Variant report

Variant	rs12991189
Chromosome Location	chr2:99854284-99854285
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr2:99795164..99797878-chr2:99854234..99856098,2	K562	blood:
2	chr2:99853855..99856752-chr2:99861068..99863308,2	K562	blood:

Variant related genes	Relation type
ENSG00000185414	Chromatin interaction
ENSG00000241962	Chromatin interaction
ENSG00000158411	Chromatin interaction

Extended variants
information (count: 90 )
Associated
traits (count: 7 )

rSNPs within LD-proxies of this variant (count:66)

rs_ID	r²[population]
rs11123765	0.84[EUR][1000 genomes]
rs11123770	0.91[AFR][1000 genomes];0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1133977	0.89[EUR][1000 genomes]
rs1133978	0.89[EUR][1000 genomes]
rs11674894	0.92[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs11683107	0.90[EUR][1000 genomes]
rs11683188	0.89[EUR][1000 genomes]
rs11685759	0.84[EUR][1000 genomes]
rs11688004	0.89[EUR][1000 genomes]
rs11689265	0.85[EUR][1000 genomes]
rs11692336	0.89[EUR][1000 genomes]
rs11692669	0.84[EUR][1000 genomes]
rs11695751	0.82[EUR][1000 genomes]
rs11883676	0.80[EUR][1000 genomes]
rs11895749	0.89[EUR][1000 genomes]
rs12613624	0.89[EUR][1000 genomes]
rs12619780	0.88[EUR][1000 genomes]
rs12621007	0.85[EUR][1000 genomes]
rs12987548	0.87[EUR][1000 genomes]
rs12992930	0.80[EUR][1000 genomes]
rs12999417	0.91[EUR][1000 genomes]
rs13000731	0.92[EUR][1000 genomes]
rs13008171	0.89[EUR][1000 genomes]
rs13023501	0.88[EUR][1000 genomes]
rs13023744	0.82[EUR][1000 genomes]
rs13026928	0.81[EUR][1000 genomes]
rs13030961	0.85[EUR][1000 genomes]
rs13031919	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs13033012	0.92[EUR][1000 genomes]
rs1453563	0.89[EUR][1000 genomes]
rs17759607	0.89[EUR][1000 genomes]
rs2309581	0.80[EUR][1000 genomes]
rs2516830	0.90[EUR][1000 genomes]
rs2516833	0.90[EUR][1000 genomes]
rs2516834	0.82[EUR][1000 genomes]
rs2516835	0.92[EUR][1000 genomes]
rs2632260	0.84[EUR][1000 genomes]
rs2632277	0.84[EUR][1000 genomes]
rs2632283	0.92[EUR][1000 genomes]
rs2632284	0.82[EUR][1000 genomes]
rs2964969	0.80[EUR][1000 genomes]
rs2969379	0.84[EUR][1000 genomes]
rs34252185	0.82[EUR][1000 genomes]
rs34272114	0.89[EUR][1000 genomes]
rs36071868	0.82[EUR][1000 genomes]
rs4340581	0.81[EUR][1000 genomes]
rs4347885	0.91[EUR][1000 genomes]
rs4850897	0.90[EUR][1000 genomes]
rs4851187	0.81[EUR][1000 genomes]
rs4851188	0.88[EUR][1000 genomes]
rs6542866	0.92[EUR][1000 genomes]
rs6542868	0.93[EUR][1000 genomes]
rs6542870	0.80[EUR][1000 genomes]
rs6708878	0.93[EUR][1000 genomes]
rs6717723	0.83[EUR][1000 genomes]
rs6727749	0.93[EUR][1000 genomes]
rs6751927	0.82[EUR][1000 genomes]
rs6753063	0.80[EUR][1000 genomes]
rs6753650	0.82[EUR][1000 genomes]
rs6756650	0.80[EUR][1000 genomes]
rs6757661	0.80[EUR][1000 genomes]
rs720228	0.82[EUR][1000 genomes]
rs720229	0.88[EUR][1000 genomes]
rs7572660	0.80[EUR][1000 genomes]
rs7604557	0.82[EUR][1000 genomes]
rs7608938	0.93[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:24 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv431424	chr2:99652682-100494682	Flanking Active TSS Enhancers Strong transcription Weak transcription ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers Active TSS Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	49 gene(s)	inside rSNPs	diseases
2	nsv1013507	chr2:99729047-99861692	Weak transcription Strong transcription Enhancers Active TSS Flanking Active TSS Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	20 gene(s)	inside rSNPs	diseases
3	nsv961842	chr2:99781138-99886836	Weak transcription Strong transcription Flanking Active TSS Enhancers Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	15 gene(s)	inside rSNPs	diseases
4	nsv515702	chr2:99827733-99922967	Strong transcription Weak transcription Enhancers ZNF genes & repeats Flanking Active TSS Active TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region	10 gene(s)	inside rSNPs	diseases
5	nsv458685	chr2:99827733-99922967	Enhancers Weak transcription Strong transcription Flanking Active TSS ZNF genes & repeats Active TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region	10 gene(s)	inside rSNPs	diseases
6	nsv582519	chr2:99827733-99922967	Enhancers Weak transcription Strong transcription Flanking Active TSS Active TSS ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region	10 gene(s)	inside rSNPs	diseases
7	nsv874698	chr2:99827733-99924918	Enhancers Strong transcription Weak transcription Active TSS Flanking Active TSS Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region	10 gene(s)	inside rSNPs	diseases
8	nsv1001784	chr2:99838079-99910328	Weak transcription Strong transcription Active TSS Enhancers Flanking Active TSS ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region	6 gene(s)	inside rSNPs	diseases
9	nsv535840	chr2:99838079-99910328	Weak transcription Flanking Active TSS ZNF genes & repeats Enhancers Strong transcription Active TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region	6 gene(s)	inside rSNPs	diseases
10	nsv458696	chr2:99838203-99922967	ZNF genes & repeats Strong transcription Weak transcription Enhancers Active TSS Flanking Active TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region	10 gene(s)	inside rSNPs	diseases
11	nsv582520	chr2:99838203-99922967	Enhancers Weak transcription Strong transcription Flanking Active TSS ZNF genes & repeats Active TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region	10 gene(s)	inside rSNPs	diseases
12	nsv997436	chr2:99840131-99916886	Strong transcription Weak transcription Enhancers Flanking Active TSS ZNF genes & repeats Active TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region	6 gene(s)	inside rSNPs	diseases
13	nsv1009872	chr2:99840131-99924543	Weak transcription ZNF genes & repeats Enhancers Strong transcription Active TSS Flanking Active TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region	10 gene(s)	inside rSNPs	diseases
14	nsv1001194	chr2:99840131-99928323	Weak transcription Strong transcription Flanking Active TSS Enhancers ZNF genes & repeats Active TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region	10 gene(s)	inside rSNPs	diseases
15	esv2762746	chr2:99840143-99916898	Weak transcription Enhancers Strong transcription Flanking Active TSS Active TSS ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region	6 gene(s)	inside rSNPs	diseases
16	nsv1005118	chr2:99841951-99924543	Weak transcription Strong transcription Enhancers ZNF genes & repeats Flanking Active TSS Active TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region	10 gene(s)	inside rSNPs	diseases
17	nsv1001736	chr2:99846306-99916886	Weak transcription Strong transcription Flanking Active TSS Enhancers ZNF genes & repeats Active TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region	6 gene(s)	inside rSNPs	diseases
18	nsv1009459	chr2:99846306-99918895	Enhancers ZNF genes & repeats Weak transcription Strong transcription Flanking Active TSS Active TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region	7 gene(s)	inside rSNPs	diseases
19	nsv1002169	chr2:99846306-99924543	Weak transcription Flanking Active TSS Strong transcription Enhancers ZNF genes & repeats Active TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region	10 gene(s)	inside rSNPs	diseases
20	esv2751904	chr2:99847882-99913998	Weak transcription Strong transcription Enhancers ZNF genes & repeats Active TSS Flanking Active TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region	6 gene(s)	inside rSNPs	diseases
21	nsv1001235	chr2:99847890-99913998	Enhancers Weak transcription Strong transcription Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Active TSS	TF binding region CpG island Chromatin interactive region	6 gene(s)	inside rSNPs	diseases
22	nsv582521	chr2:99847890-99922967	Weak transcription Enhancers Strong transcription Flanking Active TSS ZNF genes & repeats Active TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region	10 gene(s)	inside rSNPs	diseases
23	nsv1007566	chr2:99847890-99924543	Enhancers Weak transcription Strong transcription Flanking Active TSS ZNF genes & repeats Active TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region	10 gene(s)	inside rSNPs	diseases
24	nsv999059	chr2:99847890-99926934	Enhancers Weak transcription Bivalent Enhancer Flanking Active TSS Strong transcription Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region	10 gene(s)	inside rSNPs	diseases

mRNA abundance (count:7)

SNP	Gene	Cis/trans	Tissue	Source
rs12991189	TSGA10	cis	lung	GTEx
rs12991189	TSGA10	cis	Skin Sun Exposed Lower leg	GTEx
rs12991189	TSGA10	cis	Thyroid	GTEx
rs12991189	LIPT1	Cis_1M	lymphoblastoid	RTeQTL
rs12991189	TSGA10	Cis_1M	lymphoblastoid	RTeQTL
rs12991189	MITD1	Cis_1M	lymphoblastoid	RTeQTL
rs12991189	TSGA10	cis	multi-tissue	Pritchard

Chromatin state (count:3 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:99818200-99854600	Weak transcription	Left Ventricle	heart
2	chr2:99840800-99874400	Weak transcription	Aorta	Aorta
3	chr2:99853600-99863200	Weak transcription	Esophagus	oesophagus

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