Variant report

Variant	rs6940280
Chromosome Location	chr6:128056719-128056720
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 70 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:57)

rs_ID	r²[population]
rs10872324	0.88[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.92[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.92[TSI][hapmap];0.91[AMR][1000 genomes];0.82[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs11154427	0.82[GIH][hapmap]
rs11753398	0.89[AMR][1000 genomes];0.81[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs11961168	0.88[CEU][hapmap];1.00[CHB][hapmap];0.83[CHD][hapmap];0.92[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.92[TSI][hapmap];0.97[AMR][1000 genomes];0.92[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11967147	0.88[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[AMR][1000 genomes];0.82[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs12153861	0.82[GIH][hapmap]
rs12191259	0.88[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs12193548	0.82[GIH][hapmap]
rs12194548	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12205922	0.82[GIH][hapmap]
rs12206913	0.82[GIH][hapmap]
rs12214409	0.82[CEU][hapmap];0.85[CHB][hapmap];1.00[CHD][hapmap];0.92[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.88[TSI][hapmap];0.91[AMR][1000 genomes];0.82[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs12660845	0.82[CHB][hapmap];0.81[ASN][1000 genomes]
rs12660847	0.82[CHB][hapmap]
rs12661098	0.82[CHB][hapmap];0.81[ASN][1000 genomes]
rs12661121	0.82[CHB][hapmap];0.84[ASN][1000 genomes]
rs12663768	0.82[CHB][hapmap]
rs12664881	0.82[CHB][hapmap]
rs12665235	0.88[CEU][hapmap];0.81[YRI][hapmap];0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12665648	0.81[ASN][1000 genomes]
rs13215234	0.94[AMR][1000 genomes];0.91[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs13219045	0.94[CEU][hapmap];1.00[CHB][hapmap];0.83[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.92[TSI][hapmap];0.89[AMR][1000 genomes];0.85[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1333767	1.00[CHB][hapmap];0.83[CHD][hapmap];1.00[JPT][hapmap]
rs17055025	0.82[CHB][hapmap];0.81[ASN][1000 genomes]
rs17055029	0.82[CHB][hapmap]
rs17055044	0.82[CHB][hapmap]
rs17301984	0.82[CHB][hapmap]
rs199148	0.82[ASN][1000 genomes]
rs269992	1.00[CHB][hapmap];1.00[JPT][hapmap];0.80[ASN][1000 genomes]
rs269993	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs269994	0.82[GIH][hapmap]
rs269997	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs269998	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs270009	1.00[CHB][hapmap];1.00[JPT][hapmap];0.80[ASN][1000 genomes]
rs270010	1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[ASN][1000 genomes]
rs270012	0.85[CHB][hapmap];0.83[CHD][hapmap];1.00[JPT][hapmap]
rs58586522	0.81[ASN][1000 genomes]
rs59993660	0.84[ASN][1000 genomes]
rs623345	0.85[CHB][hapmap];0.83[CHD][hapmap];1.00[JPT][hapmap]
rs669722	0.80[ASN][1000 genomes]
rs68018843	0.91[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs6902009	0.91[AMR][1000 genomes];0.82[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs6902933	0.82[CHB][hapmap];0.81[ASN][1000 genomes]
rs6905527	0.88[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6934865	1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[ASN][1000 genomes]
rs6935078	0.82[CHB][hapmap]
rs6935256	0.88[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs6939770	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7744896	0.88[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.92[TSI][hapmap];0.97[AMR][1000 genomes];0.92[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7768836	0.88[CEU][hapmap];1.00[CHB][hapmap];0.90[JPT][hapmap]
rs7772357	0.93[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs7774647	1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[ASN][1000 genomes]
rs7776202	0.85[CHB][hapmap]
rs920992	0.82[GIH][hapmap]
rs9482835	1.00[CHB][hapmap];0.83[CHD][hapmap];1.00[JPT][hapmap];0.92[ASN][1000 genomes]
rs9491858	1.00[CHB][hapmap];0.83[CHD][hapmap];1.00[JPT][hapmap];0.92[ASN][1000 genomes]
rs9491859	0.85[CHB][hapmap];0.83[CHD][hapmap];1.00[JPT][hapmap];0.90[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:13 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv886638	chr6:127954614-128087172	Enhancers Strong transcription Weak transcription ZNF genes & repeats Active TSS Flanking Active TSS Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
2	nsv886639	chr6:127954614-128109244	Strong transcription Weak transcription Enhancers ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Active TSS Flanking Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
3	nsv886640	chr6:127961263-128096587	Strong transcription Weak transcription Enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Flanking Active TSS Active TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
4	nsv886641	chr6:127971136-128085283	Weak transcription Strong transcription Enhancers ZNF genes & repeats Genic enhancers Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
5	nsv886642	chr6:127971136-128096587	Weak transcription Enhancers ZNF genes & repeats Strong transcription Genic enhancers Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
6	nsv886643	chr6:127971136-128109244	Strong transcription Enhancers Weak transcription ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
7	nsv886644	chr6:127976408-128109244	Weak transcription Genic enhancers Enhancers Strong transcription ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
8	nsv886645	chr6:127977160-128085283	Strong transcription Enhancers Weak transcription Genic enhancers ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region	3 gene(s)	inside rSNPs	diseases
9	nsv886646	chr6:127977160-128087172	Weak transcription Strong transcription Enhancers Genic enhancers ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region	3 gene(s)	inside rSNPs	diseases
10	nsv886647	chr6:127977160-128109244	Enhancers Weak transcription Strong transcription Genic enhancers ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	3 gene(s)	inside rSNPs	diseases
11	nsv886648	chr6:127983009-128109244	Enhancers Weak transcription Genic enhancers Strong transcription ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
12	nsv830799	chr6:128033100-128194511	Genic enhancers Enhancers Weak transcription Strong transcription Flanking Active TSS Transcr. at gene 5' and 3' Active TSS ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS	Chromatin interactive region	n/a	inside rSNPs	diseases
13	nsv518548	chr6:128046713-128062827	Weak transcription Enhancers Bivalent Enhancer Strong transcription Genic enhancers	Chromatin interactive region	n/a	inside rSNPs	n/a

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs6940280	THEMIS	cis	parietal	SCAN

Chromatin state (count:16 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:128039800-128069200	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
2	chr6:128045600-128069200	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
3	chr6:128047200-128082400	Weak transcription	Primary T cells fromperipheralblood	blood
4	chr6:128047600-128060800	Weak transcription	Thymus	Thymus
5	chr6:128052600-128058200	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
6	chr6:128053800-128057800	Strong transcription	Fetal Thymus	thymus
7	chr6:128054200-128058200	Weak transcription	Stomach Mucosa	stomach
8	chr6:128054400-128058600	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
9	chr6:128055200-128069000	Weak transcription	Primary T killer memory cells from peripheral blood	blood
10	chr6:128055600-128057800	Weak transcription	Primary T helper naive cells from peripheral blood	blood
11	chr6:128055600-128058200	Weak transcription	Primary T cells from cord blood	blood
12	chr6:128055600-128058400	Weak transcription	Primary T helper cells fromperipheralblood	blood
13	chr6:128055800-128058400	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
14	chr6:128056200-128056800	Strong transcription	Primary T helper naive cells fromperipheralblood	blood
15	chr6:128056400-128060400	Enhancers	Primary T helper cells PMA-I stimulated	--
16	chr6:128056600-128058400	Weak transcription	Fetal Brain Male	brain

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