Variant report

Variant	rs41960
Chromosome Location	chr7:117974788-117974789
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 128 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:119)

rs_ID	r²[population]
rs10085904	0.91[CEU][hapmap];0.85[CHB][hapmap];0.89[GIH][hapmap];0.85[JPT][hapmap];0.91[TSI][hapmap]
rs10226152	0.84[EUR][1000 genomes]
rs10227326	0.84[EUR][1000 genomes]
rs10229589	0.84[EUR][1000 genomes]
rs10252627	0.91[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs10267938	0.86[EUR][1000 genomes]
rs10487390	0.84[EUR][1000 genomes]
rs10487393	1.00[YRI][hapmap]
rs1054032	1.00[CEU][hapmap];1.00[CHB][hapmap];0.93[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.93[TSI][hapmap];0.84[EUR][1000 genomes]
rs1061731	1.00[CEU][hapmap];1.00[CHB][hapmap];0.93[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.93[TSI][hapmap];0.84[EUR][1000 genomes]
rs1117254	0.81[EUR][1000 genomes]
rs11486992	1.00[CEU][hapmap];0.93[CHD][hapmap];1.00[GIH][hapmap];0.93[TSI][hapmap];0.84[EUR][1000 genomes]
rs11543742	0.83[EUR][1000 genomes]
rs11761947	0.92[EUR][1000 genomes]
rs11768889	0.93[EUR][1000 genomes]
rs11770353	0.81[EUR][1000 genomes]
rs11979012	1.00[CEU][hapmap];0.95[CHB][hapmap];0.93[CHD][hapmap];1.00[GIH][hapmap];0.84[JPT][hapmap];0.95[TSI][hapmap];0.83[EUR][1000 genomes]
rs12112697	0.87[CEU][hapmap]
rs12537795	0.91[CEU][hapmap];0.85[CHB][hapmap]
rs12667103	0.83[EUR][1000 genomes]
rs13224397	0.93[EUR][1000 genomes]
rs13224733	0.86[EUR][1000 genomes]
rs17584234	0.91[EUR][1000 genomes]
rs17584359	0.93[EUR][1000 genomes]
rs194577	0.93[EUR][1000 genomes]
rs194578	0.84[AFR][1000 genomes];0.93[EUR][1000 genomes]
rs194579	0.90[AFR][1000 genomes];0.93[EUR][1000 genomes]
rs2041527	0.83[CEU][hapmap]
rs2058416	0.82[EUR][1000 genomes]
rs2058417	0.86[EUR][1000 genomes]
rs20598	0.90[AFR][1000 genomes];0.93[EUR][1000 genomes]
rs2109858	1.00[YRI][hapmap]
rs2191920	0.82[EUR][1000 genomes]
rs2192233	0.84[EUR][1000 genomes]
rs2402322	0.84[EUR][1000 genomes]
rs2402359	0.83[EUR][1000 genomes]
rs2896242	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[EUR][1000 genomes]
rs34029977	0.93[EUR][1000 genomes]
rs34847140	0.92[EUR][1000 genomes]
rs35382009	0.92[EUR][1000 genomes]
rs3802012	0.83[EUR][1000 genomes]
rs4141028	0.83[EUR][1000 genomes]
rs41900	0.86[EUR][1000 genomes]
rs41901	0.86[EUR][1000 genomes]
rs41902	0.86[EUR][1000 genomes]
rs41905	0.86[EUR][1000 genomes]
rs41906	0.85[EUR][1000 genomes]
rs41909	0.86[EUR][1000 genomes]
rs41910	0.88[EUR][1000 genomes]
rs41911	0.88[EUR][1000 genomes]
rs41915	0.89[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs41916	0.89[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs41926	0.89[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs41933	0.92[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs41934	0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs41935	0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs41938	0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs41939	0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs41945	0.90[AFR][1000 genomes];0.90[EUR][1000 genomes]
rs41946	0.90[AFR][1000 genomes];0.93[EUR][1000 genomes]
rs41947	0.93[EUR][1000 genomes]
rs41948	0.93[EUR][1000 genomes]
rs41949	0.93[EUR][1000 genomes]
rs41950	0.93[EUR][1000 genomes]
rs41951	0.93[EUR][1000 genomes]
rs41952	0.93[EUR][1000 genomes]
rs41953	0.93[EUR][1000 genomes]
rs41954	0.93[EUR][1000 genomes]
rs41955	0.90[AFR][1000 genomes];0.93[EUR][1000 genomes]
rs41956	0.93[EUR][1000 genomes]
rs41957	0.93[EUR][1000 genomes]
rs41958	0.93[EUR][1000 genomes]
rs41959	0.91[EUR][1000 genomes]
rs41961	0.90[AFR][1000 genomes];0.93[EUR][1000 genomes]
rs41963	0.90[AFR][1000 genomes];0.93[EUR][1000 genomes]
rs41964	0.93[EUR][1000 genomes]
rs41966	0.90[AFR][1000 genomes];0.91[EUR][1000 genomes]
rs41967	0.93[EUR][1000 genomes]
rs41968	0.90[AFR][1000 genomes];0.92[EUR][1000 genomes]
rs41969	0.90[AFR][1000 genomes];0.93[EUR][1000 genomes]
rs41970	0.93[EUR][1000 genomes]
rs41977	0.90[AFR][1000 genomes];0.93[EUR][1000 genomes]
rs41978	0.90[EUR][1000 genomes]
rs41979	0.93[EUR][1000 genomes]
rs41980	0.93[EUR][1000 genomes]
rs41982	0.93[EUR][1000 genomes]
rs41983	0.92[EUR][1000 genomes]
rs41984	0.93[EUR][1000 genomes]
rs41985	0.92[EUR][1000 genomes]
rs41986	0.90[AFR][1000 genomes];0.93[EUR][1000 genomes]
rs41987	0.90[AFR][1000 genomes];0.93[EUR][1000 genomes]
rs41988	0.93[EUR][1000 genomes]
rs41990	0.93[EUR][1000 genomes]
rs41991	0.93[EUR][1000 genomes]
rs41993	0.93[EUR][1000 genomes]
rs41994	0.92[EUR][1000 genomes]
rs41995	0.92[EUR][1000 genomes]
rs41996	0.84[AFR][1000 genomes];0.92[EUR][1000 genomes]
rs41997	0.92[EUR][1000 genomes]
rs42234	0.93[EUR][1000 genomes]
rs42376	0.93[EUR][1000 genomes]
rs4727865	0.93[EUR][1000 genomes]
rs5002233	0.84[EUR][1000 genomes]
rs68189275	0.93[EUR][1000 genomes]
rs6942513	0.83[CEU][hapmap]
rs6944524	0.84[EUR][1000 genomes]
rs6946855	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[EUR][1000 genomes]
rs6948096	0.84[EUR][1000 genomes]
rs6964911	0.91[CEU][hapmap];0.85[CHB][hapmap];0.86[EUR][1000 genomes]
rs6965144	0.84[EUR][1000 genomes]
rs7796145	0.84[EUR][1000 genomes]
rs7796148	0.84[EUR][1000 genomes]
rs7797855	0.84[EUR][1000 genomes]
rs7799229	0.91[CEU][hapmap];0.80[CHB][hapmap];0.85[JPT][hapmap]
rs7805314	0.84[EUR][1000 genomes]
rs881802	0.91[CEU][hapmap];0.94[GIH][hapmap];0.85[JPT][hapmap];0.90[MKK][hapmap];0.95[TSI][hapmap];0.84[EUR][1000 genomes]
rs9655829	1.00[CEU][hapmap];1.00[CHB][hapmap];0.93[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.93[TSI][hapmap];0.84[EUR][1000 genomes]
rs979652	0.91[CEU][hapmap];1.00[CHB][hapmap];0.93[CHD][hapmap];1.00[GIH][hapmap];0.92[JPT][hapmap];0.93[TSI][hapmap];0.84[EUR][1000 genomes]
rs989899	0.82[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:9 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv869971	chr7:117420583-118274149	Weak transcription Enhancers Active TSS Flanking Active TSS Strong transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	40 gene(s)	inside rSNPs	diseases
2	nsv889090	chr7:117865940-118067460	Flanking Active TSS Enhancers Weak transcription Bivalent Enhancer Active TSS ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
3	nsv1029103	chr7:117917362-118035987	Flanking Active TSS Weak transcription Enhancers Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS	Chromatin interactive region	n/a	inside rSNPs	diseases
4	esv2764014	chr7:117917374-118035999	Bivalent Enhancer Flanking Active TSS Weak transcription Enhancers ZNF genes & repeats Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS	Chromatin interactive region	n/a	inside rSNPs	diseases
5	nsv608262	chr7:117926753-118036133	Enhancers Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Weak transcription ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS	Chromatin interactive region	n/a	inside rSNPs	diseases
6	nsv429805	chr7:117940049-118026049	Enhancers Bivalent Enhancer Weak transcription Flanking Active TSS Active TSS ZNF genes & repeats	Chromatin interactive region	n/a	inside rSNPs	diseases
7	esv1804964	chr7:117960973-118188573	Enhancers Weak transcription Active TSS Flanking Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
8	esv1803022	chr7:117970170-117998574	Enhancers Weak transcription	Chromatin interactive region	n/a	inside rSNPs	n/a
9	nsv608263	chr7:117973445-118058927	Enhancers Weak transcription Flanking Active TSS Active TSS	Chromatin interactive region	1 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs41960	ANKRD7	cis	parietal	SCAN
rs41960	NAA38	cis	lymphoblastoid	seeQTL
rs41960	LSM8	cis	multi-tissue	Pritchard
rs41960	ANKRD7	cis	cerebellum	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:117964400-117986800	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
2	chr7:117970800-117975800	Weak transcription	Dnd41	blood

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