Variant report

Variant	rs6842919
Chromosome Location	chr4:106958170-106958171
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 218 )
Associated
traits (count: 5 )

rSNPs within LD-proxies of this variant (count:216)

rs_ID	r²[population]
rs10000428	0.96[CEU][hapmap];0.87[EUR][1000 genomes]
rs10002288	0.99[ASN][1000 genomes]
rs10003024	0.95[CEU][hapmap];0.85[MKK][hapmap];0.97[TSI][hapmap];0.87[EUR][1000 genomes]
rs10004611	0.95[CEU][hapmap];0.87[EUR][1000 genomes]
rs10008428	0.96[CEU][hapmap];0.87[EUR][1000 genomes]
rs10008773	0.93[AFR][1000 genomes];0.96[EUR][1000 genomes]
rs10017969	0.87[EUR][1000 genomes]
rs10025052	0.96[AFR][1000 genomes];0.85[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10027207	0.87[EUR][1000 genomes]
rs10030019	0.91[CEU][hapmap];0.92[CHB][hapmap];0.94[JPT][hapmap];0.85[YRI][hapmap];0.88[AFR][1000 genomes];0.85[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10049933	0.87[EUR][1000 genomes]
rs10084928	0.92[CHB][hapmap];1.00[CHD][hapmap];0.94[JPT][hapmap];0.97[ASN][1000 genomes]
rs10516532	0.92[CHB][hapmap];1.00[CHD][hapmap];0.94[JPT][hapmap];0.97[ASN][1000 genomes]
rs10516533	0.93[ASN][1000 genomes]
rs11097912	0.91[CEU][hapmap];0.92[CHB][hapmap];0.94[JPT][hapmap];0.85[YRI][hapmap];0.88[AFR][1000 genomes];0.85[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11097914	0.97[ASN][1000 genomes]
rs11097916	0.97[ASN][1000 genomes]
rs11097917	0.90[CHB][hapmap];0.94[JPT][hapmap];0.97[ASN][1000 genomes]
rs11097919	0.92[CHB][hapmap];1.00[CHD][hapmap];0.94[JPT][hapmap];0.97[ASN][1000 genomes]
rs11097924	0.93[ASN][1000 genomes]
rs11097925	0.93[ASN][1000 genomes]
rs11725254	0.80[ASN][1000 genomes]
rs11732251	1.00[CEU][hapmap];0.95[EUR][1000 genomes]
rs11732791	0.91[CEU][hapmap];0.98[TSI][hapmap];0.81[EUR][1000 genomes]
rs11931386	0.81[EUR][1000 genomes]
rs11932523	0.96[CEU][hapmap];0.85[MKK][hapmap];1.00[TSI][hapmap];0.93[EUR][1000 genomes]
rs11942153	0.91[AFR][1000 genomes];0.85[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12499891	0.97[ASN][1000 genomes]
rs12502764	0.93[ASN][1000 genomes]
rs12503753	0.95[ASN][1000 genomes]
rs12504704	0.92[CHB][hapmap];0.94[JPT][hapmap];0.97[ASN][1000 genomes]
rs12504721	0.93[ASN][1000 genomes]
rs12505689	0.99[ASN][1000 genomes]
rs12506062	0.92[CHB][hapmap];1.00[CHD][hapmap];0.94[JPT][hapmap];0.97[ASN][1000 genomes]
rs12506658	0.97[ASN][1000 genomes]
rs12507429	0.92[CHB][hapmap];1.00[CHD][hapmap];0.94[JPT][hapmap];0.96[ASN][1000 genomes]
rs12507867	0.99[ASN][1000 genomes]
rs12507874	0.87[ASN][1000 genomes]
rs12508432	0.93[ASN][1000 genomes]
rs12508552	0.97[ASN][1000 genomes]
rs12509366	0.86[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12509640	0.91[CEU][hapmap];0.92[CHB][hapmap];1.00[CHD][hapmap];0.95[GIH][hapmap];0.88[JPT][hapmap];0.86[TSI][hapmap];0.84[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs12509865	0.92[CHB][hapmap];0.94[JPT][hapmap];0.97[ASN][1000 genomes]
rs12510058	0.93[ASN][1000 genomes]
rs12510966	0.91[CEU][hapmap];0.92[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.94[JPT][hapmap];0.86[TSI][hapmap];0.85[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12511305	0.92[CHB][hapmap];1.00[CHD][hapmap];0.94[JPT][hapmap];0.94[ASN][1000 genomes]
rs12512683	0.88[AFR][1000 genomes];0.85[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12512877	0.92[CHB][hapmap];0.94[JPT][hapmap];0.91[ASN][1000 genomes]
rs12512903	0.92[CHB][hapmap];1.00[CHD][hapmap];0.94[JPT][hapmap];0.91[ASN][1000 genomes]
rs12512966	0.92[CHB][hapmap];1.00[CHD][hapmap];0.94[JPT][hapmap];0.97[ASN][1000 genomes]
rs12513317	0.92[CHB][hapmap];0.94[JPT][hapmap];0.97[ASN][1000 genomes]
rs12513345	0.83[CEU][hapmap]
rs12639678	0.99[ASN][1000 genomes]
rs12639869	0.93[ASN][1000 genomes]
rs12641015	0.93[ASN][1000 genomes]
rs12641037	0.92[CHB][hapmap];0.94[JPT][hapmap];0.91[ASN][1000 genomes]
rs12642059	0.93[ASN][1000 genomes]
rs12642227	0.97[ASN][1000 genomes]
rs12642691	0.96[CEU][hapmap];0.85[MKK][hapmap];0.98[TSI][hapmap];0.83[EUR][1000 genomes]
rs12642900	0.92[CHB][hapmap];0.94[JPT][hapmap];0.85[YRI][hapmap];0.88[AFR][1000 genomes];0.85[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12643397	0.97[ASN][1000 genomes]
rs12644259	0.92[CHB][hapmap];1.00[CHD][hapmap];0.94[JPT][hapmap];0.93[ASN][1000 genomes]
rs12645271	0.90[CHB][hapmap];0.94[JPT][hapmap];0.97[ASN][1000 genomes]
rs12645698	0.89[ASN][1000 genomes]
rs12645743	0.87[ASN][1000 genomes]
rs12646263	0.95[ASN][1000 genomes]
rs12646485	0.97[ASN][1000 genomes]
rs12647078	0.97[ASN][1000 genomes]
rs12649709	0.93[ASN][1000 genomes]
rs12651360	0.93[ASN][1000 genomes]
rs13101612	0.96[CEU][hapmap];0.85[MKK][hapmap];0.98[TSI][hapmap];0.83[EUR][1000 genomes]
rs13113845	0.81[EUR][1000 genomes]
rs13114479	0.81[EUR][1000 genomes]
rs13121614	0.80[EUR][1000 genomes]
rs13138528	0.96[CEU][hapmap];0.84[MKK][hapmap];0.98[TSI][hapmap];0.81[EUR][1000 genomes]
rs17036613	0.82[CHB][hapmap];1.00[CHD][hapmap];0.94[JPT][hapmap];0.93[ASN][1000 genomes]
rs17259572	0.99[ASN][1000 genomes]
rs17273093	0.92[CHB][hapmap];0.94[JPT][hapmap];0.97[ASN][1000 genomes]
rs17273445	0.97[ASN][1000 genomes]
rs17274017	0.93[ASN][1000 genomes]
rs17333287	0.92[CHB][hapmap];0.94[JPT][hapmap];0.93[ASN][1000 genomes]
rs2290607	0.92[CHB][hapmap];0.94[JPT][hapmap];0.97[ASN][1000 genomes]
rs28391259	0.84[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs28394440	0.95[EUR][1000 genomes]
rs28467469	0.91[EUR][1000 genomes]
rs28507027	0.97[ASN][1000 genomes]
rs28765420	0.95[ASN][1000 genomes]
rs28784652	0.91[EUR][1000 genomes]
rs28787305	0.97[ASN][1000 genomes]
rs28814088	0.91[ASN][1000 genomes]
rs28822186	0.88[AFR][1000 genomes];0.87[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs28845843	0.95[EUR][1000 genomes]
rs28866820	0.97[ASN][1000 genomes]
rs28868894	0.97[ASN][1000 genomes]
rs28875879	0.97[ASN][1000 genomes]
rs28897193	0.87[AFR][1000 genomes];0.84[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs34193646	0.93[ASN][1000 genomes]
rs34899289	0.93[ASN][1000 genomes]
rs34961213	0.93[ASN][1000 genomes]
rs35518913	0.97[ASN][1000 genomes]
rs3775090	0.93[ASN][1000 genomes]
rs4306956	0.83[AMR][1000 genomes];0.95[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs4307042	0.87[EUR][1000 genomes]
rs4314353	0.91[EUR][1000 genomes]
rs4323181	0.97[ASN][1000 genomes]
rs4337798	0.97[ASN][1000 genomes]
rs4337799	0.97[ASN][1000 genomes]
rs4339284	0.97[ASN][1000 genomes]
rs4355394	0.93[AFR][1000 genomes];0.94[EUR][1000 genomes]
rs4364267	1.00[CEU][hapmap];0.89[YRI][hapmap];0.93[AFR][1000 genomes];0.95[EUR][1000 genomes]
rs4374692	0.91[CEU][hapmap];0.84[MKK][hapmap];0.98[TSI][hapmap];0.81[EUR][1000 genomes]
rs4382109	0.96[CEU][hapmap];0.84[MKK][hapmap];0.98[TSI][hapmap];0.87[EUR][1000 genomes]
rs4422480	0.97[ASN][1000 genomes]
rs4429790	0.92[CHB][hapmap];1.00[CHD][hapmap];0.94[JPT][hapmap];0.97[ASN][1000 genomes]
rs4458525	0.92[CHB][hapmap];0.94[JPT][hapmap];0.97[ASN][1000 genomes]
rs4466113	0.97[ASN][1000 genomes]
rs4470632	0.91[AFR][1000 genomes];0.94[EUR][1000 genomes]
rs4508971	0.96[CEU][hapmap];0.85[MKK][hapmap];1.00[TSI][hapmap];0.91[EUR][1000 genomes]
rs4521418	0.96[ASN][1000 genomes]
rs4569824	0.81[EUR][1000 genomes]
rs4577583	1.00[CEU][hapmap];0.95[EUR][1000 genomes]
rs4600995	0.96[CEU][hapmap];0.84[MKK][hapmap];0.98[TSI][hapmap];0.87[EUR][1000 genomes]
rs55633564	0.85[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs55634475	0.97[ASN][1000 genomes]
rs55833794	0.97[ASN][1000 genomes]
rs56009469	0.93[ASN][1000 genomes]
rs56135499	0.97[ASN][1000 genomes]
rs56222430	0.89[ASN][1000 genomes]
rs56231393	0.93[ASN][1000 genomes]
rs56260521	0.97[ASN][1000 genomes]
rs56329826	0.97[ASN][1000 genomes]
rs56333662	0.93[ASN][1000 genomes]
rs56341229	0.97[ASN][1000 genomes]
rs56775039	0.93[ASN][1000 genomes]
rs57246774	0.97[ASN][1000 genomes]
rs59784613	0.97[ASN][1000 genomes]
rs60538413	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs61544154	0.93[ASN][1000 genomes]
rs62321365	0.84[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6533237	0.96[EUR][1000 genomes]
rs6533240	0.92[CHB][hapmap];0.94[JPT][hapmap];0.97[ASN][1000 genomes]
rs6533242	0.81[EUR][1000 genomes]
rs6533243	0.93[ASN][1000 genomes]
rs6810877	0.95[ASN][1000 genomes]
rs6815014	0.86[CHB][hapmap];0.94[JPT][hapmap];0.97[ASN][1000 genomes]
rs6816614	0.97[ASN][1000 genomes]
rs6818197	0.92[CHB][hapmap];1.00[CHD][hapmap];0.94[JPT][hapmap];0.97[ASN][1000 genomes]
rs6818626	0.97[ASN][1000 genomes]
rs6819081	0.96[CEU][hapmap];0.83[MKK][hapmap];0.95[TSI][hapmap];0.83[EUR][1000 genomes]
rs6822692	0.97[ASN][1000 genomes]
rs6823347	0.96[AFR][1000 genomes];0.84[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6824682	0.86[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6828362	0.86[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6829795	0.92[CHB][hapmap];1.00[CHD][hapmap];0.94[JPT][hapmap];0.97[ASN][1000 genomes]
rs6835216	0.83[CHB][hapmap];0.88[JPT][hapmap];0.97[ASN][1000 genomes]
rs6836198	0.96[CEU][hapmap];0.84[MKK][hapmap];0.98[TSI][hapmap];0.87[EUR][1000 genomes]
rs6843331	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6843870	0.92[CHB][hapmap];1.00[CHD][hapmap];0.94[JPT][hapmap];0.97[ASN][1000 genomes]
rs6844324	0.97[ASN][1000 genomes]
rs6846579	0.91[CEU][hapmap];0.92[CHB][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];0.94[JPT][hapmap];0.86[TSI][hapmap];0.84[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6852388	0.95[EUR][1000 genomes]
rs6853554	0.83[CEU][hapmap]
rs72489522	0.97[ASN][1000 genomes]
rs72677306	0.87[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs72876575	0.93[ASN][1000 genomes]
rs72893620	0.93[ASN][1000 genomes]
rs7340989	0.90[ASN][1000 genomes]
rs7438546	1.00[CEU][hapmap];0.95[EUR][1000 genomes]
rs7655054	0.97[ASN][1000 genomes]
rs7657962	0.91[CEU][hapmap];0.82[CHB][hapmap];1.00[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.86[TSI][hapmap];0.85[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7657975	0.91[CHB][hapmap];0.94[JPT][hapmap];0.97[ASN][1000 genomes]
rs7658011	0.99[ASN][1000 genomes]
rs7658701	0.97[ASN][1000 genomes]
rs7661499	0.92[ASN][1000 genomes]
rs7661565	0.92[CHB][hapmap];0.94[JPT][hapmap];0.97[ASN][1000 genomes]
rs7662219	0.93[ASN][1000 genomes]
rs7662291	0.93[ASN][1000 genomes]
rs7662395	0.93[ASN][1000 genomes]
rs7662592	0.91[CEU][hapmap];0.92[CHB][hapmap];0.94[JPT][hapmap];0.86[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7662806	0.97[ASN][1000 genomes]
rs7662836	0.97[ASN][1000 genomes]
rs7663321	0.95[CEU][hapmap];0.82[YRI][hapmap]
rs7664032	0.97[ASN][1000 genomes]
rs7664188	0.92[CHB][hapmap];0.94[JPT][hapmap];0.97[ASN][1000 genomes]
rs7665946	0.93[ASN][1000 genomes]
rs7667719	0.93[ASN][1000 genomes]
rs7668276	0.96[CEU][hapmap];0.81[EUR][1000 genomes]
rs7668477	0.92[CHB][hapmap];0.94[JPT][hapmap];0.93[ASN][1000 genomes]
rs7669087	0.92[CHB][hapmap];0.95[CHD][hapmap];0.94[JPT][hapmap];0.97[ASN][1000 genomes]
rs7669212	0.93[ASN][1000 genomes]
rs7671145	0.92[CHB][hapmap];1.00[CHD][hapmap];0.94[JPT][hapmap];0.95[ASN][1000 genomes]
rs7673101	0.96[CEU][hapmap];0.87[EUR][1000 genomes]
rs7673949	0.93[ASN][1000 genomes]
rs7674381	0.86[ASN][1000 genomes]
rs7674466	0.91[ASN][1000 genomes]
rs7674931	0.93[ASN][1000 genomes]
rs7675728	0.99[ASN][1000 genomes]
rs7677248	0.93[AFR][1000 genomes];0.85[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7678229	0.92[CHB][hapmap];0.89[JPT][hapmap];0.97[ASN][1000 genomes]
rs7678847	0.94[ASW][hapmap];0.91[CEU][hapmap];0.92[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.94[JPT][hapmap];0.95[LWK][hapmap];0.96[MKK][hapmap];0.84[TSI][hapmap];0.84[YRI][hapmap];0.88[AFR][1000 genomes];0.86[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7681257	0.91[CHB][hapmap];1.00[JPT][hapmap];0.97[ASN][1000 genomes]
rs7682646	0.96[CEU][hapmap];0.85[EUR][1000 genomes]
rs7687657	0.89[AFR][1000 genomes];0.92[EUR][1000 genomes]
rs7688411	0.93[ASN][1000 genomes]
rs7689298	0.95[EUR][1000 genomes]
rs7692069	0.96[AFR][1000 genomes];0.85[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7692652	0.96[CEU][hapmap];0.84[MKK][hapmap];0.98[TSI][hapmap]
rs7693333	0.96[CEU][hapmap];0.98[TSI][hapmap];0.87[EUR][1000 genomes]
rs7693448	0.91[CEU][hapmap];0.82[MKK][hapmap];0.95[TSI][hapmap];0.81[EUR][1000 genomes]
rs7698386	0.96[ASN][1000 genomes]
rs7699768	0.92[CHB][hapmap];0.94[JPT][hapmap];0.97[ASN][1000 genomes]
rs9684658	0.93[ASN][1000 genomes]
rs9685018	0.95[ASN][1000 genomes]
rs9685464	0.88[AFR][1000 genomes];0.86[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9991091	0.86[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs9996093	0.95[CEU][hapmap];0.87[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 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

mRNA abundance (count:5)

SNP	Gene	Cis/trans	Tissue	Source
rs6842919	TBCK	cis	lymphoblastoid	seeQTL
rs6842919	ELOVL6	cis	cerebellum	SCAN
rs6842919	SCYE1	Cis_1M	lymphoblastoid	RTeQTL
rs6842919	TBCK	cis	parietal	SCAN
rs6842919	MGC16169	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:29 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:106953800-106959600	Enhancers	HepG2	liver
2	chr4:106954400-106959200	Weak transcription	Pancreas	Pancrea
3	chr4:106954800-106959200	Weak transcription	iPS-20b Cell Line	embryonic stem cell
4	chr4:106955000-106969600	Weak transcription	NHLF	lung
5	chr4:106955200-106966600	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
6	chr4:106956000-106960600	Weak transcription	Fetal Lung	lung
7	chr4:106956000-106961400	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
8	chr4:106956000-106969800	Weak transcription	Muscle Satellite Cultured Cells	--
9	chr4:106956200-106958400	Enhancers	Fetal Heart	heart
10	chr4:106956200-106960800	Weak transcription	NHDF-Ad	bronchial
11	chr4:106956200-106967200	Weak transcription	Skeletal Muscle Female	skeletal muscle
12	chr4:106956200-106967400	Weak transcription	Primary hematopoietic stem cells short term culture	blood
13	chr4:106956200-106968200	Weak transcription	Fetal Stomach	stomach
14	chr4:106956200-106969600	Weak transcription	HUES6 Cell Line	embryonic stem cell
15	chr4:106956200-106970000	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
16	chr4:106956400-106959000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
17	chr4:106956400-106959200	Weak transcription	Fetal Kidney	kidney
18	chr4:106956400-106966600	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
19	chr4:106956600-106961600	Weak transcription	Psoas Muscle	Psoas
20	chr4:106956600-106969200	Weak transcription	Fetal Muscle Leg	muscle
21	chr4:106956800-106970800	Weak transcription	HSMMtube	muscle
22	chr4:106957400-106958200	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
23	chr4:106957400-106958200	Enhancers	iPS-18 Cell Line	embryonic stem cell
24	chr4:106957400-106959200	Enhancers	HUES64 Cell Line	embryonic stem cell
25	chr4:106957600-106958400	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
26	chr4:106957600-106958400	Enhancers	Fetal Adrenal Gland	Adrenal Gland
27	chr4:106957800-106959000	Weak transcription	iPS-15b Cell Line	embryonic stem cell
28	chr4:106957800-106959200	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
29	chr4:106958000-106966600	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived

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