Variant report

Variant	rs4306956
Chromosome Location	chr4:106942261-106942262
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-TBCK-1	chr4:106940966-106943635	XLOC_004040

Extended variants
information (count: 116 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:90)

rs_ID	r²[population]
rs10000428	0.95[CEU][hapmap];0.88[EUR][1000 genomes]
rs10003024	0.94[CEU][hapmap];0.88[EUR][1000 genomes]
rs10004611	0.95[CEU][hapmap];0.88[EUR][1000 genomes]
rs10008428	0.95[CEU][hapmap];0.88[EUR][1000 genomes]
rs10008773	0.95[EUR][1000 genomes]
rs10017969	0.87[EUR][1000 genomes]
rs10018910	0.84[CEU][hapmap]
rs10025052	0.82[EUR][1000 genomes]
rs10027207	0.88[EUR][1000 genomes]
rs10030019	0.90[CEU][hapmap];0.82[EUR][1000 genomes]
rs10049933	0.88[EUR][1000 genomes]
rs11097912	0.90[CEU][hapmap];0.82[EUR][1000 genomes]
rs11725254	1.00[ASN][1000 genomes]
rs11732251	1.00[CEU][hapmap];0.93[EUR][1000 genomes]
rs11732791	0.82[EUR][1000 genomes]
rs11931386	0.82[EUR][1000 genomes]
rs11932523	0.95[CEU][hapmap];0.91[EUR][1000 genomes]
rs11942153	0.83[EUR][1000 genomes]
rs12505689	0.81[ASN][1000 genomes]
rs12507867	0.81[ASN][1000 genomes]
rs12509366	0.81[EUR][1000 genomes]
rs12509640	0.89[CEU][hapmap];0.81[EUR][1000 genomes]
rs12510966	0.89[CEU][hapmap];0.83[EUR][1000 genomes]
rs12512683	0.82[EUR][1000 genomes]
rs12513345	0.90[CEU][hapmap]
rs12639678	0.81[ASN][1000 genomes]
rs12642691	0.95[CEU][hapmap];0.84[EUR][1000 genomes]
rs12642900	0.80[EUR][1000 genomes]
rs13101612	0.95[CEU][hapmap];0.84[EUR][1000 genomes]
rs13113845	0.82[EUR][1000 genomes]
rs13114479	0.82[EUR][1000 genomes]
rs13121614	0.82[EUR][1000 genomes]
rs13138528	0.82[EUR][1000 genomes]
rs17272618	0.84[CEU][hapmap]
rs28391259	0.82[EUR][1000 genomes]
rs28394440	0.94[EUR][1000 genomes]
rs28467469	0.90[EUR][1000 genomes]
rs28784652	0.90[EUR][1000 genomes]
rs28822186	0.82[EUR][1000 genomes]
rs28845843	0.93[EUR][1000 genomes]
rs28897193	0.82[EUR][1000 genomes]
rs4307042	0.87[EUR][1000 genomes]
rs4314353	0.90[EUR][1000 genomes]
rs4355394	0.94[EUR][1000 genomes]
rs4364267	1.00[CEU][hapmap];0.94[EUR][1000 genomes]
rs4374692	0.82[EUR][1000 genomes]
rs4382109	0.95[CEU][hapmap];0.87[EUR][1000 genomes]
rs4470632	0.94[EUR][1000 genomes]
rs4508971	0.95[CEU][hapmap];0.90[EUR][1000 genomes]
rs4577583	1.00[CEU][hapmap];0.94[EUR][1000 genomes]
rs4600995	0.95[CEU][hapmap];0.87[EUR][1000 genomes]
rs55633564	0.83[EUR][1000 genomes]
rs60538413	0.83[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs62321365	0.82[EUR][1000 genomes]
rs6533237	0.92[EUR][1000 genomes]
rs6533242	0.81[EUR][1000 genomes]
rs6819081	0.95[CEU][hapmap];0.84[EUR][1000 genomes]
rs6823347	0.82[EUR][1000 genomes]
rs6824682	0.83[EUR][1000 genomes]
rs6828362	0.82[EUR][1000 genomes]
rs6835216	0.81[CEU][hapmap]
rs6836198	0.95[CEU][hapmap];0.87[EUR][1000 genomes]
rs6842919	0.83[AMR][1000 genomes];0.95[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs6843331	0.83[AMR][1000 genomes];0.96[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs6844105	0.86[CEU][hapmap]
rs6846579	0.89[CEU][hapmap];0.81[EUR][1000 genomes]
rs6852388	0.92[EUR][1000 genomes]
rs6853554	0.89[CEU][hapmap]
rs72677306	0.82[EUR][1000 genomes]
rs7438546	1.00[CEU][hapmap];0.93[EUR][1000 genomes]
rs7657962	0.89[CEU][hapmap];0.82[CHB][hapmap];0.83[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs7657975	0.81[CEU][hapmap]
rs7662592	0.90[CEU][hapmap];0.81[EUR][1000 genomes]
rs7663321	0.95[CEU][hapmap]
rs7664188	0.81[CEU][hapmap]
rs7668276	0.82[EUR][1000 genomes]
rs7673101	0.95[CEU][hapmap];0.88[EUR][1000 genomes]
rs7675728	0.81[ASN][1000 genomes]
rs7677248	0.82[EUR][1000 genomes]
rs7678847	0.89[CEU][hapmap];0.82[EUR][1000 genomes]
rs7682646	0.95[CEU][hapmap];0.85[EUR][1000 genomes]
rs7687657	0.93[EUR][1000 genomes]
rs7689298	0.91[EUR][1000 genomes]
rs7692069	0.83[EUR][1000 genomes]
rs7692652	0.95[CEU][hapmap]
rs7693333	0.95[CEU][hapmap];0.87[EUR][1000 genomes]
rs7693448	0.82[EUR][1000 genomes]
rs9685464	0.82[EUR][1000 genomes]
rs9991091	0.82[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs9996093	0.95[CEU][hapmap];0.88[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:26 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1014993	chr4:106796019-106980727	Enhancers Flanking Bivalent TSS/Enh Weak transcription Bivalent/Poised TSS Bivalent Enhancer Strong transcription Active TSS Genic enhancers Flanking Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
2	nsv522792	chr4:106895964-106982793	Weak transcription Enhancers Strong transcription ZNF genes & repeats Flanking Active TSS Active TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
3	esv2422027	chr4:106936604-106946435	Enhancers Weak transcription ZNF genes & repeats Flanking Active TSS Bivalent Enhancer	TF binding region Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
4	esv1842775	chr4:106938490-106942261	Enhancers Flanking Active TSS Weak transcription Bivalent Enhancer	Chromatin interactive region lncRNA	n/a	inside rSNPs	diseases
5	esv1850962	chr4:106938490-106942261	Flanking Active TSS Enhancers Bivalent Enhancer Weak transcription	Chromatin interactive region lncRNA	n/a	inside rSNPs	diseases
6	esv3465900	chr4:106938503-106945201	Enhancers Bivalent Enhancer Weak transcription Flanking Active TSS	TF binding region Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
7	esv3512204	chr4:106939353-106944351	Enhancers Bivalent Enhancer Flanking Active TSS Weak transcription	TF binding region Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
8	esv3512202	chr4:106939700-106944356	Enhancers Flanking Active TSS Bivalent Enhancer Weak transcription	TF binding region Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
9	esv3512200	chr4:106939753-106944301	Enhancers Flanking Active TSS Weak transcription Bivalent Enhancer	TF binding region Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
10	esv18236	chr4:106940112-106943263	Weak transcription Enhancers Flanking Active TSS Bivalent Enhancer	Chromatin interactive region lncRNA	n/a	inside rSNPs	diseases
11	nsv819910	chr4:106940232-106945512	Enhancers Flanking Active TSS Weak transcription Bivalent Enhancer ZNF genes & repeats	TF binding region Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
12	esv3465898	chr4:106940339-106943358	Enhancers Flanking Active TSS Weak transcription Bivalent Enhancer	Chromatin interactive region lncRNA	n/a	inside rSNPs	diseases
13	esv1843313	chr4:106940351-106942261	Bivalent Enhancer Enhancers Weak transcription Flanking Active TSS	Chromatin interactive region lncRNA	n/a	inside rSNPs	diseases
14	esv3512199	chr4:106940360-106943377	Bivalent Enhancer Weak transcription Enhancers Flanking Active TSS	Chromatin interactive region lncRNA	n/a	inside rSNPs	diseases
15	esv3512203	chr4:106940364-106943371	Enhancers Weak transcription Bivalent Enhancer Flanking Active TSS	Chromatin interactive region lncRNA	n/a	inside rSNPs	diseases
16	esv3512198	chr4:106940382-106943313	Enhancers Weak transcription Flanking Active TSS Bivalent Enhancer	Chromatin interactive region lncRNA	n/a	inside rSNPs	diseases
17	esv3465895	chr4:106940391-106943324	Flanking Active TSS Enhancers Bivalent Enhancer Weak transcription	Chromatin interactive region lncRNA	n/a	inside rSNPs	diseases
18	esv3465899	chr4:106940404-106943294	Enhancers Flanking Active TSS Bivalent Enhancer Weak transcription	Chromatin interactive region lncRNA	n/a	inside rSNPs	diseases
19	esv3512201	chr4:106940410-106943316	Enhancers Flanking Active TSS Weak transcription Bivalent Enhancer	Chromatin interactive region lncRNA	n/a	inside rSNPs	diseases
20	esv3512206	chr4:106940412-106943318	Enhancers Bivalent Enhancer Flanking Active TSS Weak transcription	Chromatin interactive region lncRNA	n/a	inside rSNPs	diseases
21	nsv822679	chr4:106940436-106942896	Enhancers Bivalent Enhancer Weak transcription Flanking Active TSS	Chromatin interactive region lncRNA	n/a	inside rSNPs	diseases
22	esv3465896	chr4:106940454-106943270	Weak transcription Enhancers Bivalent Enhancer Flanking Active TSS	Chromatin interactive region lncRNA	n/a	inside rSNPs	diseases
23	esv3512205	chr4:106940464-106943271	Enhancers Weak transcription Flanking Active TSS Bivalent Enhancer	Chromatin interactive region lncRNA	n/a	inside rSNPs	diseases
24	esv3465901	chr4:106940468-106943269	Flanking Active TSS Enhancers Weak transcription Bivalent Enhancer	Chromatin interactive region lncRNA	n/a	inside rSNPs	diseases
25	esv3512207	chr4:106940468-106943269	Bivalent Enhancer Enhancers Weak transcription Flanking Active TSS	Chromatin interactive region lncRNA	n/a	inside rSNPs	diseases
26	esv1849804	chr4:106940744-106942261	Enhancers Weak transcription Bivalent Enhancer Flanking Active TSS	Chromatin interactive region lncRNA	n/a	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs4306956	SCYE1	Cis_1M	lymphoblastoid	RTeQTL
rs4306956	MGC16169	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:9 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:106935000-106948400	Weak transcription	Aorta	Aorta
2	chr4:106939800-106942400	Enhancers	NHDF-Ad	bronchial
3	chr4:106940400-106943000	Enhancers	HSMMtube	muscle
4	chr4:106941000-106943200	Enhancers	Fetal Heart	heart
5	chr4:106941000-106944000	Enhancers	Primary hematopoietic stem cells short term culture	blood
6	chr4:106941200-106944400	Enhancers	Primary hematopoietic stem cells	blood
7	chr4:106941400-106943800	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
8	chr4:106942000-106942400	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
9	chr4:106942000-106942600	Weak transcription	HSMM	muscle

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