Variant report

Variant	rs961679
Chromosome Location	chr7:33458535-33458536
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 102 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:98)

rs_ID	r²[population]
rs10464225	0.92[CEU][hapmap];0.94[GIH][hapmap];0.94[TSI][hapmap];0.86[EUR][1000 genomes]
rs10486529	0.92[CEU][hapmap];0.84[EUR][1000 genomes]
rs10486530	0.92[CEU][hapmap];0.84[EUR][1000 genomes]
rs10951387	0.92[CEU][hapmap];0.84[EUR][1000 genomes]
rs11763712	0.92[CEU][hapmap];0.90[GIH][hapmap];0.97[TSI][hapmap];0.86[EUR][1000 genomes]
rs11764582	0.92[CEU][hapmap];0.84[EUR][1000 genomes]
rs11764921	0.84[AFR][1000 genomes];0.84[EUR][1000 genomes]
rs11765727	0.81[EUR][1000 genomes]
rs11766818	0.86[EUR][1000 genomes]
rs11769334	0.86[EUR][1000 genomes]
rs11769528	0.87[CHB][hapmap];0.90[CHD][hapmap];0.91[JPT][hapmap];0.87[ASN][1000 genomes]
rs11769616	0.92[CEU][hapmap];0.90[GIH][hapmap];0.97[TSI][hapmap];0.86[EUR][1000 genomes]
rs11771086	0.92[CEU][hapmap];0.81[EUR][1000 genomes]
rs11773450	0.92[CEU][hapmap];0.87[EUR][1000 genomes]
rs11773504	0.92[CEU][hapmap];0.93[GIH][hapmap];0.89[TSI][hapmap];0.84[EUR][1000 genomes]
rs11976613	0.92[CEU][hapmap]
rs11977450	0.84[EUR][1000 genomes]
rs11978733	0.92[CEU][hapmap];0.81[EUR][1000 genomes]
rs11982544	0.80[EUR][1000 genomes]
rs12056024	0.86[AFR][1000 genomes];0.81[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs12056065	0.81[EUR][1000 genomes]
rs12056267	0.92[CEU][hapmap];0.84[EUR][1000 genomes]
rs12666753	0.92[CEU][hapmap];0.86[TSI][hapmap]
rs12701289	0.92[CEU][hapmap]
rs13224392	0.92[CEU][hapmap];0.89[TSI][hapmap]
rs13225608	0.81[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs13227256	0.91[JPT][hapmap];0.87[ASN][1000 genomes]
rs13230868	0.92[CEU][hapmap];0.87[EUR][1000 genomes]
rs13234292	0.92[CEU][hapmap];0.87[EUR][1000 genomes]
rs13234403	0.92[CEU][hapmap];0.86[EUR][1000 genomes]
rs13236865	0.92[CEU][hapmap]
rs13236885	0.92[CEU][hapmap];0.87[EUR][1000 genomes]
rs13238407	0.81[EUR][1000 genomes]
rs13239022	0.92[CEU][hapmap];0.87[EUR][1000 genomes]
rs13438256	1.00[JPT][hapmap]
rs1419899	0.91[CEU][hapmap];0.85[EUR][1000 genomes]
rs1419922	0.86[ASW][hapmap];0.92[CEU][hapmap];0.94[GIH][hapmap];1.00[LWK][hapmap];0.82[MEX][hapmap];0.96[MKK][hapmap];0.97[TSI][hapmap];0.87[YRI][hapmap];0.88[AFR][1000 genomes];0.81[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs1419923	0.92[CEU][hapmap];0.87[YRI][hapmap];0.88[AFR][1000 genomes];0.81[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs17170142	0.92[CEU][hapmap]
rs17170174	0.92[CEU][hapmap]
rs17170175	0.92[CEU][hapmap]
rs17170202	0.84[EUR][1000 genomes]
rs17170203	0.92[CEU][hapmap];0.94[GIH][hapmap];0.94[TSI][hapmap];0.84[EUR][1000 genomes]
rs17170220	0.92[CEU][hapmap];0.90[GIH][hapmap];0.97[TSI][hapmap];0.87[EUR][1000 genomes]
rs17170225	0.92[CEU][hapmap];0.87[EUR][1000 genomes]
rs17170226	0.92[CEU][hapmap];0.87[EUR][1000 genomes]
rs17170229	0.92[CEU][hapmap];0.87[EUR][1000 genomes]
rs17170246	0.86[ASW][hapmap];0.92[CEU][hapmap];0.94[GIH][hapmap];1.00[LWK][hapmap];0.83[MEX][hapmap];0.96[MKK][hapmap];0.97[TSI][hapmap];0.87[YRI][hapmap];0.86[AFR][1000 genomes];0.81[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs17170247	0.92[CEU][hapmap];0.94[GIH][hapmap];0.82[LWK][hapmap];0.83[MEX][hapmap];0.97[TSI][hapmap];0.84[EUR][1000 genomes]
rs17170253	0.86[ASW][hapmap];0.92[CEU][hapmap];0.94[GIH][hapmap];1.00[LWK][hapmap];0.83[MEX][hapmap];0.91[MKK][hapmap];0.97[TSI][hapmap];0.87[YRI][hapmap];0.88[AFR][1000 genomes];0.84[EUR][1000 genomes]
rs17170269	0.90[JPT][hapmap];0.88[ASN][1000 genomes]
rs17170271	0.81[JPT][hapmap]
rs1833138	0.88[AFR][1000 genomes];0.81[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs1861298	0.92[CEU][hapmap];0.86[TSI][hapmap]
rs2041417	0.81[JPT][hapmap]
rs2109526	0.87[CHB][hapmap];0.87[CHD][hapmap];0.85[GIH][hapmap];0.91[JPT][hapmap];0.83[MEX][hapmap];0.89[ASN][1000 genomes]
rs2392232	0.99[ASN][1000 genomes]
rs34305091	0.84[AFR][1000 genomes];0.84[EUR][1000 genomes]
rs34711685	0.96[AFR][1000 genomes];0.84[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs35067143	0.81[EUR][1000 genomes]
rs35557465	0.86[EUR][1000 genomes]
rs35822718	0.88[ASN][1000 genomes]
rs35850465	0.87[EUR][1000 genomes]
rs35940003	0.87[EUR][1000 genomes]
rs3735420	0.87[EUR][1000 genomes]
rs3779239	1.00[JPT][hapmap]
rs3823763	1.00[CHB][hapmap];0.98[CHD][hapmap];0.95[JPT][hapmap];0.94[ASN][1000 genomes]
rs3884597	1.00[JPT][hapmap]
rs4270862	0.84[EUR][1000 genomes]
rs4270863	0.92[CEU][hapmap];0.84[EUR][1000 genomes]
rs4604335	1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[ASN][1000 genomes]
rs4723278	0.92[CEU][hapmap];0.81[EUR][1000 genomes]
rs4723279	0.81[EUR][1000 genomes]
rs4723280	0.92[CEU][hapmap];0.86[EUR][1000 genomes]
rs4723287	0.80[AFR][1000 genomes];0.84[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs4723289	0.91[JPT][hapmap];0.88[ASN][1000 genomes]
rs60118903	0.88[AFR][1000 genomes];0.81[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs6944723	1.00[CHB][hapmap];0.98[CHD][hapmap];1.00[JPT][hapmap];0.97[ASN][1000 genomes]
rs6952877	0.92[CEU][hapmap];0.89[TSI][hapmap]
rs6953348	0.92[CEU][hapmap]
rs6965729	0.85[CEU][hapmap];0.94[GIH][hapmap];0.97[TSI][hapmap];0.87[EUR][1000 genomes]
rs6966188	0.92[CEU][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];0.84[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs6968365	0.92[CEU][hapmap];0.85[EUR][1000 genomes]
rs71532573	0.81[EUR][1000 genomes]
rs71532575	0.87[EUR][1000 genomes]
rs71532577	0.84[EUR][1000 genomes]
rs71532578	0.89[ASN][1000 genomes]
rs740888	0.91[JPT][hapmap];0.83[ASN][1000 genomes]
rs7776754	0.85[EUR][1000 genomes]
rs7777101	0.92[CEU][hapmap]
rs7783612	0.92[CEU][hapmap];0.89[TSI][hapmap]
rs7798938	0.87[ASN][1000 genomes]
rs7810388	0.91[CEU][hapmap]
rs929524	0.92[CEU][hapmap];0.87[EUR][1000 genomes]
rs9638888	0.92[CEU][hapmap]
rs9638889	0.92[CEU][hapmap];0.89[TSI][hapmap]
rs9639675	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9784973	1.00[JPT][hapmap]

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	nsv606610	chr7:33218763-33486316	Weak transcription Enhancers Strong transcription Active TSS Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
2	nsv1016416	chr7:33241443-33559477	Enhancers Weak transcription ZNF genes & repeats Strong transcription Flanking Active TSS Active TSS Bivalent Enhancer Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
3	nsv916660	chr7:33272493-33506384	Weak transcription Enhancers Strong transcription ZNF genes & repeats Flanking Active TSS Active TSS Genic enhancers Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
4	nsv830944	chr7:33389892-33549882	Weak transcription Strong transcription ZNF genes & repeats Enhancers Active TSS Flanking Active TSS Genic enhancers Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs961679	BBS9	cis	lymphoblastoid	seeQTL
rs961679	BBS9	cis	parietal	SCAN

Chromatin state (count:23 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:33454800-33476800	Weak transcription	Aorta	Aorta
2	chr7:33455200-33462600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
3	chr7:33456800-33458600	Enhancers	NHDF-Ad	bronchial
4	chr7:33457200-33458600	Enhancers	ES-WA7 Cell Line	embryonic stem cell
5	chr7:33457200-33458800	Enhancers	HSMM	muscle
6	chr7:33457400-33458600	Enhancers	ES-I3 Cell Line	embryonic stem cell
7	chr7:33457400-33458800	Enhancers	HUES48 Cell Line	embryonic stem cell
8	chr7:33457600-33458600	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
9	chr7:33457600-33458800	Enhancers	iPS-15b Cell Line	embryonic stem cell
10	chr7:33457600-33458800	Enhancers	NH-A	brain
11	chr7:33457600-33459200	Enhancers	HUES64 Cell Line	embryonic stem cell
12	chr7:33458000-33458800	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
13	chr7:33458200-33458600	Flanking Active TSS	iPS-20b Cell Line	embryonic stem cell
14	chr7:33458200-33458600	Enhancers	Osteobl	bone
15	chr7:33458200-33458800	Enhancers	HUES6 Cell Line	embryonic stem cell
16	chr7:33458200-33458800	Enhancers	iPS-18 Cell Line	embryonic stem cell
17	chr7:33458200-33458800	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
18	chr7:33458200-33461200	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
19	chr7:33458200-33462600	Weak transcription	H1 Cell Line	embryonic stem cell
20	chr7:33458200-33466400	Weak transcription	Esophagus	oesophagus
21	chr7:33458400-33462600	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
22	chr7:33458400-33465000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
23	chr7:33458400-33465000	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin

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