Variant report

Variant	rs6956549
Chromosome Location	chr7:13073750-13073751
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 141 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:130)

rs_ID	r²[population]
rs10429149	0.84[AMR][1000 genomes]
rs10488243	1.00[CHB][hapmap];0.89[CHD][hapmap];1.00[GIH][hapmap];0.95[JPT][hapmap];0.90[MEX][hapmap];0.88[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs10950428	0.83[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs10950431	0.92[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs10950432	0.92[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs10950433	0.92[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs10950434	0.92[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs11975327	0.81[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap];0.87[AMR][1000 genomes];0.85[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs11983822	0.88[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs12056050	0.89[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs12056168	0.92[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs12056220	0.92[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs12112648	0.87[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs12113090	0.82[CEU][hapmap];0.84[GIH][hapmap];0.91[JPT][hapmap];0.85[MEX][hapmap]
rs12530565	0.88[AMR][1000 genomes];0.87[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12530643	0.84[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs12530651	0.89[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs12531362	0.82[CEU][hapmap];0.85[JPT][hapmap]
rs12531363	0.82[CEU][hapmap];0.91[JPT][hapmap]
rs12532653	0.90[ASN][1000 genomes]
rs12533128	0.91[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs12534513	0.91[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs12534537	0.92[ASN][1000 genomes]
rs12534546	0.91[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs12536140	0.90[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs12536193	0.91[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs12537378	0.86[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs12537712	0.86[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs12539699	0.91[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs12671480	0.81[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs12672647	0.91[AMR][1000 genomes];0.87[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs16877655	0.84[AMR][1000 genomes]
rs17166605	0.93[AMR][1000 genomes];0.85[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs17166608	0.95[AMR][1000 genomes];0.87[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs17166610	0.88[AMR][1000 genomes];0.99[ASN][1000 genomes]
rs17166612	0.97[AMR][1000 genomes];0.93[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs17166614	0.84[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs17166626	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs17166643	0.87[AFR][1000 genomes];0.97[AMR][1000 genomes];0.86[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs17166651	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs17166653	1.00[CEU][hapmap];1.00[GIH][hapmap];0.92[TSI][hapmap];0.94[EUR][1000 genomes]
rs17166655	1.00[CEU][hapmap];0.81[CHD][hapmap];1.00[GIH][hapmap];0.84[TSI][hapmap];0.90[EUR][1000 genomes]
rs17166658	0.88[CEU][hapmap];0.81[CHD][hapmap];1.00[GIH][hapmap];0.84[TSI][hapmap];0.90[EUR][1000 genomes]
rs17166671	0.87[CEU][hapmap];1.00[CHB][hapmap];0.89[CHD][hapmap];1.00[GIH][hapmap];0.95[JPT][hapmap];0.84[TSI][hapmap];0.93[AMR][1000 genomes];0.91[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs17166673	1.00[CHB][hapmap];0.95[JPT][hapmap];0.90[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs17166674	0.92[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs17166683	0.84[AMR][1000 genomes]
rs17166689	0.87[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs17166711	0.93[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs17166712	0.84[AMR][1000 genomes]
rs17166756	0.81[CEU][hapmap];0.91[JPT][hapmap]
rs1861237	0.87[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs1981639	0.82[CEU][hapmap];0.91[JPT][hapmap]
rs2005878	0.90[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs2006291	0.89[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs2110650	0.86[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs2160193	0.89[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs2191043	0.82[CEU][hapmap];0.83[JPT][hapmap]
rs2215222	0.82[AMR][1000 genomes]
rs2215950	0.83[ASN][1000 genomes]
rs28639785	0.88[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs34125302	0.95[AMR][1000 genomes];0.89[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs34404228	0.87[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs34932308	0.86[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs35023832	0.87[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs35432593	0.84[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs4236278	0.91[JPT][hapmap]
rs4636097	0.87[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs4719347	0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4721177	0.92[AMR][1000 genomes];0.84[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs55957561	0.90[AMR][1000 genomes];0.81[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs57459966	0.92[AMR][1000 genomes];0.83[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs59675898	0.86[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs60020188	0.81[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs60345281	0.86[AMR][1000 genomes];0.82[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs60705466	0.97[AMR][1000 genomes];0.91[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs61232028	0.86[AMR][1000 genomes];0.82[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs61639094	0.86[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs6460997	0.93[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs6460999	0.84[AMR][1000 genomes]
rs6461000	0.84[AMR][1000 genomes]
rs6461007	0.91[JPT][hapmap]
rs6942805	0.82[AMR][1000 genomes]
rs6949649	0.92[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs6950122	0.87[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs6950438	0.87[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs6950752	0.95[AFR][1000 genomes];0.97[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6964875	0.85[CEU][hapmap];0.90[JPT][hapmap]
rs6969380	0.83[AMR][1000 genomes]
rs6969769	0.88[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs6974627	0.81[CEU][hapmap];0.91[JPT][hapmap]
rs6977552	0.90[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs73255876	0.83[AMR][1000 genomes]
rs73259988	0.92[AMR][1000 genomes];0.82[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs73259991	0.86[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs73261908	0.93[AMR][1000 genomes];0.91[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs73261911	0.88[AMR][1000 genomes];0.87[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs73261913	0.91[AMR][1000 genomes];0.86[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs73261923	0.97[AMR][1000 genomes];0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs73261936	0.92[AMR][1000 genomes];0.91[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs73261949	0.91[EUR][1000 genomes]
rs73261950	0.82[EUR][1000 genomes]
rs73261954	0.88[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs73261964	0.91[AMR][1000 genomes];0.87[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs73261983	0.88[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs736198	0.86[AMR][1000 genomes]
rs738052	0.89[AMR][1000 genomes];0.81[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs763534	0.86[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs7777911	0.86[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs7778632	0.90[AMR][1000 genomes];0.85[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7778887	0.91[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs7783710	0.84[AMR][1000 genomes]
rs7787776	0.83[AMR][1000 genomes]
rs7787998	0.84[AMR][1000 genomes];0.82[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7788257	0.83[AMR][1000 genomes]
rs7788484	0.82[CEU][hapmap];0.91[JPT][hapmap]
rs7789174	0.87[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs7789528	0.90[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs7789970	0.82[CEU][hapmap];0.91[JPT][hapmap]
rs7790328	0.82[CEU][hapmap];0.91[JPT][hapmap]
rs7790665	0.82[CEU][hapmap];0.91[JPT][hapmap]
rs7790770	0.91[JPT][hapmap]
rs7793289	0.87[AMR][1000 genomes]
rs7793405	0.89[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs7793573	0.92[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs7797104	0.86[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs7799356	0.81[CEU][hapmap]
rs7802485	0.83[AMR][1000 genomes]
rs7802872	0.84[AMR][1000 genomes]
rs9639142	0.82[CEU][hapmap];0.91[JPT][hapmap]

Variant overlapped rSNPs/rCNVs (count:11 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv932020	chr7:12676890-13239551	Enhancers Flanking Active TSS Weak transcription Active TSS Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	42 gene(s)	inside rSNPs	diseases
2	nsv868830	chr7:12712753-13517417	Flanking Active TSS Enhancers Weak transcription ZNF genes & repeats Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	43 gene(s)	inside rSNPs	diseases
3	nsv606235	chr7:12781381-13205950	Weak transcription Enhancers Flanking Active TSS Bivalent Enhancer Active TSS ZNF genes & repeats Genic enhancers Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
4	nsv1020568	chr7:12802640-13183737	Enhancers Flanking Active TSS Weak transcription Active TSS ZNF genes & repeats Strong transcription Bivalent Enhancer Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
5	nsv464384	chr7:12907178-13077065	Enhancers Weak transcription Active TSS ZNF genes & repeats Flanking Active TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
6	nsv606238	chr7:12907178-13077065	Enhancers Flanking Active TSS Weak transcription Active TSS ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
7	nsv1029771	chr7:12927648-13153855	Weak transcription Enhancers ZNF genes & repeats Flanking Active TSS Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
8	nsv538736	chr7:12927648-13153855	Enhancers Flanking Active TSS Active TSS Weak transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
9	nsv1026624	chr7:12963907-13123408	Enhancers Weak transcription Active TSS Flanking Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
10	nsv1019173	chr7:13063854-13585360	Active TSS Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
11	nsv538737	chr7:13063854-13585360	Weak transcription Enhancers Active TSS Flanking Active TSS ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs6956549	TSPAN13	cis	parietal	SCAN
rs6956549	ARL4A	cis	parietal	SCAN

Chromatin state (count:17 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:13070000-13075200	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
2	chr7:13070800-13074600	Enhancers	HUES64 Cell Line	embryonic stem cell
3	chr7:13071200-13075200	Enhancers	iPS-18 Cell Line	embryonic stem cell
4	chr7:13071400-13075000	Enhancers	ES-I3 Cell Line	embryonic stem cell
5	chr7:13071600-13074600	Enhancers	HUES48 Cell Line	embryonic stem cell
6	chr7:13071800-13073800	Enhancers	Rectal Smooth Muscle	rectum
7	chr7:13071800-13073800	Enhancers	A549	lung
8	chr7:13071800-13075400	Enhancers	iPS-15b Cell Line	embryonic stem cell
9	chr7:13072000-13082200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
10	chr7:13072200-13075400	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
11	chr7:13072400-13074800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
12	chr7:13072400-13075000	Enhancers	iPS-20b Cell Line	embryonic stem cell
13	chr7:13072400-13080600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
14	chr7:13072600-13073800	Weak transcription	H1 Cell Line	embryonic stem cell
15	chr7:13072800-13074200	Weak transcription	HUES6 Cell Line	embryonic stem cell
16	chr7:13073000-13073800	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
17	chr7:13073600-13075000	Weak transcription	Colon Smooth Muscle	Colon

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