7:83616528-83687622	Flanking Active TSS Strong transcription Weak transcription Enhancers ZNF genes & repeats Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer	Chromatin interactive region	n/a	inside rSNPs	diseases
5	esv3352967	chr7:83626144-83684599	Strong transcription Weak transcription Enhancers Flanking Active TSS Genic enhancers Active TSS Bivalent Enhancer ZNF genes & repeats	Chromatin interactive region	n/a	inside rSNPs	diseases
6	nsv888626	chr7:83651854-83698177	Active TSS Enhancers Weak transcription Strong transcription ZNF genes & repeats Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer	Chromatin interactive region	n/a	inside rSNPs	diseases
7	nsv888627	chr7:83659577-83708238	Enhancers Weak transcription Active TSS Strong transcription Flanking Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer	Chromatin interactive region	n/a	inside rSNPs	diseases
8	nsv888628	chr7:83659577-83722691	Enhancers Weak transcription Flanking Active TSS Active TSS Strong transcription ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer	Chromatin interactive region	n/a	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs41323648	SEMA3A	cis	lymphoblastoid	seeQTL

Chromatin state (count:40 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:83652200-83680200	Weak transcription	Stomach Smooth Muscle	stomach
2	chr7:83668400-83674200	Weak transcription	H9 Cell Line	embryonic stem cell
3	chr7:83668400-83676000	Weak transcription	Fetal Muscle Leg	muscle
4	chr7:83669400-83674800	Enhancers	HepG2	liver
5	chr7:83669800-83673800	Weak transcription	Brain Germinal Matrix	brain
6	chr7:83670200-83685000	Weak transcription	iPS-18 Cell Line	embryonic stem cell
7	chr7:83671000-83673800	Enhancers	Osteobl	bone
8	chr7:83671400-83674400	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
9	chr7:83671800-83677600	Weak transcription	iPS-15b Cell Line	embryonic stem cell
10	chr7:83671800-83687400	Weak transcription	Fetal Intestine Large	intestine
11	chr7:83672000-83673800	Strong transcription	HUES64 Cell Line	embryonic stem cell
12	chr7:83672000-83674200	Enhancers	Muscle Satellite Cultured Cells	--
13	chr7:83672000-83676200	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
14	chr7:83672000-83684600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
15	chr7:83672000-83685800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
16	chr7:83672200-83674200	Enhancers	Fetal Heart	heart
17	chr7:83672600-83673600	Flanking Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
18	chr7:83672800-83673600	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
19	chr7:83672800-83673800	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
20	chr7:83672800-83673800	Enhancers	Colon Smooth Muscle	Colon
21	chr7:83672800-83673800	Enhancers	NH-A	brain
22	chr7:83672800-83674200	Enhancers	Stomach Mucosa	stomach
23	chr7:83672800-83674600	Strong transcription	iPS-20b Cell Line	embryonic stem cell
24	chr7:83672800-83674600	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
25	chr7:83672800-83674600	Strong transcription	Fetal Lung	lung
26	chr7:83672800-83676000	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
27	chr7:83673000-83673800	Enhancers	Breast Myoepithelial Primary Cells	Breast
28	chr7:83673000-83674000	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
29	chr7:83673000-83674400	Genic enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
30	chr7:83673000-83674400	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
31	chr7:83673000-83674800	Strong transcription	HUES48 Cell Line	embryonic stem cell
32	chr7:83673200-83673600	Enhancers	Cortex derived primary cultured neurospheres	brain
33	chr7:83673200-83673800	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
34	chr7:83673200-83674400	Strong transcription	HUES6 Cell Line	embryonic stem cell
35	chr7:83673200-83674400	Enhancers	Rectal Smooth Muscle	rectum
36	chr7:83673200-83674400	Genic enhancers	NHDF-Ad	bronchial
37	chr7:83673200-83678200	Weak transcription	Hela-S3	cervix
38	chr7:83673200-83688200	Weak transcription	NHLF	lung
39	chr7:83673400-83675800	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
40	chr7:83673400-83676400	Weak transcription	A549	lung

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