Variant report

Variant	rs270043
Chromosome Location	chr6:128186131-128186132
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 27 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:24)

rs_ID	r²[population]
rs187938	0.86[AFR][1000 genomes];0.82[EUR][1000 genomes]
rs270004	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[AMR][1000 genomes];0.92[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs270006	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[AMR][1000 genomes];0.92[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs270024	0.88[CEU][hapmap];0.82[CHB][hapmap];0.95[GIH][hapmap];0.95[TSI][hapmap];0.88[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs270025	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.84[AFR][1000 genomes];0.94[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs270027	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs270028	1.00[CEU][hapmap];1.00[CHB][hapmap];0.96[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap];0.95[TSI][hapmap];0.86[AMR][1000 genomes];0.93[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs270029	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs270030	1.00[CEU][hapmap];1.00[CHB][hapmap];0.96[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];0.82[YRI][hapmap];0.80[AFR][1000 genomes];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs270031	0.87[AMR][1000 genomes];0.93[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs270032	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs270033	0.85[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.96[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.99[MKK][hapmap];0.95[TSI][hapmap];0.93[YRI][hapmap];0.85[AFR][1000 genomes];0.96[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs270035	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[AMR][1000 genomes];0.93[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs270036	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[YRI][hapmap];0.91[AFR][1000 genomes];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs270038	0.81[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs270042	0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs270046	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[YRI][hapmap];0.94[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs270047	0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7738306	0.96[CEU][hapmap];0.93[CHB][hapmap];1.00[JPT][hapmap];0.80[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7767438	0.81[MKK][hapmap]
rs875336	0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9398854	0.86[YRI][hapmap]
rs9482842	0.96[CEU][hapmap];0.93[CHB][hapmap];0.87[CHD][hapmap];1.00[JPT][hapmap];0.87[MEX][hapmap];0.93[MKK][hapmap];0.85[TSI][hapmap];0.80[AMR][1000 genomes];0.82[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs9491876	0.96[CEU][hapmap];0.93[CHB][hapmap];0.87[CHD][hapmap];0.80[GIH][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap];0.85[TSI][hapmap];0.83[EUR][1000 genomes];0.92[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	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
2	esv1849854	chr6:128143774-128287313	Weak transcription Active TSS Enhancers Strong transcription ZNF genes & repeats Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region	2 gene(s)	inside rSNPs	diseases
3	nsv1024516	chr6:128184182-128298278	Enhancers Weak transcription Active TSS Flanking Active TSS Strong transcription ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region miRNA target site	2 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs270043	THEMIS	cis	parietal	SCAN

Chromatin state (count:22 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:128178800-128190800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
2	chr6:128179200-128190400	Weak transcription	Brain Cingulate Gyrus	brain
3	chr6:128180400-128189600	Weak transcription	Brain Inferior Temporal Lobe	brain
4	chr6:128180400-128190600	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
5	chr6:128180600-128189600	Weak transcription	Brain Substantia Nigra	brain
6	chr6:128183800-128187000	Enhancers	Primary T killer naive cells fromperipheralblood	blood
7	chr6:128184200-128186200	Strong transcription	Primary T helper 17 cells PMA-I stimulated	--
8	chr6:128184400-128186400	Genic enhancers	Primary T cells from cord blood	blood
9	chr6:128184600-128186200	Genic enhancers	Primary T helper naive cells from peripheral blood	blood
10	chr6:128184600-128186800	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
11	chr6:128185400-128187400	Enhancers	Primary T helper naive cells fromperipheralblood	blood
12	chr6:128185600-128186200	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
13	chr6:128185600-128186200	Genic enhancers	Fetal Thymus	thymus
14	chr6:128185600-128186400	Genic enhancers	Thymus	Thymus
15	chr6:128185600-128186600	Enhancers	Fetal Intestine Large	intestine
16	chr6:128185600-128187200	Genic enhancers	Primary T helper cells PMA-I stimulated	--
17	chr6:128185800-128186600	Enhancers	Primary T killer memory cells from peripheral blood	blood
18	chr6:128185800-128186600	Enhancers	HepG2	liver
19	chr6:128186000-128186200	Genic enhancers	Primary T helper cells fromperipheralblood	blood
20	chr6:128186000-128186400	Enhancers	Rectal Mucosa Donor 31	rectum
21	chr6:128186000-128186400	Enhancers	Sigmoid Colon	Sigmoid Colon
22	chr6:128186000-128186600	Genic enhancers	Primary T cells fromperipheralblood	blood

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