Variant report

Variant	rs9998009
Chromosome Location	chr4:26983753-26983754
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 31 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:27)

rs_ID	r²[population]
rs10007132	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10010180	0.96[YRI][hapmap]
rs10019691	0.97[ASN][1000 genomes]
rs10022599	0.81[CEU][hapmap];0.93[GIH][hapmap];0.81[TSI][hapmap]
rs10030655	0.85[CEU][hapmap];0.93[GIH][hapmap];0.82[TSI][hapmap]
rs1012550	1.00[CHB][hapmap];0.94[JPT][hapmap];0.96[ASN][1000 genomes]
rs10433805	1.00[ASW][hapmap];0.90[CEU][hapmap];0.93[LWK][hapmap];0.87[MEX][hapmap];0.94[MKK][hapmap];0.85[TSI][hapmap];1.00[YRI][hapmap];0.85[AFR][1000 genomes]
rs10470823	0.85[CEU][hapmap];0.93[GIH][hapmap];0.82[TSI][hapmap]
rs10939141	0.85[CEU][hapmap]
rs10939147	0.91[CHB][hapmap];0.83[CHD][hapmap];0.82[MEX][hapmap];0.92[YRI][hapmap];0.81[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs1122045	0.86[CEU][hapmap];0.92[GIH][hapmap]
rs12331378	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs13115054	0.90[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.88[ASN][1000 genomes]
rs13127603	0.85[CEU][hapmap];0.93[GIH][hapmap];0.82[TSI][hapmap]
rs13140015	0.88[AMR][1000 genomes];0.87[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs16878653	1.00[CHB][hapmap];0.97[CHD][hapmap];0.94[JPT][hapmap];0.88[TSI][hapmap];0.88[ASN][1000 genomes]
rs16878671	0.97[ASN][1000 genomes]
rs28572642	0.82[ASN][1000 genomes]
rs2871256	0.95[CHB][hapmap];0.94[JPT][hapmap];0.86[YRI][hapmap];0.82[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs4692136	0.95[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.88[AMR][1000 genomes];0.87[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6830950	0.90[CEU][hapmap];0.82[MEX][hapmap];0.84[TSI][hapmap]
rs6833149	0.96[ASN][1000 genomes]
rs6855865	0.95[CHB][hapmap];0.90[CHD][hapmap];0.94[JPT][hapmap];0.82[MEX][hapmap];0.82[TSI][hapmap];0.96[ASN][1000 genomes]
rs6856381	0.96[ASN][1000 genomes]
rs7655631	0.80[CEU][hapmap]
rs7693687	0.90[CEU][hapmap];0.82[MEX][hapmap];0.84[MKK][hapmap];0.82[TSI][hapmap]
rs7695335	0.95[CEU][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	nsv470021	chr4:26721578-27067027	Active TSS Strong transcription Enhancers Weak transcription Flanking Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	diseases
2	nsv461312	chr4:26844674-27078376	Enhancers Weak transcription Active TSS Flanking Active TSS Bivalent/Poised TSS Strong transcription ZNF genes & repeats Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
3	nsv593872	chr4:26844674-27078376	Enhancers Weak transcription ZNF genes & repeats Flanking Active TSS Strong transcription Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
4	nsv1000568	chr4:26886920-27049554	Strong transcription Weak transcription Enhancers Active TSS ZNF genes & repeats Genic enhancers Flanking Active TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region	2 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs9998009	C4orf52	cis	parietal	SCAN
rs9998009	STIM2	cis	uninvolved skin	skin_eQTL
rs9998009	STIM2	cis	normal skin	skin_eQTL
rs9998009	STIM2	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:36 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:26961800-26994000	Weak transcription	Monocytes-CD14+_RO01746	blood
2	chr4:26963600-26994200	Weak transcription	Sigmoid Colon	Sigmoid Colon
3	chr4:26966600-26986400	Weak transcription	HSMM	muscle
4	chr4:26966600-26989000	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
5	chr4:26966600-26994600	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
6	chr4:26966800-26985200	Weak transcription	Muscle Satellite Cultured Cells	--
7	chr4:26966800-26986400	Weak transcription	Primary T killer memory cells from peripheral blood	blood
8	chr4:26967600-26986400	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
9	chr4:26975800-27003200	Weak transcription	Aorta	Aorta
10	chr4:26977800-26988600	Weak transcription	Fetal Thymus	thymus
11	chr4:26978000-26987400	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
12	chr4:26978000-26994600	Weak transcription	Fetal Stomach	stomach
13	chr4:26978200-26984600	Weak transcription	Cortex derived primary cultured neurospheres	brain
14	chr4:26978400-27019200	Weak transcription	Fetal Intestine Small	intestine
15	chr4:26978800-26988600	Weak transcription	Fetal Muscle Leg	muscle
16	chr4:26979600-26988600	Weak transcription	Thymus	Thymus
17	chr4:26980400-26984200	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
18	chr4:26980400-26984400	Weak transcription	Pancreas	Pancrea
19	chr4:26980400-26988600	Weak transcription	Ovary	ovary
20	chr4:26980400-26994800	Weak transcription	Breast Myoepithelial Primary Cells	Breast
21	chr4:26980400-27019400	Weak transcription	Left Ventricle	heart
22	chr4:26980600-26984600	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
23	chr4:26980600-26984800	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
24	chr4:26980600-26984800	Weak transcription	Primary T helper cells fromperipheralblood	blood
25	chr4:26980600-26986000	Weak transcription	Psoas Muscle	Psoas
26	chr4:26980600-26986600	Weak transcription	Primary T cells fromperipheralblood	blood
27	chr4:26980600-26986600	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
28	chr4:26980800-26985800	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
29	chr4:26980800-26985800	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
30	chr4:26981200-26985800	Weak transcription	Primary T cells from cord blood	blood
31	chr4:26981200-26986600	Weak transcription	Primary B cells from peripheral blood	blood
32	chr4:26981200-26986600	Weak transcription	GM12878-XiMat	blood
33	chr4:26983000-26985200	Weak transcription	Fetal Lung	lung
34	chr4:26983400-26984400	Strong transcription	Primary B cells from cord blood	blood
35	chr4:26983400-26986600	Weak transcription	Primary hematopoietic stem cells	blood
36	chr4:26983600-26984600	Weak transcription	Primary T helper cells PMA-I stimulated	--

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